SubtiWiki - User contributions [en]

Pgk

2010-03-19T08:36:40Z

Npietac:

* '''Description:''' phosphoglycerate kinase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgk''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglycerate kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42,0 kDa, 4.77
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1182 bp, 394 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tpi]]'', ''[[gapA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15398]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgk_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33930

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11062]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + 3-phospho-D-glycerate = ADP + 1,3-bisphosphoglycerate (according to Swiss-Prot)

* '''Protein family:''' phosphoglycerate kinase family (according to Swiss-Prot)
* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Two Substrate Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Domains:'''
** nucleotide binding domain (ATP) (350–353)
** 2x substrate binding domain (21–23), (59–62)

* '''Modification:''' phosphorylation on Ser-183 AND Thr-299 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+ or Mn2+ [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Effectors of protein activity:'''
** Inhibited by Co2+, NDP and NMP [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1PHP 1PHP] (Geobacillus stearothermophilus), ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=57113 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P40924 P40924]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33930]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.2.3 2.7.2.3]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:'''
** ''[[cggR]]'': [[SigA]] {{PubMed|11489127}}
** ''[[pgk]]'': [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP699 (''pgk''::''cat''), available in [[Stülke]] lab
* GP707 (''pgk''::''erm''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1102 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP95 (N-terminal Strep-tag, in [[pGP172]]), available in [[Stülke]] lab
** pGP91 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab
** pGP1513 (expression in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:''' pGP514 (in [[pAC6]]), a series of promoter deletion variants is also available in [[pAC6]], available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 16479537, 12850135 , 17726680, 11489127 ,17505547 , 17218307 7154941 12682299 </pubmed>

[[Category:Protein-coding genes]]

GapB

2010-03-19T08:35:19Z

Npietac:

* '''Description:''' glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent, gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde-3-phosphate dehydrogenase 2
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || anabolic enzyme in gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37,3 kDa, 6.47
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1020 bp, 340 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[speD]]'', ''[[ytcD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14862]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29020

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12592]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H (according to Swiss-Prot)
** This reaction is part of the gluconeogenesis

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''
** Nucleotid bindinge domain (12-13)
** 2x Glyceraldehyde 3-phosphate binding domain (151-153) & (210-211)

* '''Modification:'''

* '''Cofactor(s):''' NADP (preferentially) and NAD [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34425 O34425]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29020]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.59 1.2.1.59]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[gapB]]-[[speD]]'' {{PubMed|15720552}}

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

* '''Regulation:'''
** repressed in the presence of glucose (70-fold) ([[CcpN]]) {{PubMed|15720552}}

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP701 (''gapB''::''spec''), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed> 16479537,10799476,10844697 ,15720552,18586936,17114254</pubmed>

[[Category:Protein-coding genes]]

GapB

2010-03-19T08:34:06Z

Npietac:

* '''Description:''' glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent, gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde-3-phosphate dehydrogenase 2
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || anabolic enzyme in gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37,3 kDa, 6.47
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1020 bp, 340 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[speD]]'', ''[[ytcD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14862]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29020

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12592]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H (according to Swiss-Prot)
** This reaction is part of the gluconeogenesis

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''
** Nucleotid bindinge domain (12-13)
** 2x Glyceraldehyde 3-phosphate binding domain (151-153) & (210-211)

* '''Modification:'''

* '''Cofactor(s):''' NADP (preferentially) and NAD [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34425 O34425]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29020]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.59 1.2.1.59]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[gapB]]-[[speD]]'' {{PubMed|15720552}}

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

* '''Regulation:'''
** repressed in the presence of glucose (70-fold) ([[CcpN]]) {{PubMed|15720552}}

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP701 (''gapB''::''spec'')

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed> 16479537,10799476,10844697 ,15720552,18586936,17114254</pubmed>

[[Category:Protein-coding genes]]

Pyk

2010-03-19T08:32:35Z

Npietac:

* '''Description:''' pyruvate kinase, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pyk''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytzA]]'', ''[[pfkA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14878]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pyk_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29180

===Phenotypes of a mutant ===

Unable to grow with non-PTS carbohydrates (such as glucitol or glycerol) as single carbon source.

=== 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+BG12661]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ADP + phosphoenolpyruvate --> ATP + pyruvate
** The reaction is irreversible under physiological conditions

* '''Protein family:''' PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], phosphorylation on Ser536 or Ser546 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], please note that the Ser is not on position 536 but rather at 538

* '''Cofactor(s):''' Mg2+, K+

* '''Effectors of protein activity:'''
** Activated by PEP (Hill Coefficient 1,8) [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Allosterically activated by AMP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Activation by r5p and ADP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Inhibition by ADP and f16bp in high concentrations; and ATP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2E28 2E28] (Geobacillus stearothermophilus)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80885 P80885]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29180]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]

=== Additional information===
The enzyme is a tetramer with four active sites [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[pfkA]]-[[pyk]]-[[ytzA]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:'''
** twofold induced by glucose {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP589 (''pyk''::''cat''), available in [[Stülke]] lab
* GP600 (''pyk''::''erm''), available in [[Stülke]] lab

* '''Expression vector:'''
** expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab
** expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Stülke]] lab
** expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Stülke]] lab
** expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Stülke]] lab

* '''lacZ fusion:''' see ''[[pfkA]]''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 </pubmed>

[[Category:Protein-coding genes]]

Eno

2010-03-19T08:29:05Z

Npietac:

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''eno''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:eno_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33900

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H2O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Domains:'''
** substrate binding domain (366–369)

* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3ES8 3ES8] (from ''Oceanobacillus iheyensis'', complex with Mg(2+) and malate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]

