SubtiWiki - User contributions [en]

PfkA

2009-01-13T22:44:24Z

82.82.75.193:

* '''Description:''' phosphofructokinase, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pfkA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pfk''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphofructokinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34,1 kDa, 6.14
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accA]]'', ''[[pyk]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pfkA_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pfkA_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:pfkA_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2985630 - 2986586

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12644]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate

* '''Protein family:''' phosphofructokinase family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** 3 x nucleotide binding domain (ATP) (21–25), (154–158), (171–187)

* '''Modification:'''

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

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

* '''Interactions:''' [[Pyk]]-PfkA

* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=58449 NCBI], Mutant form, complex with fructose-6-phosphate ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=21480 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34529]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29190]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.11]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''pfkA [[pyk]]''

* '''Sigma factor:'''

* '''Regulation:''' twofold induced by glucose

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. subm.
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

Pgi

2009-01-13T22:44:09Z

82.82.75.193:

* '''Description:''' glucose 6-phosphate isomerase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgi''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yugL ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glucose-6-phosphate isomerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50.4 kDa, 4.85
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1353 bp, 451 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yugK]]'', ''[[yugM]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pgi_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pgi_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgi_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 3219772 - 3221124

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12366]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glucose 6-phosphate = D-fructose 6-phosphate

* '''Protein family:''' GPI family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation (STY)

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

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

* '''Interactions:'''

* '''Localization:''' cytoplasm

=== Database entries ===

* '''Structure:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=54052 NCBI], ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=11544 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80860]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31350]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.9]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''pgi''

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

# Lee et al. (2008) Crystallization and preliminary crystallographic study of the phosphoglucose isomerase from Bacillus subtilis. Acta Cryst. Sect. F 64:1181-1183. [http://www.ncbi.nlm.nih.gov/sites/entrez/19052382 PubMed]
# Lin and Prasad (1975) Selection of a mutant of Bacillus subtilis deficient in glucose-6-phosphate dehydrogenase and phosphoglucoisomerase. J. Gen. Microbiol. 83:419-421. [http://www.ncbi.nlm.nih.gov/sites/entrez/4214896 PubMed]
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
# Prasad and Freese (1974) Cell lysis of Bacillus subtilis caused by intracellular accumulation of glucose-1-phosphate. J. Bacteriol. 118:1111-1122. [http://www.ncbi.nlm.nih.gov/sites/entrez/4275311 PubMed]
# Stülke, J., Martin-Verstraete, I., Glaser, P. & Rapoport, G. (2001) Characterization of glucose repression resistant mutants of Bacillus subtilis: identification of the glcR gene. Arch. Microbiol. 175: 441-449. [http://www.ncbi.nlm.nih.gov/sites/entrez/11491085 PubMed]

SigL

2009-01-13T22:43:51Z

82.82.75.193:

* '''Description:''' Sigma subunit of the RNA polymerase, Sigma-54, Sigma L 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma-54 factor (sigma-L)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of arginin, acetoin, and fructose, required for cold adaptation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49,5 kDa, 7.79
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvfG]]'', ''[[yvfH]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sigL_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sigL_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigL_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 3511532 - 3512839

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10748]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Binding to promoters of the -12, -24 type

* '''Protein family:''' sigma-54 factor family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** DNA binding domain (H-T-H motif) (324–343)
** pron box domain (413–421)
** 3 x Compositional bias domain (6–21),(32–53),(112–136)

* '''Modification:'''

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

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

* '''Interactions:''' SigL-[[RpoB]]-[[RpoC]]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P24219]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34200]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:''' neg. regulated by [[CcpA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+16166551 PubMed]

* '''Regulatory mechanism:''' transcriptional roadblock

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]

=Your additional remarks=

=References=

# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

YmdB

2009-01-13T22:43:13Z

82.82.75.193:

* '''Description:''' unknown function 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymdB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || YmdB protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown function
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29,1 kDa, 6.50
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymdA]]'', ''[[spoVS]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ymdB_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ymdB_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:ymdB_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 1768211 - 1769002

===Phenotypes of a mutant ===

strong overexpression of [[Hag]]

=== Database entries ===

* '''DBTBS entry:'''

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' negative effector of the expression of ''[[hag]]'' and other members of the [[SigD]] regulon

* '''Protein family:'''

* '''Paralogous protein(s):''' similar to unknown proteins

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31775]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16970]

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

=== Additional information===
has a negative effect on ''[[hag]]'' expression

=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]''

* '''Sigma factor:'''

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there

=Biological materials =

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Rny

2009-01-13T22:42:52Z

82.82.75.193:

* '''Description:''' required for the processing of the ''[[gapA]]'' operon mRNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rny''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2',3'-cyclic-nucleotide 2'-phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || required for the processing of the ''[[gapA]]'' operon mRNA
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdbX]]'', ''[[ymdB]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rny_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rny_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:rny_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 1766580 - 1768139

===Phenotypes of a mutant ===

essential

=== Database entries ===

* '''DBTBS entry:'''

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' required for the processing of the ''[[gapA]]'' operon mRNA

* '''Protein family:''' 2',3' cyclic nucleotide phosphodiesterase family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** transmembrane domain (4–24)
** KH domain (210–273)
** HD domain (336–429)

* '''Modification:'''

* '''Cofactor(s):''' metal-dependent

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

* '''Interactions:'''

* '''Localization:''' Single-pass membrane protein

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31774]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16960]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16]

=== Additional information===

required for the processing of the ''[[gapA]]'' operon mRNA
=Expression and regulation=

* '''Operon:''' ''[[rny]]-[[ymdB]]''

* '''Sigma factor:'''

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there

=Biological materials =

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. subm.
# Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed]

