Difference between revisions of "Sandbox"

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−
* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]]<br/><br/>
+
* '''Description:''' D-alanine transfer from Dcp to undecaprenol-phosphate <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''eno''
+
|''dltB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-4r ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || D-alanine transfer from Dcp to undecaprenol-phosphate
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of teichoic acid
 +
acid (D-alanyl transfer from Dcp to undecaprenol-phosphate)
 
|-
 
|-
−
|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/Eno Eno]
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 9.944 
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1185 bp, 395 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dltA]]'', ''[[dltC]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15877&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dltB_context.gif]]
−
|-
 
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15395&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:eno_context.gif]]
 
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
−
|colspan="2" |'''Expression'''<br/>[[Image:eno_expression.png|500px]]<div align="right"> <small>[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=eno_3476555_3477847_-1 Expression at a glance]</small></div>
+
|colspan="2" |'''Expression'''<br/>[[Image:dltB_expression.png|400px]]<div align="right"> <small>[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dltB_3953783_3954970_1 Expression at a glance]</small></div>
 
|}
 
|}
−
 
−
 
−
<br/><br/><br/><br/><br/><br/>
 
−
 
  
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
Line 40: Line 33:
 
__TOC__
 
__TOC__
  
−
 
+
<br/><br/>
−
 
 
−
<br/><br/><br/><br/>
 
−
 
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[carbon core metabolism]]}},
+
{{SubtiWiki category|[[cell wall synthesis]]}},
−
{{SubtiWiki category|[[membrane proteins]]}},
+
{{SubtiWiki category|[[transporters/ other]]}},
−
{{SubtiWiki category|[[phosphoproteins]]}},
+
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
−
{{SubtiWiki category|[[universally conserved proteins]]}}
+
{{SubtiWiki category|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},
 +
{{SubtiWiki category|[[membrane proteins]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[CggR regulon]]}}
+
{{SubtiWiki regulon|[[SigD regulon]]}},
 +
{{SubtiWiki regulon|[[SigM regulon]]}},
 +
{{SubtiWiki regulon|[[SigX regulon]]}},
 +
{{SubtiWiki regulon|[[Spo0A regulon]]}},
 +
{{SubtiWiki regulon|[[stringent response]]}},
 +
{{SubtiWiki regulon|[[YvrHb regulon]]}}
  
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
−
* '''Locus tag:''' BSU33900
+
 
 +
* '''Locus tag:''' BSU38510
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
* no growth on LB, requires glucose and malate
 
−
* essential according to Kobayashi et al. on LB  [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dltABCDE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10550]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
 +
  
 
=The protein=
 
=The protein=
Line 75: Line 73:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H<sub>2</sub>O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' enolase family (according to Swiss-Prot)
+
* '''Protein family:''' membrane-bound acyltransferase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 83: Line 81:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
+
* '''Kinetic information:'''
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** substrate binding domain (366–369)
 
  
−
* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
* '''Modification:'''
  
−
* '''Cofactor(s):''' Mg2+
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
−
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
 
  
 
* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
−
** forms octamers {{PubMed|22198292}}
 
−
** part of the [[RNA degradosome]]  {{PubMed|19193632}}
 
−
** [[Eno]]-[[PfkA]] {{PubMed|19193632}}, K(D) of the interaction: 40 nM {{PubMed|22198292}}
 
−
** [[Eno]]-[[Rny]] {{PubMed|19193632,21803996}}, K(D) of the interaction: 100 nM {{PubMed|22198292}}
 
−
** [[Eno]]-[[CshA]] {{PubMed|20572937}}
 
  
−
* '''[[Localization]]:'''
+
* '''[[Localization]]:'''  
−
** cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
** membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
** membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]
 
−
** exported, this requires a long, unbent α-helix (from A108 to L126)  {{PubMed|15003462,21856851}}
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''  
+
* '''Structure:'''
−
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4A3R 4A3R] {{PubMed|22198292}}
 
−
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W6T 1W6T] (from ''Streptococcus pneumoniae'') {{PubMed|15476816}}
 
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39580 P39580]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38510]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
 
−
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
 
−
* [[universally conserved protein]]
 
−
* extensive information on the structure and enzymatic properties of Eno can be found at [http://www.proteopedia.org/wiki/index.php/Enolase Proteopedia]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
 +
* '''Operon:''' ''[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]]'' {{PubMed|7797557}}
  
−
* '''Operon:'''
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dltB_3953783_3954970_1 dltB] {{PubMed|22383849}}
−
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
 
