SubtiWiki - User contributions [en]

RrcM

2013-03-14T13:11:24Z

Fmeyer: /* Biological materials */

* '''Description:''' regulatory RNA, [[small RNAs|ncRNA]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rrcM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA regulator of central metabolism
|-
|style="background:#ABCDEF;" align="center"|'''Function''' ||control of central metabolism
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrhK]]'', ''[[yrhJ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The [[RrcM regulon]]: =
=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:'''

* '''Structure:'''

=== Additional information===

=The RNA=

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1464 (cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|20709900}}
<pubmed> 20525796</pubmed>

[[Category:small RNA]]

RrcM

2013-03-14T13:10:55Z

Fmeyer: /* Biological materials */

* '''Description:''' regulatory RNA, [[small RNAs|ncRNA]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rrcM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA regulator of central metabolism
|-
|style="background:#ABCDEF;" align="center"|'''Function''' ||control of central metabolism
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrhK]]'', ''[[yrhJ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The [[RrcM regulon]]: =
=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:'''

* '''Structure:'''

=== Additional information===

=The RNA=

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''GP1464 (cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|20709900}}
<pubmed> 20525796</pubmed>

[[Category:small RNA]]

CitB

2012-11-02T08:49:03Z

Fmeyer: /* Biological materials */

* '''Description:''' [[trigger enzymes|trigger enzyme]]: aconitase and RNA binding protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU18000 citB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitB CitB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13684]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[trigger enzyme]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpC regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The [[CitB regulon]]: ''[[feuA]]-[[feuB]]-[[feuC]]-[[ybbA]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
* ''B. subtilis'' aconitase is both an enzyme and an RNA binding protein ([[moonlighting proteins|moonlighting protein]]) [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
* extensive information on the structure and enzymatic properties of CitB can be found at [http://www.proteopedia.org/wiki/index.php/Aconitase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 citB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1310745}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** expressed upon transition into the stationary phase ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed], indirect negative regulation by [[AbrB]] {{PubMed|20817675}}
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed2]
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[FsrA]]: translational repression {{PubMed|18697947}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP683 (erm), available in [[Jörg Stülke]]'s lab
** GP1441 (spc), available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citB''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:
**GP1439 (''citB''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
**pGP1810 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''
** pGP700 (in [[pAC5]]), available in [[Jörg Stülke]]'s lab

* '''GFP fusion:''' GP1434 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:''' available in [[Linc Sonenshein]]'s lab

* '''FLAG-tag construct:'''
** GP1144 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
** GP1145 (kan), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480</pubmed>

[[Category:Protein-coding genes]]

CitB

2012-11-02T08:47:01Z

Fmeyer: /* Biological materials */

* '''Description:''' [[trigger enzymes|trigger enzyme]]: aconitase and RNA binding protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU18000 citB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitB CitB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13684]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[trigger enzyme]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpC regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The [[CitB regulon]]: ''[[feuA]]-[[feuB]]-[[feuC]]-[[ybbA]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
* ''B. subtilis'' aconitase is both an enzyme and an RNA binding protein ([[moonlighting proteins|moonlighting protein]]) [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
* extensive information on the structure and enzymatic properties of CitB can be found at [http://www.proteopedia.org/wiki/index.php/Aconitase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 citB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1310745}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** expressed upon transition into the stationary phase ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed], indirect negative regulation by [[AbrB]] {{PubMed|20817675}}
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed2]
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[FsrA]]: translational repression {{PubMed|18697947}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP683 (erm), available in [[Jörg Stülke]]'s lab
** GP1441 (spc), available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citB''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:
**''' GP1439 (''citB''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
**pGP1810 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''
** pGP700 (in [[pAC5]]), available in [[Jörg Stülke]]'s lab

* '''GFP fusion:''' GP1434 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:''' available in [[Linc Sonenshein]]'s lab

* '''FLAG-tag construct:'''
** GP1144 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
** GP1145 (kan), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480</pubmed>

[[Category:Protein-coding genes]]

Mdh

2012-11-02T08:45:56Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29120 mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mdh_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-156 {{PubMed|22517742}}
** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
* The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
* extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719(spc) & GP1150(spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
** GP1438(''mdh''-''Strep'' ''(spc)'') & GP1440(''mdh''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1431 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''YFP fusion:''' GP1429 (spc, based on [[pGP1871]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1130 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742</pubmed>

[[Category:Protein-coding genes]]

GndA

2012-11-02T08:43:17Z

Fmeyer: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU23860 gndA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:gndA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 gndA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1514 (''gndA''::''kan''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1777 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
** pGP1789 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP1389]]) (available in [[Stülke]] lab)
** GP1408 (''gndA''-''Strep'' ''(spc)'') & GP1410 (''gndA''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
** GP1408 (kan, resistance cassette exchange in GP1403), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|15231785}}
<pubmed>17218307 19407374</pubmed>

[[Category:Protein-coding genes]]

GndA

2012-11-02T08:42:01Z

Fmeyer: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU23860 gndA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:gndA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 gndA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1514 (''gndA''::''kan''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1777 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
** pGP1789 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP1389]]) (available in [[Stülke]] lab)
** GP1408 (''gndA''-''Strep'' ''(spc)'') & GP1410 (''gndA''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
** GP1408 (kan, resistance cassette exchange in GP1403), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|15231785}}
<pubmed>17218307 19407374</pubmed>

[[Category:Protein-coding genes]]

CitZ

2012-11-02T08:40:25Z

Fmeyer: /* Biological materials */

* '''Description:''' citrate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29140 citZ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitZ CitZ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[ytwI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citZ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA, 2-oxoglutarate and NADH [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
** [http://www.rcsb.org/pdb/101/motm.do?momID=93 A discussion of citrate synthase structure]
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===
* extensive information on the structure and enzymatic properties of CitZ can be found at [http://www.proteopedia.org/wiki/index.php/Citrate_synthase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 citZ] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** repression by glucose (6.7-fold) ([[CcpA]]) {{PubMed|12100558,12850135}}
** repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''
** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab
** 1A999 ( ''citZ''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1776 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
** pGP1761 (expression with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>3013232 </pubmed>
==Original publications==
<pubmed>10348849,8045899,,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 20525796 20933603 22900538 </pubmed>

[[Category:Protein-coding genes]]