PckA

2009-01-13T22:42:32Z

82.82.75.193:

* '''Description:''' phosphoenolpyruvate carboxykinase synthesises phosphoenolpyrovat out of oxalacetate 

{| 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 phosphoenolpyrovat
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pckA_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pckA_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:pckA_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 3128579 - 3130159

===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 + CO(2)

* '''Protein family:''' 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:'''

* '''Localization:''' cytoplasm

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P54418]

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

* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?4.1.1.49]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]

* '''Regulation:''' repressed (35-times) Glc, repressor [[CcpN]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]

* '''Regulatory mechanism:''' transcription repression

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
# Tännler et al. (2008) CcpN controls central carbon fluxes in ''Bacillus subtilis''. J. Bacteriol. 190: 6178-6187. [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]

PtsI

2009-01-13T22:42:15Z

82.82.75.193:

* '''Description:''' Enzyme I, general (non sugar-specific) component of the PTS. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein ([[PtsH |HPr]]) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptsI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphotransferase system (PTS) enzyme I
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || PTS-dependent sugar transport
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62,9 kDa, 4.59
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1710 bp, 570 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pstH]]'', ''[[splA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsI_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsI_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:ptsI_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 1458959 - 1460668

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10201]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' PEP-dependent autophosphorylation on His-189, transfer of the phosphoryl group to [[PtsH |HPr]] (His-15)

* '''Protein family:''' PEP-utilizing enzyme family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
**HPr binding site (N-Terminal Domain)
**pyruvate binding site (C-Terminal Domain)
**pyrophosphate/phosphate carrier histidine (central Domain)

* '''Modification:''' transient autophosphorylation on His-189, in vivo also phosphorylated on Ser-44 or Ser-46

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

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P08838]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13910]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.3.9]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
**''[[ptsG]]-[[ptsH]]-[[ptsI]]''
**''[[ptsH]]-[[ptsI]]''

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11902727 PubMed]
* '''Regulation:''' induction by glucose (''[[ptsG]]''), constitutive (''[[ptsH]]'')

* '''Regulatory mechanism:''' ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent RNA-switch

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

[[Josef Deutscher]], Paris-Grignon, France

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

=Your additional remarks=

=References=

# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
# Pompeo F, Luciano J, Galinier A. (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in Bacillus subtilis? ''J Bacteriol.'' '''189(3):''' 1154-7. [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]

PtsH

2009-01-13T22:41:35Z

82.82.75.193:

* '''Description:''' HPr, General component of the sugar phosphotransferase system (PTS). 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptsH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || histidine-containing phosphocarrier protein HPr of the PTS
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || PTS-dependent sugar trnasport and carbon catabolite repression
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9,1 kDa, 4.58
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 264 bp, 88 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptsG]]'', ''[[ptsI]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsH_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsH_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:ptsH_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 1458693 - 1458956

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10200]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein HPr N(pi)-phospho-L-histidine + protein EIIA = protein [[PtsH|HPr]] + protein EIIA N(tau)-phospho-L-histidine

* '''Protein family:''' HPr family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' HPr Domain (2–88)

* '''Modification:''' phosphorylations: transient phosphorylation by [[PtsI |Enzyme I]] of the PTS on His-15, regulatory phosphorylation on Ser-46 by [[HprK]], weak phosphorylation on Ser-12

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

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

* '''Interactions:''' [[GapA]]-[[PtsH|HPr]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed], [[PtsH|HPr]]-[[MtlR]], [[PtsH|HPr]]-[[LicR]], [[PtsH|HPr]]-[[LevR]],[[PtsH|HPr]]-[[ManR]], [[YesS]]-[[PtsH|HPr]] (HPr-His-P), [[PtsH|HPr]]-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12432959 PubMed], [[PtsH|HPr]]-[[RbsR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16519689 PubMed], [[HprK]]-[[PtsH|HPr]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]

* '''Localization:''' Cytoplasm

=== Database entries ===

* '''Structure:''' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=58038 NCBI], complex of L. Casei HprK with B. Subtilis HPr [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=20417 NCBI], complex of L. Casei HprK with B. Subtilis HPr-Ser-P [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=20418 NCBI]

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P08877]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.11.-]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
**''[[ptsG]]-[[ptsH]]-[[ptsI]]''
**''ptsH-[[ptsI]]''

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11902727 PubMed]

* '''Regulation:''' induction by glucose (''[[ptsG]]''), constitutive (''[[ptsH]]'')

* '''Regulatory mechanism:''' ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent RNA-switch

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

[[Josef Deutscher]], Paris-Grignon, France

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

[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]

[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]

[[Boris Görke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

[[Anne Galinier]], University of Marseille, France

=Your additional remarks=

=References=

# Macek B, Mijakovic I, Olsen JV (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. ''Mol Cell Proteomics'' '''6(4):''' 697-707. [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

# Müller W, Horstmann N, Hillen W (2006) The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis ''FEBS J.'' '''273(6):''' 1251-61. [http://www.ncbi.nlm.nih.gov/sites/entrez/16519689 PubMed]
# Pompeo ''et al.'' (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in ''Bacillus subtilis''? J Bacteriol 189, 1154-1157.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]