−
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}  
 
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=eno_3476555_3477847_-1 eno] {{PubMed|22383849}}
+
* '''Sigma factor:''' [[SigD]] {{PubMed|7797557}}, [[SigM]] {{PubMed|18179421}}, [[SigX]] {{PubMed|14762009}}
−
 
 
−
* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}  
 
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
+
** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}
−
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
+
** repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|7797557}}
−
** ''[[pgk]]'': constitutive {{PubMed|11489127}}
+
** expression is reduced in a [[SigV]] mutant {{PubMed|21926231}}
  
−
* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}
+
* '''Regulatory mechanism:'''  
 +
** activated by [[YvrHb]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
 +
** [[Spo0A]]: transcription repression {{PubMed|7797557}}
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 146: Line 128:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''  
+
* '''Mutant:'''
−
** GP594 (''eno''::''cat''), available in [[Stülke]] lab
 
−
** GP599 (''eno''::''erm''), available in [[Stülke]] lab
 
−
** GP698 (''eno''-''[[pgm]]''::''cat''), available in [[Stülke]] lab
 
−
 
 
−
* '''Expression vector:'''
 
−
** pGP1426 (expression of ''[[eno]]'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
 
−
** pGP1500 (expression of ''[[pgm]]'' and ''[[eno]]'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
 
−
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
 
−
** pGP1276 (N-terminal Strep-tag, purification from ''E. coli'', in [[pGP172]]), available in [[Stülke]] lab
 
−
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
 
−
** GP1215 (''eno''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
 
  
 +
* '''Expression vector:'''
 +
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
−
** see ''[[pgk]]''
 
−
 
−
* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab
 
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''GFP fusion:'''
  
−
* '''FLAG-tag construct:''' GP1214 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Stülke]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
==Reviews==
+
'''Additional publications:''' {{PubMed|21856855,21926231}}
−
<pubmed> 8994873 </pubmed>
+
<pubmed>14762009,12028417 ,7797557,18763711, </pubmed>
−
==Subcellular localization of enolase==
 
−
'''Additional publications:''' {{PubMed|21856851}}
 
−
<pubmed> 16479537 18763711 15003462 20497499 </pubmed>
 
−
 
 
−
==Other original publications==
 
−
<pubmed> 17726680, 17218307, 12850135, 19193632, 11489127, 8021172, 17505547, 25885, 20572937 15476816 9988532 ,21803996 22198292 </pubmed>
 
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 10:46, 18 April 2012

  • Description: D-alanine transfer from Dcp to undecaprenol-phosphate

Gene name dltB
Synonyms ipa-4r
Essential no
Product D-alanine transfer from Dcp to undecaprenol-phosphate
Function biosynthesis of teichoic acid

acid (D-alanyl transfer from Dcp to undecaprenol-phosphate)

MW, pI 46 kDa, 9.944
Gene length, protein length 1185 bp, 395 aa
Immediate neighbours dltA, dltC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DltB context.gif
This image was kindly provided by SubtiList
Expression
DltB expression.png







Categories containing this gene/protein

cell wall synthesis, transporters/ other, biosynthesis of cell wall components, cell envelope stress proteins (controlled by SigM, V, W, X, Y), membrane proteins

This gene is a member of the following regulons

SigD regulon, SigM regulon, SigX regulon, Spo0A regulon, stringent response, YvrHb regulon

The gene

Basic information

  • Locus tag: BSU38510

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: membrane-bound acyltransferase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
    • RelA dependent downregulation (Class I) during stringent response PubMed
    • repressed under conditions that trigger sporulation (Spo0A) PubMed
    • expression is reduced in a SigV mutant PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Additional publications: PubMed

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

Min Cao, John D Helmann
The Bacillus subtilis extracytoplasmic-function sigmaX factor regulates modification of the cell envelope and resistance to cationic antimicrobial peptides.
J Bacteriol: 2004, 186(4);1136-46
[PubMed:14762009] [WorldCat.org] [DOI] (P p)

K Stephenson, C L Jensen, S T Jørgensen, C R Harwood
Simultaneous inactivation of the wprA and dltB genes of Bacillus subtilis reduces the yield of alpha-amylase.
Lett Appl Microbiol: 2002, 34(6);394-7
[PubMed:12028417] [WorldCat.org] [DOI] (P p)

M Perego, P Glaser, A Minutello, M A Strauch, K Leopold, W Fischer
Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. Identification of genes and regulation.
J Biol Chem: 1995, 270(26);15598-606
[PubMed:7797557] [WorldCat.org] [DOI] (P p)

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