SdhB

2012-11-02T08:36:01Z

Fmeyer: /* Biological materials */

* '''Description:''' succinate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (iron-sulfur protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28430 sdhB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SdhB SdhB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysmA]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14803]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sdhB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhB_2905571_2906332_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sdhB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10353]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' succinate dehydrogenase/fumarate reductase iron-sulfur protein family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[SdhA]]-[[SdhB]], [[SdhB]]-[[SdhC]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)

* '''[[Localization]]:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P08066 P08066]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28430]

* '''E.C. number:'''EC 1.3.99.1

=== Additional information===
* This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
** One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
** Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
** The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* extensive information on the structure and enzymatic properties of succinate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/Succinate_Dehydrogenase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhB_2905571_2906332_-1 sdhB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[FsrA]]: translation inhibition {{PubMed|22389480}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1436 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1426 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>1707123,6401289,1324713,3036777,2495271,3027051,7748886,2837411,12560550, 3910107 6799760 22389480</pubmed>

[[Category:Protein-coding genes]]

CitB

2012-11-02T08:35:34Z

Fmeyer: /* Biological materials */

* '''Description:''' [[trigger enzymes|trigger enzyme]]: aconitase and RNA binding protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU18000 citB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitB CitB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13684]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[trigger enzyme]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpC regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The [[CitB regulon]]: ''[[feuA]]-[[feuB]]-[[feuC]]-[[ybbA]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
* ''B. subtilis'' aconitase is both an enzyme and an RNA binding protein ([[moonlighting proteins|moonlighting protein]]) [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
* extensive information on the structure and enzymatic properties of CitB can be found at [http://www.proteopedia.org/wiki/index.php/Aconitase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 citB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1310745}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** expressed upon transition into the stationary phase ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed], indirect negative regulation by [[AbrB]] {{PubMed|20817675}}
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed2]
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[FsrA]]: translational repression {{PubMed|18697947}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP683 (erm), available in [[Jörg Stülke]]'s lab
** GP1441 (spc), available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citB''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:''' GP1439 (''citB''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''
** pGP700 (in [[pAC5]]), available in [[Jörg Stülke]]'s lab

* '''GFP fusion:''' GP1434 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:''' available in [[Linc Sonenshein]]'s lab

* '''FLAG-tag construct:'''
** GP1144 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
** GP1145 (kan), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480</pubmed>

[[Category:Protein-coding genes]]

SucD

2012-11-02T08:35:03Z

Fmeyer: /* Biological materials */

* '''Description:''' succinyl-CoA synthetase (alpha subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (alpha subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16100 sucD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SucD SucD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[dprA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13483]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sucD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sucD_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ATP synthesis]]}},
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16100

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' succinate/malate CoA ligase alpha subunit family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** GTP is not accepted by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''[[SubtInteract|Interactions]]:'''
** [[SucC]]-[[SucD]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80865 P80865]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16100]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
* extensive information on the structure and enzymatic properties of succinyl-CoA synthetase can be found at [http://www.proteopedia.org/wiki/index.php/Succinyl-Coa_Synthetase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[sucD]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 sucD] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab
** 1A1008 ( ''sucD''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1008&Search=1A1008 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1435 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1425 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 11976317 20933603</pubmed>

[[Category:Protein-coding genes]]

CitG

2012-11-02T08:33:52Z

Fmeyer: /* Biological materials */

* '''Description:''' fumarase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fumarate hydratase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU33040 citG]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitG CitG]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.475
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1386 bp, 462 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuxN]], [[yvzF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15294]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citG_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33040

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citG.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10384]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate = fumarate + H2O (according to Swiss-Prot)

* '''Protein family:''' Fumarase subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[AnsB]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3R6Q 3R6Q] (aspartase from ''Bacillus'' sp. YM55-1, 43% identity, 77% similarity) {{PubMed|21661762}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P07343 P07343]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33040]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.2 4.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citG]]'' {{PubMed|3923430}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 citG] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|3130545,2509422,2509423}}, [[SigH]] {{PubMed|3130545,2509422}}

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP718 (spec), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1122 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)

* '''lacZ fusion:'''
** pGP387 (in [[pAC7]]), available in [[Jörg Stülke]]'s lab

* '''GFP fusion:''' GP1433 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1132 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21661762}}
<pubmed>2509422,3923430 ,3130545 2509423 20933603</pubmed>

[[Category:Protein-coding genes]]

YtsJ

2012-11-02T08:33:19Z

Fmeyer: /* Biological materials */

* '''Description:''' malic enzyme, forms a transhydrogenation cycle with [[MalS]] for balancing of NADPH 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ytsJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || malate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29220 ytsJ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 5.046
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accD]]'', ''[[dnaE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14882]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ytsJ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytsJ_2989900_2991132_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytsJ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29220

===Phenotypes of a mutant ===

Poor growth with malate as single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/16788182 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytsJ.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13922]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NADP+ = pyruvate + CO2 + NADPH (according to Swiss-Prot) malate <--> pyruvate

* '''Protein family:''' malic enzymes family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MleA]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] cytoplasm protein [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=1WW8 1WW8] (from ''Pyrococcus horikoshii'', 46% identity, 63% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34962 O34962]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29220]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.38 1.1.1.38]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ytsJ]]'' {{PubMed|9387221}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytsJ_2989900_2991132_-1 ytsJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**GP612 (spc), available in [[Jörg Stülke]]'s lab
**GP1143 (spc), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1432 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:'''

* '''FLAG-tag construct:''' GP1131 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22740702}}
<pubmed>16479537, 16788182 ,12949160 9387221</pubmed>

[[Category:Protein-coding genes]]

PckA

2012-11-02T08:32:53Z

Fmeyer: /* Biological materials */

* '''Description:''' phosphoenolpyruvate carboxykinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pckA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoenolpyruvate carboxykinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of phosphoenolpyruvate
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30560 pckA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/PckA PckA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15034]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pckA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pckA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpN regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30560

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2 (according to Swiss-Prot) ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)

* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family (according to Swiss-Prot) phosphoenolpyruvate carboxykinase [ATP] family

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** Nucleotide binding Domain (233–240)

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), cytoplasm

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54418 P54418]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30560]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.49 4.1.1.49]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pckA]]'' {{PubMed|9387221}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 pckA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|15720552}}

* '''Regulation:'''
** repressed by glucose (35-fold) [[CcpN]] {{PubMed|15720552,12850135}}

* '''Regulatory mechanism:'''
** [[CcpN]]: transcription repression {{PubMed|15720552}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A1005 ( ''pckA''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1005&Search=1A1005 BGSC]
** 1A996 ( ''pckA''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A996&Search=1A996 BGSC]
** GP1147 (''pckA''::''neo''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab)
** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1430 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1129 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>12850135 15720552 18586936, 9387221 20933603 22190493 </pubmed>