1. Arnaud M, Vary P, Zagorec M, Klier A, Débarbouillé M, Postma P, Rapoport G (1992) Regulation of the sacPA operon of Bacillus subtilis: identification of phosphotransferase system components involved in SacT activity. J Bacteriol 174:3161-3170
2. Deutscher, J., Kessler, U., Alpert, C. A., and Hengstenberg, W. (1984) Bacterial phosphoenolpyruvate-dependent phosphotransferase system: P-ser-HPr and its possible regulatory function. Biochemistry 23: 4455-4460.
3. Deutscher, J., Küster, E., Bergstedt, U., Charrier, V., and Hillen, W. 1995. Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in Gram-positive bacteria. Mol. Microbiol. 15: 1049-1053.
4. Eisermann, R., Deutscher, J., Gonzy-Tréboul, G., and Hengstenberg, W. (1988) Site-directed mutagenesis with the ptsH gene of Bacillus subtilis. J Biol Chem 263: 17050-17054.
5. Frisby, D., and Zuber, P. 1994. Mutations in pts cause catabolite-resistant sporulation and altered regulation of spo0H in Bacillus subtilis. J. Bacteriol. 176: 2587-2595.
6. Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the Bacillus subtilis xyn cre and catabolite repression of the xyn operon. J Mol Biol 1999, 286:307-314.
7. Görke, B., Fraysse, L. & Galinier, A. Drastic differences in Crh and HPr synthesis levels reflect their different impacts on catabolite repression in Bacillus subtilis. J. Bacteriol. 186, 2992-2995 (2004).
8. Lindner, C., Galinier, A., Hecker, M. & Deutscher, J. Regulation of the activity of the Bacillus subtilis antiterminator LicT by multiple PEP-dependent, enzyme I- and HPr-catalysed phosphorylation. Mol. Microbiol. 31, 995-1006 (1999).
9. Lindner, C., Hecker, M., Le Coq, D. & Deutscher, J. Bacillus subtilis mutant LicT antiterminators exhibiting enzyme I- and HPr-independent antitermination affect catabolite repression of the bglPH operon. J. Bacteriol. 184, 4819-4828 (2002).
10. Martin-Verstraete, I., Charrier, V., Stülke, J., Galinier, A., Erni, B., Rapoport, G., & Deutscher, J. (1998) Antagonistic effects of dual PTS catalyzed phosphorylation on the Bacillus subtilis transcriptional activator LevR. Mol. Microbiol. 28: 293-303.
11. Martin-Verstraete, I., Deutscher, J., and Galinier, A. (1999) Phosphorylation of HPr and Crh by HprK, early steps in the catabolite repression signalling pathway for the Bacillus subtilis levanase operon. J Bacteriol 181: 2966-2969.
12. Reizer, J., Sutrina, S. L., Saier, Jr., M. H., Stewart, G. C., Peterkofsky, A., and Reddy, P. (1989) Mechanistic and physiological consequences of HPr(Ser) phosphorylation on the activities of the phosphoenolpyruvate:sugar phosphotransferase system in Gram-positive bacteria: studies with site-specific mutants of HPr. EMBO J 8: 2111-2120.
13. Schmalisch, M., Bachem, S. & Stülke, J. (2003) Control of the Bacillus subtilis antiterminator protein GlcT by phosphorylation: Elucidation of the phosphorylation chain leading to inactivation of GlcT. J. Biol. Chem. 278: 51108-51115.
14. Schumacher, M. A. et al. Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P. Cell 118, 731-741 (2004).
15. Singh, K. D., Halbedel, S., Görke, B. & Stülke, J. (2007) Control of the phosphorylation state of the HPr protein of the phosphotransferase system in Bacillus subtilis: implication of the protein phosphatase PrpC. J. Mol. Microbiol. Biotechnol. 13: 165-171.
16. Singh, K. D., Schmalisch, M. H., Stülke, J. & Görke, B. (2008) Carbon catabolite repression in Bacillus subtilis: A quantitative analysis of repression exerted by different carbon sources. J. Bacteriol. 190: 7275-7284.
17. Stülke, J., Martin-Verstraete, I., Charrier, V., Klier, A., Deutscher, J. & Rapoport, G. (1995) The HPr protein of the phosphotransferase system links induction and catabolite repression of the Bacillus subtilis levanase operon. J. Bacteriol. 177: 6928-6936.
18. Tortosa, P., Aymerich, S., Lindner, C., Saier, M.H., Jr., Reizer, J. and Le Coq, D. (1997) Multiple phosphorylation of SacY, a Bacillus subtilis antiterminator negatively controlled by the phosphotransferase system. J. Biol. Chem. 272, 17230-17237.

PtsG

2009-01-13T22:41:13Z

82.82.75.193:

* '''Description:''' Major glucose permease of the PTS, EIICBA(Glc) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ptsG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ptsX, crr''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glucose-specific enzyme IICBA component
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || glucose transport and phosphorylation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 75,3 kDa, 5.40
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2097 bp, 699 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glcT]]'', ''[[ptsH]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsG_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsG_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:ptsG_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 1456496 - 1458592

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10198]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transport and phosphorylation of glucose, receives a phosphate from [[PtsH |HPr]] at the IIA domain (His-620), the phosphate group is then transferred to the IIB domain (Cys-461) an finally to the incoming glucose. In the absence of glucose, PtsG phosphorylates and thereby inactivates the transcriptional antiterminator [[GlcT]].

* '''Protein family:''' PTS enzyme II, glucose family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** 11x transmembrane domain (16–36, 89–109, 139–159, 180–200, 233–253, 283–303, 313–333, 338–358, 365–385, 388–408)
** PTS EIIC domain ( 1-424)
** PTS EIIB domain (439–520)
** PTS EIIA domain (568–672)

* '''Modification:''' transient phosphorylation ([[PtsH |HPr]]-dependent) on His-620, then internal phosphotransfer from His-620 to Cys-461

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

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

* '''Interactions:''' PtsG-[[PtsH |HPr]], PtsG-[[GlcT]] (for phosphorylation of [[GlcT]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14527945 PubMed]

* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 NCBI]

=== Database entries ===

* '''Structure:''' IIA domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=56258 NCBI], NMR IIA domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=55395 NCBI]

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P20166]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13890]

* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?2.7.1.69]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
**''[[ptsG]]-[[ptsH]]-[[ptsI]]''
**''[[ptsH]]-[[ptsI]]''

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11902727 PubMed]

* '''Regulation:''' induction by glucose

* '''Regulatory mechanism:''' transcriptional antitermination via the [[GlcT]]-dependent RNA-switch [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9765562 PubMed]
* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

# Stülke J, Martin-Verstraete I, Zagorec M (1997) Induction of the ''Bacillus subtilis ptsGHI'' operon by glucose is controlled by a novel antiterminator, ''GlcT Mol Microbiol.'' '''25:''' 65-78. [http://www.ncbi.nlm.nih.gov/sites/entrez/11902727 PubMed]
# Bachem S, Stülke J. (1998) Regulation of the ''Bacillus subtilis'' GlcT antiterminator protein by components of the phosphotransferase system. ''J Bacteriol.'' '''180:''' 5319-26 [http://www.ncbi.nlm.nih.gov/sites/entrez/9765562 PubMed]
# Bachem, S., Faires, N., & Stülke, J. (1997) Characterization of the presumptive phosphorylation sites of the Bacillus subtilis glucose permease by site-directed mutagenesis: Implication in glucose transport and catabolite repression. FEMS Microbiol. L. 156: 233-238. [http://www.ncbi.nlm.nih.gov/sites/entrez/9513271 PubMed]
# Gonzy-Tréboul, G., de Waard, J. H., Zagorec, M., and Postma, P.W. (1991). The glucose permease of the phosphotransferase system of Bacillus subtilis: Evidence for IIGlc and IIIGlc domains. Mol. Microbiol. 5, 1241-1249. [http://www.ncbi.nlm.nih.gov/sites/entrez/1956301 PubMed]
# Langbein, I., Bachem, S. & Stülke, J. (1999) Specific interaction of the RNA binding domain of the Bacillus subtilis transcriptional antiterminator GlcT with its RNA target, RAT. J. Mol. Biol. 293: 795-805. [http://www.ncbi.nlm.nih.gov/sites/entrez/10543968 PubMed]
# Schilling, O., Herzberg, C., Hertrich, T., Vörsmann, H., Jessen, D., Hübner, S., Titgemeyer, F. & Stülke, J. (2006) Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples. Nucl. Acids Res. 34: 6102-6115. [http://www.ncbi.nlm.nih.gov/sites/entrez/17074746 PubMed]
# Schilling, O., Langbein, I., Müller, M., Schmalisch, M. & Stülke, J. (2004) A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity. Nucl. Acids Res. 32: 2853-2864. [http://www.ncbi.nlm.nih.gov/sites/entrez/15155854 PubMed]
# Schmalisch, M., Bachem, S. & Stülke, J. (2003) Control of the Bacillus subtilis antiterminator protein GlcT by phosphorylation: Elucidation of the phosphorylation chain leading to inactivation of GlcT. J. Biol. Chem. 278: 51108-51115. [http://www.ncbi.nlm.nih.gov/sites/entrez/14527945 PubMed]

Crh

2009-01-13T22:40:51Z

82.82.75.193:

* '''Description:''' "Catabolite rpression HPr-like protein", Cofactor of the [[CcpA]] transcription factor 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''crh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvcM''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || catabolite repression HPr-like protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolite repression
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9,2 kDa, 4.70
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 255 bp, 85 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcL]]'', ''[[yvcN]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/crh_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/crh_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:crh_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 3568325 - 3568579

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:'''

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12403]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[PtsH]],HPr family

* '''Paralogous protein(s):''' [[PtsH |HPr]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' HPr domain (1–85)

* '''Modification:''' phosphorylation at Ser46 by [[HPrK]]

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

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

* '''Interactions:''' Crh-[[ThiC]], Crh-[[MgsA]], Crh-[[GapA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed], Crh-[[Hag]], Crh-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed], [[HprK]]-Crh [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=24634 NCBI], dimer [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=64943 NCBI], CcpA-Crh-DNA complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], dimeric phosphor-Crh [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39567 NCBI]
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O06976]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34740]

=== Additional information===

Crh does not possess the phosphorylation site usedfor PTS phosphotransfer (His-15 in [[PtsH]]), it can only be phosphorylated on Ser-46

=Expression and regulation=

* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

[[Boris Görke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]

[[Anne Galinier]], University of Marseille, France

=Your additional remarks=

=References=

# Juy M, Penin F, Favier A (2003) Dimerization of Crh by reversible 3D domain swapping induces structural adjustments to its monomeric homologue Hpr. ''J Mol Biol.'' '''332(4):'''767-76. [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed]
# Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the Bacillus subtilis xyn cre and catabolite repression of the xyn operon. J Mol Biol 1999, 286:307-314. [http://www.ncbi.nlm.nih.gov/sites/entrez/9973552 PubMed]
# Galinier, A., Haiech, J., Kilhoffer, M.-C., Jaquinod, M., Stülke, J., Deutscher, J., & Martin-Verstraete, I. (1997) The Bacillus subtilis crh gene encodes a HPr-like protein involved in carbon catabolite repression. Proc. Natl. Acad. Sci. USA 94: 8439-8444. [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
# Görke, B., Fraysse, L. & Galinier, A. Drastic differences in Crh and HPr synthesis levels reflect their different impacts on catabolite repression in Bacillus subtilis. J. Bacteriol. 186, 2992-2995 (2004). [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed]
# Martin-Verstraete, I., Deutscher, J., and Galinier, A. (1999) Phosphorylation of HPr and Crh by HprK, early steps in the catabolite repression signalling pathway for the Bacillus subtilis levanase operon. J Bacteriol 181: 2966-2969. [http://www.ncbi.nlm.nih.gov/sites/entrez/10217795 PubMed]
# Pompeo ''et al.'' (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in ''Bacillus subtilis''? J Bacteriol 189, 1154-1157.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
# Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation. J. Biol. Chem. 281, 6793-6800 (2006). [http://www.ncbi.nlm.nih.gov/sites/entrez/16316990 PubMed]