[[Category:Protein-coding genes]]

Mdh

2012-11-02T08:31:31Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29120 mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mdh_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-156 {{PubMed|22517742}}
** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
* The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
* extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719(spc) & GP1150(spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Jörg Stülke]]'s lab
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
** GP1438(''mdh''-''Strep'' ''(spc)'') & GP1440(''mdh''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1431 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''YFP fusion:''' GP1429 (spc, based on [[pGP1871]]), available in the [[Stülke]] lab

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1130 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742</pubmed>

[[Category:Protein-coding genes]]

MleN

2012-11-02T08:28:07Z

Fmeyer: /* Biological materials */

* '''Description:''' malate-H+/Na+-lactate antiporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mleN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqkI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate-H+/Na+-lactate antiporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || malate uptake
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU23560 mleN]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 7.249
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1404 bp, 468 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mleA]]'', ''[[ansB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14288]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mleN_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mleN_2452800_2454206_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mleN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transporters/ other]]}},
{{SubtiWiki category|[[utilization of specific carbon sources]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[AnsR regulon]]}},
{{SubtiWiki regulon|[[CcpA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23560

===Phenotypes of a mutant ===
abrupt arrest in the mid-logarithmic phase of growth on malate when low concentrations of protonophore were present {{PubMed|10903309}}
=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11763]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' nhaC Na(+)/H(+) antiporter family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[NhaC]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''
** membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54571 P54571]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23560]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ansA]]-[[ansB]]-[[mleN]]-[[mleA]]'' {{PubMed|22383849}}
** ''[[mleN]]-[[mleA]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mleN_2452800_2454206_-1 mleN] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[ansA]]'': [[SigA]] {{PubMed|1711029}}
** ''[[mleN]]'': [[SigA]] {{PubMed|22900538}}

* '''Regulation:'''
** ''[[ansA]]'': expressed in the presence of asparagine ([[AnsR]]) {{PubMed|11914346}}
** ''[[mleN]]'': repressed by glucose ([[CcpA]]) {{PubMed|22900538}}

* '''Regulatory mechanism:'''
** [[AnsR]]: transcription repression {{PubMed|11914346}}
** [[CcpA]]: transcription repression {{PubMed|22900538}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''GP1460 (''mleN''::''spc''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:''' pGP388 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711, 10903309 22900538 22383849 1711029 11914346</pubmed>

[[Category:Protein-coding genes]]

YwlE

2012-11-02T08:27:18Z

Fmeyer: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|protein arginine phosphatase]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywlE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipc-31d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|protein arginine phosphatase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || dephosphorylation of [[McsB]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU36930 ywlE]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 6.681
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 450 bp, 150 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywlF]]'', ''[[ywlD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15710]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ywlE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywlE_3791805_3792257_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ywlE_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[protein modification]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36930

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10941]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein arginine phosphate + H2O = protein arginine + phosphate {{PubMed|22517742}}

* '''Protein family:'''

* '''Paralogous protein(s):''' [[YfkJ]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[McsB]]-[[YwlE]] (dephosphorylation of [[McsB]]) {{PubMed|20852588,21622759}}

* '''[[Localization]]:''' weak oligomerization, results in inactivation of YwlE {{PubMed|19678837}}

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1ZGG 1ZGG]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39155 P39155]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36930]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.48 3.1.3.48]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywlE_3791805_3792257_-1 ywlE] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**''ywlE::aphA3'' available from [[Ulf Gerth]]'s lab
**''ywlE::tet'' available from [[Ulf Gerth]]'s lab
**''ywlE::spec'' available from [[Ulf Gerth]]'s lab
**GP1458 (''ywlE''::''aphA3''), available in [[Stülke]] lab
**GP1459 (''ywlE''::''tet''), available in [[Stülke]] lab

* '''Expression vector:''' for expression, purification in E. coli with N-terminal His-tag, pRSETA available in [[Ulf Gerth]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:''' available in [[Ulf Gerth]]'s lab

=Labs working on this gene/protein=
* [[Ulf Gerth]], Greifswald, Germany
=Your additional remarks=

=References=

<pubmed>16452434,15866923,15995210,19678837 21622759, 20852588 22517742</pubmed>

[[Category:Protein-coding genes]]

McsB

2012-11-02T08:25:35Z

Fmeyer: /* Biological materials */

* '''Description:''' [[protein kinases and phosphatases|protein arginine kinase]], adaptor protein, modulator of [[CtsR]]-dependent repression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mcsB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[protein kinases and phosphatases|protein arginine kinase]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[CtsR]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00850 mcsB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/McsB McsB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.068
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1089 bp, 363 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcsA]]'', ''[[clpC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11861]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mcsB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcsB_102484_103575_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mcsB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[protein modification]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[sporulation proteins]]}},
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[heat shock proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CtsR regulon]]}},
{{SubtiWiki regulon|[[SigB regulon]]}},
{{SubtiWiki regulon|[[SigF regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00850

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10147]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' targets non-functional CtsR for degradation by [[ClpP]]/[[ClpC]] {{PubMed|20852588}}

* '''Protein family:''' ATP:guanido phosphotransferase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** autophosphorylation on specific arginine residues {{PubMed|20852588,21622759}}, dephosphorylation by [[YwlE]] {{PubMed|20852588,21622759}}
** autophosphorylation stimulates McsB activity as adaptor protein for [[ClpC]] {{PubMed|21622759}}

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[McsA]]-[[McsB]]-[[CtsR]], [[McsB]]-[[CtsR]] {{PubMed|20852588}}, [[McsA]]-[[McsB]]
** [[McsB]]-[[YwlE]] {{PubMed|20852588}}
** [[McsB]]-[[ClpP]]/[[ClpC]] (rapid degradation of phosphorylated McsB) {{PubMed|20852588}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37570 P37570]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00850]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcsB_102484_103575_1 mcsB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2], [[SigF]] {{PubMed|16497325}}

* '''Regulation:'''
** expressed early during sporulation in the forespore ([[SigF]]) {{PubMed|16497325}}
** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
** induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]

* '''Regulatory mechanism:'''
** [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9987115 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**''mcsB::aphA3'' availbale from the Gerth lab
**mcsBC167S::spec available from the Gerth lab
**GP1457 (''mcsB''::''aphA3''), available in [[Stülke]] lab