CcpA

2009-01-13T22:40:31Z

82.82.75.193:

* '''Description:''' Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ccpA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36,8 kDa, 5.06
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[aroA]]'', ''[[motP]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpA_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpA_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:ccpA_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 3043210 - 3044211

===Phenotypes of a mutant ===

Loss of carbon catabolite repression.
Loss of PTS-dependent sugar transport due to excessive phosphorylation of [[PtsH |HPr]] by [[HprK]].
The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcriptional regulator of carbon catabolite repression (CCR)

* '''Protein family:''' LacI family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** HTH lacI-type Domain (1 – 58)
** DNA binding Domain (6 – 25)

* '''Modification:'''

* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, Crh-Ser-46-P

* '''Effectors of protein activity:'''glucose-6-phosphate, fructose-1,6-bisphosphate [http://www.ncbi.nlm.nih.gov/pubmed/17376479?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Pubmed]

* '''Interactions:''' CcpA-[[PtsH |HPr]] [http://www.ncbi.nlm.nih.gov/pubmed/15369672?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed], CcpA-[[Crh]] [http://www.ncbi.nlm.nih.gov/pubmed/16316990?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' CcpA-Crh-DNA-complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], complex with P-Ser-[[PtsH |HPr]] and sulphate ions [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39857 NCBI]

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P25144]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ccpA]] [[motP]] [[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]

[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]

[[Milton H. Saier]], University of California at San Diego, USA [http://biology.ucsd.edu/faculty/saier.html Homepage]

[[Yasutaro Fujita]], University of Fukuyama, Japan

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

=Your additional remarks=

=References=

'''Reviews'''

# Henkin, T. M. (1996) The role of the CcpA transcriptional regulator in carbon metabolism in Bacillus subtilis. FEMS Microbiol Lett 135: 9-15. [http://www.ncbi.nlm.nih.gov/sites/entrez/8598282 PubMed]
# Warner, J. B. & Lolkema, J. S. CcpA-dependent carbon catabolite repression in bacteria. Microbiol. Mol. Biol. Rev. 67, 475-490 (2003). [http://www.ncbi.nlm.nih.gov/sites/entrez/14665673 PubMed]

'''General and physiological studies'''

# Henkin, T. M., Grundy, F. J., Nicholson, W. L. and Chambliss, G. H. (1991) Catabolite repression of -amylase gene expression in Bacillus subtilis involves a trans-acting gene product homologous to the Escherichia coli lacI and galR repressors. Mol. Microbiol. 5, 575-584. [http://www.ncbi.nlm.nih.gov/sites/entrez/1904524 PubMed]
# Faires, N., Tobisch, S., Bachem, S., Martin-Verstraete, I., Hecker, M., & Stülke, J. (1999) The catabolite control protein CcpA controls ammonium assimilation in Bacillus subtilis. J. Mol. Microbiol. Biotechnol. 1: 141-148. [http://www.ncbi.nlm.nih.gov/sites/entrez/10941796 PubMed]
# Ludwig, H., Rebhan, N., Blencke, H.-M., Merzbacher, M. & Stülke, J. (2002) Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation. Mol. Microbiol. 45: 543-553. [http://www.ncbi.nlm.nih.gov/sites/entrez/12123463 PubMed]
# Miwa, Y., M. Saikawa, and Y. Fujita. 1994. Possible function and some properties of the CcpA protein of Bacillus subtilis. Microbiology 140:2567-2575. [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed]
# Singh, K. D., Schmalisch, M. H., Stülke, J. & Görke, B. (2008) Carbon catabolite repression in Bacillus subtilis: A quantitative analysis of repression exerted by different carbon sources. J. Bacteriol. 190: 7275-7284. [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
# Terahara et al. (2006) An intergenic stem-loop mutation in the Bacillus subtilis ccpA-motPS operon increases motPS transcription and the MotPS contribution to motility ''J Bacteriol.'' '''188:''' 2701-2705. [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]
# Wacker, I., Ludwig, H., Reif, I., Blencke, H.-M., Detsch, C. & Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009. [http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]

'''Global analyses (proteome, transcriptome)'''

# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
# Moreno MS, Schneider BL, Maile RR, Weyler W, Saier Jr MH: Catabolite repression mediated by CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analysis. Mol Microbiol 2001, 39:1366-1381. [http://www.ncbi.nlm.nih.gov/sites/entrez/11251851 PubMed]
# Tobisch, S., Zühlke, D., Bernhardt, J., Stülke, J. & Hecker, M. (1999) Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis. J. Bacteriol. 181: 6996-7004. [http://www.ncbi.nlm.nih.gov/sites/entrez/10559165 PubMed]
# Yoshida, K.-I., Kobayashi, K., Miwa, Y., Kang, C.-M., Matsunaga, M., Yamaguchi, H., Tojo, S., Yamamoto, M., Nishi, R., Ogasawara, N., Nakayama, T. & Fujita, Y. (2001). Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucl Acids Res 29, 6683-6692. [http://www.ncbi.nlm.nih.gov/sites/entrez/11160890 PubMed]

'''Repression of target genes by CcpA'''

# Belitsky BR, Sonenshein, AL: CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J Bacteriol 2004, 186:3392-3398. [http://www.ncbi.nlm.nih.gov/sites/entrez/15150224 PubMed]
# Choi SK, Saier MH Jr: Regulation of sigL expression by the catabolite control protein CcpA involves a roadblock mechanism in Bacillus subtilis: potential connection between carbon and nitrogen metabolism. J Bacteriol 2005, 187:6856-6861. [http://www.ncbi.nlm.nih.gov/sites/entrez/16166551 PubMed]
# Darbon, E., Servant, P., Poncet, S., and Deutscher, J. (2002). Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control Bacillus subtilis glpFK expression. Mol. Microbiol. 43, 1039-1052. [http://www.ncbi.nlm.nih.gov/sites/entrez/11929549 PubMed]
# Grundy, F. J., Turinski, A. J., and Henkin, T. M. (1994). Catabolite regulation of Bacillus subtilis acetate and acetoin utilization genes by CcpA. J. Bacteriol. 176, 4527-4533. [http://www.ncbi.nlm.nih.gov/sites/entrez/7913927 PubMed]
# Inacio, J. M. & de Sá-Nogueira, I. trans-Acting factors and cis-elements involved in glucose repression of arabinan degradation in Bacillus subtilis. J. Bacteriol. 189, 8371-8376 (2007). [http://www.ncbi.nlm.nih.gov/sites/entrez/17827291 PubMed]
# Kim HJ, Jourlin-Castelli C, Kim SI, Sonenshein AL (2002) Regulation of the Bacillus subtilis ccpC gene by CcpA and CcpC. Mol Microbiol 43:399-410 [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002) Direct and indirect roles of CcpA in regulation of Bacillus subtilis Krebs cycle genes. Mol Microbiol 45:179-190 [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Martin-Verstraete, I., Stülke, J., Klier, A. & Rapoport, G. (1995) Two different mechanisms mediate catabolite repression of the Bacillus subtilis levanase operon. J. Bacteriol. 177: 6919-6927. [http://www.ncbi.nlm.nih.gov/sites/entrez/7592486 PubMed]

'''Positive regulation of gene expression by CcpA'''

# Grundy FJ, Waters DA, Allen SH, Henkin TM (1993) Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J Bacteriol 175:7348-7355 [http://www.ncbi.nlm.nih.gov/sites/entrez/8226682 PubMed]
# Ludwig, H., Meinken, C., Matin, A. & Stülke, J. (2002) Insufficient expression of the ilv-leu operon encoding enzymes of branched-chain amino acids biosynthesis limits growth of a Bacillus subtilis ccpA mutant. J. Bacteriol. 184: 5174-5178. [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed]
# Presecan-Siedel, E., Galinier, A., Longin, R., Deutscher, J., Danchin, A., Glaser, P. and Martin-Verstraete, I. (1999) The catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis. J. Bacteriol. 181, 6889-6897. [http://www.ncbi.nlm.nih.gov/sites/entrez/10559153 PubMed]
# Shivers, R. P., and Sonenshein, A. L. (2005) Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol 56: 1549-1559. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916605 PubMed]
# Turinsky, A. J., Grundy, F. J., Kim, J. H., Chambliss, G. H., and Henkin, T. M. 1998. Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter. J. Bacteriol. 180: 5961-5967. [http://www.ncbi.nlm.nih.gov/sites/entrez/9811655 PubMed]
# Turinsky, A. J., Moir-Blais, T. R., Grundy, F. J., and Henkin, T. M. 2000. Bacillus subtilis ccpA gene mutants specifically defective in activation of acetoin synthesis. J. Bacteriol. 182:5611-5614. [http://www.ncbi.nlm.nih.gov/sites/entrez/10986270 PubMed]

'''Control of CcpA activity'''

# Deutscher, J., Küster, E., Bergstedt, U., Charrier, V., and Hillen, W. 1995. Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in Gram-positive bacteria. Mol. Microbiol. 15: 1049-1053. [http://www.ncbi.nlm.nih.gov/sites/entrez/7623661 PubMed]
# Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the Bacillus subtilis xyn cre and catabolite repression of the xyn operon. J Mol Biol 1999, 286:307-314. [http://www.ncbi.nlm.nih.gov/sites/entrez/9973552 PubMed]
# Jones, B. E., Dossonnet, V., Küster, E., Hillen, W., Deutscher, J. & Klevit, R. E. (1997). Binding of the catabolite repressor protein CcpA to its DNA target is regulated by phosphorylation of its corepressor HPr. J Biol Chem 272, 26530-26535. [http://www.ncbi.nlm.nih.gov/sites/entrez/9334231 PubMed]

'''CcpA-DNA interaction'''

# Fujita, Y., Miwa, Y., Galinier, A. and Deutscher, J. (1995) Specific recognition of the Bacillus subtilis gnt cis-acting catabolite-responsive element by a protein complex formed between CcpA and seryl-phosphorylated HPr. Mol. Microbiol. 17, 953-960. [http://www.ncbi.nlm.nih.gov/sites/entrez/8596444 PubMed]
# Miwa, Y., Nakata, A., Ogiwara, A., Yamamota, M., and Fujita, Y. 2000. Evaluation and characterization of catabolite-responsive elements (cre) of Bacillus subtilis. Nucl. Acids Res. 28: 1206-1210. [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
# Seidel G, Diel M, Fuchsbauer N, Hillen W: Quantitative interdependence of coeffectors, CcpA and cre in carbon catabolite regulation of Bacillus subtilis. FEBS J 2005, 272:2566-2577. [http://www.ncbi.nlm.nih.gov/sites/entrez/15885105 PubMed]

'''Functional analysis of CcpA'''