* '''Expression vector:''' for expression, purification in E. coli with N-terminal His-tag, pRSETA available in Gerth lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:''' available in Gerth lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

==Reviews==
{{PubMed|19609260}}
==Original Publications==
<pubmed> 11179229,9987115, 8793870, 16497325,19226326, 9987115, 11544224, 20852588 21622759 22517742</pubmed>
'''Additional publications:''' {{PubMed|17380125,16163393,19498169}}
[[Category:Protein-coding genes]]

MaeN

2012-11-02T08:23:23Z

Fmeyer: /* Biological materials */

* '''Description:''' Na+/malate symporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''maeN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yufR ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || Na+/malate symporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || malate uptake
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU31580 maeN]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 8.411
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nupQ]]'', ''[[yufS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15147]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:maeN_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=maeN_3244770_3246116_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:maeN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transporters/ other]]}},
{{SubtiWiki category|[[utilization of specific carbon sources]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[MalR regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31580

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12353]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' sodium:citrate (SCF) symporter family (according to Swiss-Prot) 2-hydroxycarboxylate transporter family

* '''Paralogous protein(s):''' [[CimH]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O05256 O05256]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31580]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[maeN]]'' {{PubMed|21815947}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=maeN_3244770_3246116_1 maeN] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' induced by malate ([[MalR]])

* '''Regulatory mechanism:''' [[MalR]]: transcription activation

* '''Additional information:'''
** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}

=Biological materials =

* '''Mutant:'''
** 1A642 (''maeN''::Tn917, erm) (available from the [http://www.bgsc.org/ BGSC] or in [[Jörg Stülke]]'s lab)
** 1A642 ( ''maeN''::''erm''), {{PubMed|3015878}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A642&Search=1A642 BGSC]
** GP1449 (''erm''), available in [[Stülke]] lab

* '''Expression vector:'''
** expression of native ''maeN'' in ''B. subtilis'': pGP1951 (in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>16339740 </pubmed>
==Original publications==
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J'' </big>
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
<pubmed>19087206,12949159,,12949159, </pubmed>

[[Category:Protein-coding genes]]

CcpC

2012-11-02T08:18:50Z

Fmeyer: /* Biological materials */

* '''Description:''' transcriptional repressor of ''[[citZ]]'' and ''[[citB]]'' 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ccpC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykuM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor ([[LysR family]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of tricarboxylic acid branch of the TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU14140 ccpC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.932
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 879 bp, 293 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuL]]'', ''[[ykuN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13287]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ccpC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpC_1486045_1486926_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ccpC_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[regulators of core metabolism]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}
=The CcpC regulon:=
* ''[[ccpC]]'', ''[[citB]]'', ''[[citZ]]-[[icd]]-[[mdh]]''
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14140

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13297]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' [[LysR family]]

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34827 O34827]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14140]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]-[[ccpC]]'' {{PubMed|16395550}}
** ''[[ccpC]]'' {{PubMed|16395550}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpC_1486045_1486926_1 ccpC] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[ccpC]]'': [[SigA]]

* '''Regulation:'''
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 PubMed]

* '''Regulatory mechanism:'''
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 PubMed]
** [[CcpA]]: transcription repression {{PubMed|16395550}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP206 (''aphA3'') & GP1442 (''aphA3'') , available in [[Stülke]] lab

* '''Expression vector:'''
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP706, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP707 (in [[pAC5]]), available in [[Stülke]] lab, pGP711 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

=Your additional remarks=

=References=

<pubmed>17994626,,11985717,10656796 12591885 14636591, 16395550</pubmed>

[[Category:Protein-coding genes]]

CitB

2012-11-02T08:18:21Z

Fmeyer: /* Biological materials */

* '''Description:''' [[trigger enzymes|trigger enzyme]]: aconitase and RNA binding protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU18000 citB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitB CitB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13684]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[trigger enzyme]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpC regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The [[CitB regulon]]: ''[[feuA]]-[[feuB]]-[[feuC]]-[[ybbA]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
* ''B. subtilis'' aconitase is both an enzyme and an RNA binding protein ([[moonlighting proteins|moonlighting protein]]) [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
* extensive information on the structure and enzymatic properties of CitB can be found at [http://www.proteopedia.org/wiki/index.php/Aconitase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 citB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1310745}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** expressed upon transition into the stationary phase ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed], indirect negative regulation by [[AbrB]] {{PubMed|20817675}}
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed2]
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[FsrA]]: translational repression {{PubMed|18697947}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP683 (erm), available in [[Jörg Stülke]]'s lab
** GP1441 (spc), available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citB''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:''' GP1439 (''citB''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''
** pGP700 (in [[pAC5]]), available in [[Jörg Stülke]]'s lab

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:''' available in [[Linc Sonenshein]]'s lab

* '''FLAG-tag construct:'''
** GP1144 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
** GP1145 (kan), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480</pubmed>

[[Category:Protein-coding genes]]

Mdh

2012-11-02T08:16:09Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29120 mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mdh_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-156 {{PubMed|22517742}}
** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
* The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
* extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719(spc) & GP1150(spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Jörg Stülke]]'s lab
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
** GP1438(''mdh''-''Strep'' ''(spc)'') & GP1440(''mdh''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1130 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742</pubmed>

[[Category:Protein-coding genes]]

PdhD

2012-11-02T08:13:32Z

Fmeyer: /* Biological materials */

* '''Description:''' dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pdhD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citL ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle, enzyme in TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU14610 pdhD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/PdhD PdhD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.76
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1410 bp, 470 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhC]]'', ''[[slp]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13334]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pdhD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhD_1531870_1533282_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pdhD_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[stringent response]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14610

===Phenotypes of a mutant ===

* defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10210]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein N(6)-(dihydrolipoyl)lysine + NAD+ = protein N(6)-(lipoyl)lysine + NADH (according to Swiss-Prot)

* '''Protein family:''' class-I pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated (Ser/Thr/Tyr) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
** Low sensibility to NADPH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[OdhA]]-[[OdhB]]-[[PdhD]] {{PubMed|20933603}}
** [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P21880 P21880]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14610]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.8.1.4 1.8.1.4]

=== Additional information===

=Expression and regulation=

** ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]'' {{PubMed|11976308}}
** ''[[pdhC]]-[[pdhD]]'' {{PubMed|11976308}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdhD_1531870_1533282_1 pdhD] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[pdhA]]'': [[SigA]] {{PubMed|20081037}}
** ''[[pdhC]]'': [[SigA]] {{PubMed|11976308}}