# Küster, E., Hilbich, T., Dahl, M. and Hillen, W. (1999) Mutations in catabolite control protein CcpA separating growth effects from catabolite repression. J. Bacteriol. 181, 4125-4128. [http://www.ncbi.nlm.nih.gov/sites/entrez/10383986 PubMed]
# Küster-Schöck, E., Wagner, A., Völker, U., and Hillen, W. (1999) Mutations in catabolite control protein CcpA showing glucose-independent regulation in Bacillus megaterium. J Bacteriol 181: 7634-7638. [http://www.ncbi.nlm.nih.gov/sites/entrez/10601226 PubMed]
# Ludwig, H. & Stülke, J. (2001) The Bacillus subtilis catabolite control protein CcpA exerts all its regulatory functions by DNA binding. FEMS Microbiol. Lett. 203: 125-129. [http://www.ncbi.nlm.nih.gov/sites/entrez/11557150 PubMed]

'''Structural analyses'''

# Schumacher, M. A. et al. Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P. Cell 118, 731-741 (2004). [http://www.ncbi.nlm.nih.gov/sites/entrez/15369672 PubMed]
# Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation. J. Biol. Chem. 281, 6793-6800 (2006). [http://www.ncbi.nlm.nih.gov/sites/entrez/16316990 PubMed]
# Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate. J. Mol. Biol. 368, 1042-1050 (2007). [http://www.ncbi.nlm.nih.gov/sites/entrez/17376479 PubMed]

AhrC

2009-01-13T22:40:11Z

82.82.75.193:

* '''Description:''' AhrC represses the genes for arginine biosynthesis and activates the genes for arginine catabolism. 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ahrC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''argR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional regulator of arginine metabolic genes
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16,7 kDa, 5.52
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 447 bp, 149 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqxC]]'', ''[[recN]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ahrC_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ahrC_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:ahrC_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2521558 - 2522004

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10309]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcriptional activator/ repressor of genes involved in arginine metabolism

* '''Protein family:''' ArgR family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' L-arginine is the co-factor required for transcription repression/ activation

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

* '''Interactions:'''

* '''Localization:''' Cytoplasm

=== Database entries ===

* '''Structure:''' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=18637 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/18455186 PubMed],N-Terminus [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=60156 NCBI], C-Terminus [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=60157 NCBI], complex with an 18bp DNA operator [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=62912 NCBI]

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P17893]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24250]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''ahrC''-''[[recN]]''

* '''Sigma factor:'''

* '''Regulation:''' by small RNA [[sr1]]

* '''Regulatory mechanism:''' inhibtion of translation upon binding of [[sr1]] to the ''ahrC'' mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

[[Simon Phillips|Simon Phillips]], Leeds University, UK [http://www.astbury.leeds.ac.uk/People/staffpage.php?StaffID=SEVP Homepage]

[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]

=Your additional remarks=

=References=

# Van Hoy BE et al. (1990) Characterization of the ''spoIVB'' and ''recN'' loci of ''Bacillus subtilis'' ''J Bacteriol.'' '''172:''' 1306-1311. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+2106508 PubMed]
# Heidrich et al. (2006) The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol. Microbiol. 62: 520-536. [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
# Heidrich et al. (2007) In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucl. Acids Res. 35: 4331-4346. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576690 PubMed]
# Garnett et al. (2008) Structure and function of the arginine repressor-operator complex from Bacillus subtilis. J. Mol. Biol. 379: 284-298. [http://www.ncbi.nlm.nih.gov/sites/entrez/18455186 PubMed]
# Garnett et al. (2007) Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor L-arginine. Acta Cryst. Sect. F. 63: 918-921. [http://www.ncbi.nlm.nih.gov/sites/entrez/18007040 PubMed]
# Garnett et al. (2007) A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Cryst. Sect. F. 63: 914-917. [http://www.ncbi.nlm.nih.gov/sites/entrez/18007039 PubMed]
# Dennis et al. (2002) The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Cryst. Sect. D. 58:421-430. [http://www.ncbi.nlm.nih.gov/sites/entrez/11856827 PubMed]
# Makarova et al. (2001) Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2: RESEARCH0013. [http://www.ncbi.nlm.nih.gov/sites/entrez/11305941 PubMed]
# Miller et al. (1997) Operator interactions by the Bacillus subtilis arginine repressor/ activator, AhrC: novel positioning and DNA-mediated assembly of a transcriptional activator at catabolic sites. Mol. Microbiol. 26: 37-48. [http://www.ncbi.nlm.nih.gov/sites/entrez/9383188 PubMed]
# Klingel et al. (1995) A binding site for activation by the Bacillus subtilis AhrC protein, a repressor/ activator of arginine metabolism. Mol. Gen. Genet. 248:329-340. [http://www.ncbi.nlm.nih.gov/sites/entrez/7565595 PubMed]
# Czaplewski et al. (1992) Purification and initial characterization of AhrC: the regulator of arginine metabolism genes in Bacillus subtilis. Mol. Microbiol. 6:267-275. [http://www.ncbi.nlm.nih.gov/sites/entrez/1312212 PubMed]
# North et al. (1989) Nucleotide sequence of a Bacillus subtilis arginine regulatory gene and homology of its product to the Escherichia coli arginine repressor. Gene 80:29-38. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID: 2507400 PubMed]

RocR

2009-01-13T22:39:43Z

82.82.75.193:

* '''Description:''' transcriptional activator of arginine utilization operons 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rocR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional activator of arginine utilization operons
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52.6 kDa, 6.08
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyxA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocR_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocR_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:rocR_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 4144771 - 4146153

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10723]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription activation at [[SigL]]-dependent promoters of ''[[rocA|rocABC]]'', ''[[rocD|rocDEF]]'', and ''[[rocG]]''

* '''Protein family:''' [[SigL | Sigma-54]] interacting transcription activator

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
**[[SigL | Sigma-54]] factor interaction domain (143–372)
**2x nucleotid-binding domain (171–178),(233–242)
**HTH motif (434–453)

* '''Modification:'''

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

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

* '''Interactions:''' RocR-[[SigL]]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P38022]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40350]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''rocR''

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]

* '''Regulation:''' autoregulation by [[RocR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]

* '''Regulatory mechanism:''' autorepression

* '''Additional information:'''

=Biological materials =

=Labs working on this gene/protein=

[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]

=Your additional remarks=

=References=

# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

RocG

2009-01-13T22:39:11Z

82.82.75.193:

* '''Description:''' catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rocG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of GltC
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:rocG_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 3879765 - 3881036

===Phenotypes of a mutant ===

Poor growth on complex media such as LB. No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH

* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''gltAB'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''rocG''

* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]

* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])

* '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]; [[AhrC]]: transcription activation ; [[CcpA]]: transcription repression

* '''Additional information:'''

Activation by RocR requires binding of RocG to a downstream element [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]

=Biological materials =

=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=

# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
# Herzberg, C., Flórez Weidinger, L. A., Dörrbecker, B., Hübner, S., Stülke, J. & Commichau, F. M. (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 7: 4032-4035. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]
# Ali, N. O., J. Jeusset, E. Larquet, E. le Cam, B. Belitsky, A. L. Sonenshein, T. Msadek, and M. Débarbouillé. 2003. Specificity of the interaction of RocR with the rocG-rocA intergenic region in Bacillus subtilis. Microbiology 149: 739-750. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]
# Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9829940 PubMed]
# Belitsky BR, Sonenshein, AL: An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc Natl Acad Sci USA 1999, 96:10290-10295. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
# Belitsky BR, Sonenshein, AL: CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J Bacteriol 2004, 186:3392-3398. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150224 PubMed]
# Belitsky BR, Sonenshein AL (2004) Modulation of activity of Bacillus subtilis regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186:3399-3407 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150225 PubMed]
# Khan, M. I., K. Ito, H. Kim, H. Ashida, T. Ishikawa, H. Shibata, and Y. Sawa. 2005. Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis. Biosci. Biotechnol. Biochem. 69: 1861-1870. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+16244435 PubMed]
# Stillman TJ, Baker PJ, Britton KL, Rice DW Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J Mol Biol 1993, 234:1131-1139. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8263917 PubMed]

GltC

2009-01-13T22:38:38Z

82.82.75.193:

* '''Description:''' Transcriptional activator of the ''gltAB'' operon. Activates expression of the operon in the absence of arginine. 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || No
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LysR family)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || positive regulation of the glutamate synthase operon (''gltAB'')
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33.9 kDa, 5.62
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[proJ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltC_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltC_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:gltC_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2013989 - 2014888

===Phenotypes of a mutant ===
''gltC'' mutants are auxotrophic for glutamate.

=== Database entries ===

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10810]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription activation of the ''gltAB'' operon [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Protein family:''' LysR-type transcription regulator [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]

* '''Paralogous protein(s):''' none, but there are 19 members of the LysR family in ''B. subtilis''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' DNA-binding helix-turn-helix motif: AA 18 ... 37

* '''Modification:'''

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

* '''Effectors of protein activity:''' 2-oxoglutarate stimulates transcription activation, glutamate inhibits transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]

* '''Interactions:'''
** GltC-[[RocG]], This interaction takes place in the presence of glutamate. It prevents the transcription activation of the ''gltAB'' operon. Note that [[RocG]] expression is strongly regulated. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P20668 P20668]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18460 KEGG]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[gltC]]''

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

* '''Regulation:''' autoregulation by GltC

* '''Regulatory mechanism:''' autorepression

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html DBTBS]

* ''' Additional information:'''

=Biological materials =

* '''Mutant:''' GP344 (erm), GP738 (spc) (available in Stülke lab)

* '''Expression vector:''' pGP903 (N-terminal His-tag) (available in Stülke lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:''' available in 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=

# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
# Herzberg, C., Flórez Weidinger, L. A., Dörrbecker, B., Hübner, S., Stülke, J. & Commichau, F. M. (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 7: 4032-4035. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]
# Schell, M. A. (1993). Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47, 597-626. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8257110 PubMed]

GltA

2009-01-13T18:53:43Z

82.82.75.193:

* '''Description:''' large subunit of glutamate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (large subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 168 kDa, 5.47
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 4560 bp, 1520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltC]]'', ''[[gltB]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltA_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gltA_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:gltA_context.gif]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Coordinates:''' 2009283 - 2013842

===Phenotypes of a mutant ===

auxotrophic for glutamate

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10811]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH

* '''Protein family:''' glutamate synthase family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** Glutamine amidotransferase type-2 domain (22-415)
** Nucleotide binding domain (1060-1112)

* '''Modification:'''

* '''Cofactor(s):''' 3Fe-4S, FAD, FMN

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

* '''Interactions:'''

* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18763711 PubMed], cytoplasm

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39812]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18450]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.13]

=== Additional information===

subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[gltA]] [[gltB]]''

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

* '''Regulation:''' induced by sugar, repressed by arginine, ammonium required

* '''Regulatory mechanism:''' Aktivator: [[GltC]]; Repressor: [[TnrA]], pos. regulated by [[GltR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9023181 PubMed]

* '''Additional information:'''

=Biological materials =

=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=

# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
# Belitsky BR, Sonenshein AL (1997) Altered transcription activation specificity of a mutant form of Bacillus subtilis GltR, a LysR family member. J Bacteriol 179:1035-1043 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
# Belitsky, B. R., Wray, L. V., Jr., Fisher, S. H., Bohannon, D. E. & Sonenshein, A. L. (2000). Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression. J Bacteriol 182, 5939-5947. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8:4123-4136 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18763711 PubMed]