* '''Regulation:'''
** ''[[pdhA]]'': expression activated by glucose (2.0-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** subject to negative stringent control upon amino acid limitation {{PubMed|20081037}}

* '''Regulatory mechanism:'''
** stringent response: due to presence of guanine at +1 position of the transcript {{PubMed|20081037}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:''' pGP723 (in [[pAC5]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1427 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 19476487 9655937 2227213 6805383 10672230</pubmed>
==Original publications==
<pubmed>12850135 6414463 11976308 17726680 20081037 20933603</pubmed>

[[Category:Protein-coding genes]]

SdhB

2012-11-02T08:11:57Z

Fmeyer: /* Biological materials */

* '''Description:''' succinate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (iron-sulfur protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28430 sdhB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SdhB SdhB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysmA]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14803]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sdhB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhB_2905571_2906332_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sdhB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10353]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' succinate dehydrogenase/fumarate reductase iron-sulfur protein family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[SdhA]]-[[SdhB]], [[SdhB]]-[[SdhC]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)

* '''[[Localization]]:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P08066 P08066]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28430]

* '''E.C. number:'''EC 1.3.99.1

=== Additional information===
* This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
** One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
** Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
** The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* extensive information on the structure and enzymatic properties of succinate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/Succinate_Dehydrogenase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhB_2905571_2906332_-1 sdhB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[FsrA]]: translation inhibition {{PubMed|22389480}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1426 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>1707123,6401289,1324713,3036777,2495271,3027051,7748886,2837411,12560550, 3910107 6799760 22389480</pubmed>

[[Category:Protein-coding genes]]

SucD

2012-11-02T08:11:30Z

Fmeyer: /* Biological materials */

* '''Description:''' succinyl-CoA synthetase (alpha subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (alpha subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16100 sucD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SucD SucD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[dprA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13483]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sucD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sucD_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ATP synthesis]]}},
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16100

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' succinate/malate CoA ligase alpha subunit family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** GTP is not accepted by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''[[SubtInteract|Interactions]]:'''
** [[SucC]]-[[SucD]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80865 P80865]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16100]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
* extensive information on the structure and enzymatic properties of succinyl-CoA synthetase can be found at [http://www.proteopedia.org/wiki/index.php/Succinyl-Coa_Synthetase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[sucD]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 sucD] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab
** 1A1008 ( ''sucD''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1008&Search=1A1008 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1425 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 11976317 20933603</pubmed>

[[Category:Protein-coding genes]]

OdhB

2012-11-02T08:11:03Z

Fmeyer: /* Biological materials */

* '''Description:''' 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''odhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase complex
(dihydrolipoamide transsuccinylase, E2 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU19360 odhB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/OdhB OdhB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.859
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1251 bp, 417 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yocS]], [[odhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13828]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:odhB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=odhB_2107505_2108758_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:odhB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[essential genes]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19360

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10273]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine (according to Swiss-Prot)

* '''Protein family:''' sodium:bile acid symporter family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[OdhA]]-[[OdhB]]-[[PdhD]] {{PubMed|20933603}}
** [[OdhB]]-[[Icd]] {{PubMed|20933603}}

* '''[[Localization]]:'''
** membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1c4t 1C4T] (from ''Escherichia coli bl21'', 57% identity, 78% similarity) {{PubMed|10739245}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P16263 P16263]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19360]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.61 2.3.1.61]

=== Additional information===
* extensive information on the structure and enzymatic properties of 2-oxoglutarate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/2-Oxoglutarate_Dehydrogenase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[odhA]]''-''[[odhB]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=odhB_2107505_2108758_-1 odhB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1508153}}

* '''Regulation:'''
** repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** pGP1145 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1424 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 10672230</pubmed>
==Original publications==
<pubmed>2500417,,1508153,12850135 18763711 12682299,11976317 20933603</pubmed>

[[Category:Protein-coding genes]]

GndA

2012-11-02T08:09:10Z

Fmeyer: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU23860 gndA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:gndA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 gndA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1514 (''gndA''::''kan''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1789 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP1389]]) (available in [[Stülke]] lab)
** GP1408 (''gndA''-''Strep'' ''(spc)'') & GP1410 (''gndA''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
** GP1408 (kan, resistance cassette exchange in GP1403), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|15231785}}
<pubmed>17218307 19407374</pubmed>

[[Category:Protein-coding genes]]

YwjH

2012-11-02T08:08:11Z

Fmeyer: /* Biological materials */

* '''Description:''' transaldolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywjH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transaldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU37110 ywjH]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.876
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murAB]]'', ''[[fbaA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15728]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ywjH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywjH_3807754_3808392_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ywjH_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37110

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fbaA-ywjH.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10413]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' Type 3B subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-39 {{PubMed|17218307,16493705,17726680}}, ''in vitro'' phosphorylated by [[PrkC]] {{PubMed|20389117}}

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** forms decamers (dimer of pentamers) {{PubMed|22212631}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3R8R 3R8R] {{PubMed|22212631}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P19669 P19669]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37110]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.2 2.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[fbaA]]-[[ywjH]]'' {{PubMed|11489127}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywjH_3807754_3808392_-1 ywjH] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP819, available in [[Stülke]] lab
** pGP1790 (expression of ''[[ywjH]]'' in ''B. subtilis'', in [[pGP1389]]), available in [[Stülke]] lab
** GP1409 (''ywjH''-''Strep'' ''(spc)'') & GP1411 (''ywjH''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1407 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22212631}}
<pubmed> 17726680, 17218307, 16493705 11489127 20389117 21857661 </pubmed>

[[Category:Protein-coding genes]]

GndA

2012-11-02T08:04:35Z

Fmeyer: /* Biological materials */

* '''Description:''' NADP-dependent phosphogluconate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gndA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU23860 gndA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14318]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqjI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:gndA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU23860

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)

* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible reaction [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2w8z 2W8Z] (from ''Geobacillus stearothermophilus'', 83% identity, 92% similarity) {{PubMed|19407374}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80859 P80859]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23860]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]

=== Additional information===
It contains a cysteine on the active site. The enzyme is a dimer. [http://www.ncbi.nlm.nih.gov/sites/entrez/15231785 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[polY1]]-[[gndA]]'' (according to [http://dbtbs.hgc.jp/COG/prom/yqjHI.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gndA_2480750_2482159_-1 gndA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1514 (''gndA''::''kan''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1789 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP1389]]) (available in [[Stülke]] lab)
** GP1410 (''gndA''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1403 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
** GP1408 (kan, resistance cassette exchange in GP1403), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|15231785}}
<pubmed>17218307 19407374</pubmed>

[[Category:Protein-coding genes]]

Mdh

2012-11-02T08:01:31Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29120 mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mdh_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-156 {{PubMed|22517742}}
** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
* The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
* extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719(spc) & GP1150(spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Jörg Stülke]]'s lab
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1130 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742</pubmed>

[[Category:Protein-coding genes]]

Mdh

2012-11-02T08:00:31Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29120 mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mdh_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-156 {{PubMed|22517742}}
** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
* The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
* extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719(spc) & GP1150(spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Jörg Stülke]]'s lab
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1130 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742</pubmed>

[[Category:Protein-coding genes]]

PckA

2012-10-30T08:11:49Z

Fmeyer: /* Biological materials */

* '''Description:''' phosphoenolpyruvate carboxykinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pckA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoenolpyruvate carboxykinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of phosphoenolpyruvate
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30560 pckA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/PckA PckA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15034]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pckA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pckA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpN regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30560

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2 (according to Swiss-Prot) ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)

* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family (according to Swiss-Prot) phosphoenolpyruvate carboxykinase [ATP] family

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** Nucleotide binding Domain (233–240)

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), cytoplasm

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54418 P54418]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30560]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.49 4.1.1.49]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pckA]]'' {{PubMed|9387221}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 pckA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|15720552}}

* '''Regulation:'''
** repressed by glucose (35-fold) [[CcpN]] {{PubMed|15720552,12850135}}

* '''Regulatory mechanism:'''
** [[CcpN]]: transcription repression {{PubMed|15720552}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A1005 ( ''pckA''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1005&Search=1A1005 BGSC]
** 1A996 ( ''pckA''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A996&Search=1A996 BGSC]
** GP1147 (''pckA''::''neo''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Stülke]] lab)
** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1129 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>12850135 15720552 18586936, 9387221 20933603 22190493 </pubmed>

[[Category:Protein-coding genes]]

CitB

2012-10-30T08:09:40Z

Fmeyer: /* Biological materials */

* '''Description:''' [[trigger enzymes|trigger enzyme]]: aconitase and RNA binding protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU18000 citB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitB CitB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13684]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[trigger enzyme]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpC regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The [[CitB regulon]]: ''[[feuA]]-[[feuB]]-[[feuC]]-[[ybbA]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
* ''B. subtilis'' aconitase is both an enzyme and an RNA binding protein ([[moonlighting proteins|moonlighting protein]]) [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
* extensive information on the structure and enzymatic properties of CitB can be found at [http://www.proteopedia.org/wiki/index.php/Aconitase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 citB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1310745}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** expressed upon transition into the stationary phase ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed], indirect negative regulation by [[AbrB]] {{PubMed|20817675}}
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed2]
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[FsrA]]: translational repression {{PubMed|18697947}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP683 (erm) and GP1441 (spc), available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citB''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:''' pGP700 (in [[pAC5]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

* '''FLAG-tag construct:''' GP1144 (spc, based on [[pGP1331]]) and GP1145 (kan), available in the [[Stülke]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480</pubmed>

[[Category:Protein-coding genes]]

CitB

2012-10-30T08:07:39Z

Fmeyer: /* Biological materials */

* '''Description:''' [[trigger enzymes|trigger enzyme]]: aconitase and RNA binding protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU18000 citB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitB CitB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13684]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[trigger enzyme]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpC regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The [[CitB regulon]]: ''[[feuA]]-[[feuB]]-[[feuC]]-[[ybbA]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
* ''B. subtilis'' aconitase is both an enzyme and an RNA binding protein ([[moonlighting proteins|moonlighting protein]]) [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
* extensive information on the structure and enzymatic properties of CitB can be found at [http://www.proteopedia.org/wiki/index.php/Aconitase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[citB]]'' (according to [http://dbtbs.hgc.jp/COG/prom/citB.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 citB] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1310745}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** expressed upon transition into the stationary phase ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed], indirect negative regulation by [[AbrB]] {{PubMed|20817675}}
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed2]
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[FsrA]]: translational repression {{PubMed|18697947}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP683 (erm) and GP1441 (spc), available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citB''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:'''

* '''lacZ fusion:''' pGP700 (in [[pAC5]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

* '''FLAG-tag construct:''' GP1144 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480</pubmed>

[[Category:Protein-coding genes]]

YtsJ

2012-10-30T08:05:45Z

Fmeyer: /* Biological materials */

* '''Description:''' malic enzyme, forms a transhydrogenation cycle with [[MalS]] for balancing of NADPH 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ytsJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || malate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29220 ytsJ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 5.046
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accD]]'', ''[[dnaE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14882]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ytsJ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytsJ_2989900_2991132_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytsJ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29220

===Phenotypes of a mutant ===

Poor growth with malate as single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/16788182 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytsJ.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13922]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NADP+ = pyruvate + CO2 + NADPH (according to Swiss-Prot) malate <--> pyruvate

* '''Protein family:''' malic enzymes family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MleA]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] cytoplasm protein [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=1WW8 1WW8] (from ''Pyrococcus horikoshii'', 46% identity, 63% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34962 O34962]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29220]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.38 1.1.1.38]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ytsJ]]'' {{PubMed|9387221}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytsJ_2989900_2991132_-1 ytsJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**GP612 (spc), available in [[Stülke]] lab
**GP1143 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''FLAG-tag construct:''' GP1131 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>16479537, 16788182 ,12949160 9387221 22740702 </pubmed>

[[Category:Protein-coding genes]]

SucC

2012-10-30T08:03:26Z

Fmeyer: /* Biological materials */

* '''Description:''' succinyl-CoA synthetase (beta subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16090 sucC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SucC SucC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13482]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sucC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucC_1680431_1681588_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sucC_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ATP synthesis]]}},
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' ATP-grasp domain (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}
** [[SucC]]-[[SucD]] {{PubMed|20933603}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
* extensive information on the structure and enzymatic properties of succinyl-CoA synthetase can be found at [http://www.proteopedia.org/wiki/index.php/Succinyl-Coa_Synthetase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[sucD]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucC_1680431_1681588_1 sucC] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A1006 ( ''sucC''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1006&Search=1A1006 BGSC]
** GP1134 (cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 11976317 20933603 22900538 </pubmed>

[[Category:Protein-coding genes]]

CitG

2012-10-30T08:01:13Z

Fmeyer: /* Biological materials */

* '''Description:''' fumarase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fumarate hydratase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU33040 citG]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitG CitG]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.475
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1386 bp, 462 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuxN]], [[yvzF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15294]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citG_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33040

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citG.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10384]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate = fumarate + H2O (according to Swiss-Prot)

* '''Protein family:''' Fumarase subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[AnsB]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3R6Q 3R6Q] (aspartase from ''Bacillus'' sp. YM55-1, 43% identity, 77% similarity) {{PubMed|21661762}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P07343 P07343]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33040]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.2 4.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citG]]'' {{PubMed|3923430}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 citG] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|3130545,2509422,2509423}}, [[SigH]] {{PubMed|3130545,2509422}}

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP718 (spec), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1122 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP387 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1132 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|21661762}}
<pubmed>2509422,3923430 ,3130545 2509423 20933603</pubmed>

[[Category:Protein-coding genes]]

YtsJ

2012-10-30T08:00:12Z

Fmeyer: /* Biological materials */

* '''Description:''' malic enzyme, forms a transhydrogenation cycle with [[MalS]] for balancing of NADPH 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ytsJ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || malate utilization
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29220 ytsJ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 5.046
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accD]]'', ''[[dnaE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14882]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ytsJ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytsJ_2989900_2991132_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytsJ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[utilization of specific carbon sources]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29220

===Phenotypes of a mutant ===

Poor growth with malate as single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/16788182 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytsJ.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13922]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NADP+ = pyruvate + CO2 + NADPH (according to Swiss-Prot) malate <--> pyruvate

* '''Protein family:''' malic enzymes family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MleA]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] cytoplasm protein [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=1WW8 1WW8] (from ''Pyrococcus horikoshii'', 46% identity, 63% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34962 O34962]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29220]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.38 1.1.1.38]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ytsJ]]'' {{PubMed|9387221}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytsJ_2989900_2991132_-1 ytsJ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP612 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''FLAG-tag construct:''' GP1131 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>16479537, 16788182 ,12949160 9387221 22740702 </pubmed>

[[Category:Protein-coding genes]]

Mdh

2012-10-30T07:58:12Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29120 mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mdh_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-156 {{PubMed|22517742}}
** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
* The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
* extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Stülke]] lab
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Stülke]] lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1130 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742</pubmed>

[[Category:Protein-coding genes]]

PckA

2012-10-30T07:56:41Z

Fmeyer: /* Biological materials */

* '''Description:''' phosphoenolpyruvate carboxykinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pckA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoenolpyruvate carboxykinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of phosphoenolpyruvate
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30560 pckA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/PckA PckA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15034]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pckA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pckA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpN regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30560

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2 (according to Swiss-Prot) ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)

* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family (according to Swiss-Prot) phosphoenolpyruvate carboxykinase [ATP] family

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** Nucleotide binding Domain (233–240)

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}

* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), cytoplasm

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54418 P54418]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30560]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.49 4.1.1.49]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pckA]]'' {{PubMed|9387221}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pckA_3129530_3131113_1 pckA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|15720552}}

* '''Regulation:'''
** repressed by glucose (35-fold) [[CcpN]] {{PubMed|15720552,12850135}}

* '''Regulatory mechanism:'''
** [[CcpN]]: transcription repression {{PubMed|15720552}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A1005 ( ''pckA''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1005&Search=1A1005 BGSC]
** 1A996 ( ''pckA''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A996&Search=1A996 BGSC]

* '''Expression vector:'''
** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Stülke]] lab)
** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1129 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>12850135 15720552 18586936, 9387221 20933603 22190493 </pubmed>

[[Category:Protein-coding genes]]

CcpN

2012-10-30T07:53:51Z

Fmeyer: /* Biological materials */

* '''Description:''' transcriptional repressor of gluconeogenetic genes and of [[sr1]]. repression in the presence of glucose 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ccpN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqzB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || repressor of genes involved in gluconeogenesis (''[[gapB]]'','' [[pckA]]'') and of ''[[sr1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU25250 ccpN]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CcpN CcpN]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23.4 kDa, 7.22
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfL]]'', ''[[glyS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14454]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqzB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpN_2604959_2605597_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ccpN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[regulators of core metabolism]]}}

= This gene is a member of the following [[regulons]] =

=The [[CcpN regulon]]:=
* ''[[gapB]]-[[speD]]'', ''[[pckA]]'', ''[[Sr1]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25250

===Phenotypes of a mutant ===
Impaired growth on glucose due to re-routing of carbon from glycolysis to the pentose phosphate pathway [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13768]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repression of the ''[[gapB]]'', ''[[pckA]]'', and ''[[sr1]]'' genes in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** [[YqfL]] (negative effector of CcpN activity) [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
** ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** active as dimer (according to {{PubMed|20408793}})
** [[CcpN]]-[[RpoA]] {{PubMed|19726675}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34994 O34994]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25250]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ccpN]]''-''[[yqfL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpN_2604959_2605597_-1 ccpN] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]

* '''Additional information:'''
** the intracellular concentration of CcpN is about 4 myM (according to {{PubMed|20408793}}).

=Biological materials =

* '''Mutant:'''
**DB104 ''ccpN''::cat, available in [[Sabine Brantl]] lab
**GP1128 ''ccpN''::cat, available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:''' available in [[Sabine Brantl]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]

[[Uwe Sauer]], ETH Zürich, Switzerland [http://www.imsb.ethz.ch/researchgroup/sauer homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20408793 </pubmed>

==Original Publications==
<pubmed>15720552 16164558 17011578 18511073 18586936, 19726675 19732150 22190493 </pubmed>

[[Category:Protein-coding genes]]

CcpN

2012-10-30T07:52:01Z

Fmeyer: /* Biological materials */

* '''Description:''' transcriptional repressor of gluconeogenetic genes and of [[sr1]]. repression in the presence of glucose 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ccpN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqzB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || repressor of genes involved in gluconeogenesis (''[[gapB]]'','' [[pckA]]'') and of ''[[sr1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU25250 ccpN]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CcpN CcpN]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23.4 kDa, 7.22
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfL]]'', ''[[glyS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14454]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqzB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpN_2604959_2605597_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ccpN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[regulators of core metabolism]]}}

= This gene is a member of the following [[regulons]] =

=The [[CcpN regulon]]:=
* ''[[gapB]]-[[speD]]'', ''[[pckA]]'', ''[[Sr1]]''

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25250

===Phenotypes of a mutant ===
Impaired growth on glucose due to re-routing of carbon from glycolysis to the pentose phosphate pathway [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13768]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repression of the ''[[gapB]]'', ''[[pckA]]'', and ''[[sr1]]'' genes in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** [[YqfL]] (negative effector of CcpN activity) [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
** ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** active as dimer (according to {{PubMed|20408793}})
** [[CcpN]]-[[RpoA]] {{PubMed|19726675}}

* '''[[Localization]]:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34994 O34994]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25250]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ccpN]]''-''[[yqfL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpN_2604959_2605597_-1 ccpN] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]

* '''Additional information:'''
** the intracellular concentration of CcpN is about 4 myM (according to {{PubMed|20408793}}).

=Biological materials =

* '''Mutant:'''

**DB104 ''ccpN''::cat, available in [[Sabine Brantl]] lab
**GP1128 ''ccpN''::cat, available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:''' available in [[Sabine Brantl]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]

[[Uwe Sauer]], ETH Zürich, Switzerland [http://www.imsb.ethz.ch/researchgroup/sauer homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20408793 </pubmed>

==Original Publications==
<pubmed>15720552 16164558 17011578 18511073 18586936, 19726675 19732150 22190493 </pubmed>

[[Category:Protein-coding genes]]

YflS

2012-07-26T08:11:52Z

Fmeyer: /* Biological materials */

* '''Description:''' malate transporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yflS''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate transporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || malate uptake
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 9.741
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1434 bp, 478 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pel]]'', ''[[citS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12586]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yflS_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yflS_829382_830818_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yflS_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transporters/ other]]}},
{{SubtiWiki category|[[utilization of specific carbon sources]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[MalR regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU07570

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12951]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' View classification (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34726 O34726]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07570]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yflS]]'' {{PubMed|21815947}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yflS_829382_830818_1 yflS] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' induced by malate ([[MalR]])

* '''Regulatory mechanism:''' [[MalR]]: transcription activation

* '''Additional information:'''
** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}

=Biological materials =

* '''Mutant:''' GP1450 (cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J'' </big>
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
<pubmed>12949159,,12949159, </pubmed>

[[Category:Protein-coding genes]]

PGP574

2012-01-18T08:11:02Z

Fmeyer:

Vector for the expression of proteins in ''E. coli'', the [[plasmids|plasmid]] allows to fuse a Strep-tag to the C-terminus of the expressed protein

host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

constructed in the [[Stülke]] lab

in ''E. coli'': ampicillin resistance

based on pET3C

similar [[plasmid]]: [[pGP172]]

* sequencing primer:
**'''T7:''' 5’-TAATACGACTCACTATAGGG -3’
** '''NP20:''' 5’-GCAGCAGCCAACTCAGCTTCCTTTCGGGC-3’

<pubmed> 17074746 </pubmed>

PGP574

2012-01-18T08:10:19Z

Fmeyer:

Vector for the expression of proteins in ''E. coli'', the [[plasmids|plasmid]] allows to fuse a Strep-tag to the C-terminus of the expressed protein

host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

constructed in the [[Stülke]] lab

in ''E. coli'': ampicillin resistance

based on pET3C

similar [[plasmid]]: [[pGP172]]

<pubmed> 17074746 </pubmed>

* sequencing primer:
**'''T7:''' 5’-TAATACGACTCACTATAGGG -3’
** '''NP20:''' 5’-GCAGCAGCCAACTCAGCTTCCTTTCGGGC-3’

CitZ

2010-11-04T14:14:07Z

Fmeyer: /* Biological materials */

* '''Description:''' citrate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[ytwI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA, 2-oxoglutarate and NADH [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Interactions:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** repression by glucose (6.7-fold) ([[CcpA]]) {{PubMed|12100558,12850135}}
** repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''
** The mRNA has a long 5' leader region. This may indicate RNA-based regulation {{PubMed|20525796}}

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1776 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed>3013232 </pubmed>
==Original publications==
<pubmed>10348849,8045899,,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 20525796 20933603 </pubmed>

[[Category:Protein-coding genes]]

Mdh

2010-11-04T14:12:18Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Interactions:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Stülke]] lab
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Stülke]] lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603</pubmed>

[[Category:Protein-coding genes]]

Mdh

2010-11-04T14:11:43Z

Fmeyer: /* Biological materials */

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Interactions:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Stülke]] lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603</pubmed>

[[Category:Protein-coding genes]]

PckA

2010-11-04T14:10:14Z

Fmeyer: /* Biological materials */

* '''Description:''' phosphoenolpyruvate carboxykinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pckA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoenolpyruvate carboxykinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of phosphoenolpyruvate
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15034]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pckA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30560

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2 (according to Swiss-Prot) ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)

* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family (according to Swiss-Prot) phosphoenolpyruvate carboxykinase [ATP] family

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** Nucleotide binding Domain (233–240)

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54418 P54418]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30560]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.49 4.1.1.49]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pckA]]'' {{PubMed|9387221}}

* '''Sigma factor:''' [[SigA]] {{PubMed|15720552}}

* '''Regulation:'''
** repressed by glucose (35-fold) [[CcpN]] {{PubMed|15720552,12850135}}

* '''Regulatory mechanism:'''
** [[CcpN]]: transcription repression {{PubMed|15720552}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Stülke]] lab)
** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1102 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>12850135 15720552 18586936, 9387221 20933603</pubmed>

[[Category:Protein-coding genes]]

PckA

2010-11-04T14:09:38Z

Fmeyer: /* Biological materials */

* '''Description:''' phosphoenolpyruvate carboxykinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pckA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoenolpyruvate carboxykinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of phosphoenolpyruvate
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15034]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pckA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30560

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2 (according to Swiss-Prot) ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)

* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family (according to Swiss-Prot) phosphoenolpyruvate carboxykinase [ATP] family

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** Nucleotide binding Domain (233–240)

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54418 P54418]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30560]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.49 4.1.1.49]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pckA]]'' {{PubMed|9387221}}

* '''Sigma factor:''' [[SigA]] {{PubMed|15720552}}

* '''Regulation:'''
** repressed by glucose (35-fold) [[CcpN]] {{PubMed|15720552,12850135}}

* '''Regulatory mechanism:'''
** [[CcpN]]: transcription repression {{PubMed|15720552}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** pGP1753 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1762 (for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Stülke]] lab)
** pGP1763 (for expression, purification in ''E. coli'' with N-terminal Strep-tag in [[pGP172]], available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1102 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>12850135 15720552 18586936, 9387221 20933603</pubmed>

[[Category:Protein-coding genes]]