=== Additional information===
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
* [[universally conserved protein]]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP594 (''eno''::''cat''), available in [[Stülke]] lab
* GP599 (''eno''::''erm''), available in [[Stülke]] lab
* GP698 (''eno''-''pgm''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1426 (expression of ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP399 (expression of ''eno'' from ''E. coli'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab

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

* '''Antibody:''' available in [[Stülke]] lab

=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=

<pubmed> 17726680, 17218307, 12850135 , 19193632 , 11489127, 8021172, 17505547, 25885 15003462 </pubmed>

[[Category:Protein-coding genes]]

Eno

2010-03-19T08:28:20Z

Npietac:

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''eno''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:eno_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33900

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H2O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Domains:'''
** substrate binding domain (366–369)

* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3ES8 3ES8] (from ''Oceanobacillus iheyensis'', complex with Mg(2+) and malate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]

=== Additional information===
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
* [[universally conserved protein]]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP594 (''eno''::''cat''), available in [[Stülke]] lab
* GP599 (''eno''::''erm''), available in [[Stülke]] lab
* GP698 (''eno'-''pgm''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1426 (expression of ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP399 (expression of ''eno'' from ''E. coli'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab

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

* '''Antibody:''' available in [[Stülke]] lab

=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=

<pubmed> 17726680, 17218307, 12850135 , 19193632 , 11489127, 8021172, 17505547, 25885 15003462 </pubmed>

[[Category:Protein-coding genes]]

Eno

2010-03-19T08:27:42Z

Npietac:

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''eno''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:eno_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33900

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H2O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Domains:'''
** substrate binding domain (366–369)

* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3ES8 3ES8] (from ''Oceanobacillus iheyensis'', complex with Mg(2+) and malate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]

=== Additional information===
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
* [[universally conserved protein]]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP594 (''eno''::''cat''), available in [[Stülke]] lab
* GP599 (''eno''::''erm''), available in [[Stülke]] lab
* GP698 (''eno'-''pgm'''::''cat''), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1426 (expression of ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP399 (expression of ''eno'' from ''E. coli'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab

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

* '''Antibody:''' available in [[Stülke]] lab

=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=

<pubmed> 17726680, 17218307, 12850135 , 19193632 , 11489127, 8021172, 17505547, 25885 15003462 </pubmed>

[[Category:Protein-coding genes]]

PfkA

2010-03-19T08:24:59Z

Npietac:

* '''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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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''' || ''[[pyk]]'', ''[[accA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pfkA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29190

===Phenotypes of a mutant ===

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

=== 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 (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation (Reversible) [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]

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

* '''Modification:'''

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by citrate, PEP (Hill Coefficient 3) and Ca2+ (competes with Mg2+) in ''B. licheniformes'' [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed].
** Inhibited by ATP (competitively) and f6p (non-competitively) in ''G. stearothermophillus'' [http://www.ncbi.nlm.nih.gov/pubmed/8136379 PubMed]
** Activated by GDP and ADP in lower concentrations (1mM); above that inhibition, competing with the ATP for the binding site (in ''G. stearothermophillus'') [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]

* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MTO 1MTO] (mutant, complex with fructose-6-phosphate, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=4PFK 4PFK] (Geobacillus stearothermophilus), ''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]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34529 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 2.7.1.11]

=== Additional information===
PfkA is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

=Expression and regulation=
* '''Operon:''' ''[[pfkA]]-[[pyk]]-[[ytzA]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:'''
** twofold induced by glucose {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP590 (''pfkA''::''cat''), available in [[Stülke]] lab
* GP595 (''pfkA''::''erm''), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP87, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP393, available in [[Stülke]] lab
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1422, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed> 16479537,19193632, 11489127, 8136379, 7873536 4269800 </pubmed>

[[Category:Protein-coding genes]]

FbaA

2010-03-19T08:24:22Z

Npietac:

* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywjH]]'', ''[[spo0F]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15729]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:fbaA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37120

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate (according to Swiss-Prot)

* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot)
* '''Paralogous protein(s):''' [[FbaB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Domains:'''
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)

* '''Modification:''' phosphorylation on Thr-212 and Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):''' Zn2+ (Metalloenzyme)

* '''Effectors of protein activity:'''
** Inhibited by alpha-ketoglutarate, oxaloacetate and pyruvate [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2fjk 2FJK] (from ''Thermus caldophilus'') {{PubMed|16843441}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P13243 P13243]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13]

=== Additional information===

Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution

=Expression and regulation=

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

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP591 (''fbaA''::''cat''), available in [[Stülke]] lab
* GP596 (''fbaA''::''erm''), available in [[Stülke]] lab

* '''Expression vector:'''
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1423, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP88, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP395, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP601 (in [[pAC6]])

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307, 15125960, 24624 16843441 11489127</pubmed>

[[Category:Protein-coding genes]]

GapA

2010-03-19T08:23:37Z

Npietac:

* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[cggR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15399]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33940

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
** This reaction is part of the glycolysis.

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''

* '''Modification:'''
** Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed2]
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]

* '''Cofactor(s):''' NAD+ (do not accept NADP+) [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''
** GapA-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** GapA-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1GD1 1GD1] (from ''Geobacillus stearothermophilus'')
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09124 P09124]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]

=== Additional information===

GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[cggR]]-[[gapA]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (10 fold) ([[CggR]]) {{PubMed|12850135,12622823}}

* '''Regulatory mechanism:'''
** [[CggR]]: transcription repression {{PubMed|11489127}}

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:'''
** GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).
** The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed|11489127}} The processing event requires the [[Rny|RNase Y]] {{PubMed|19193632}}.

=Biological materials =
* '''Mutant:'''
* GP592 (''gapA''::''cat''), available in [[Stülke]] lab
* GP597 (''gapA''::''erm''), available in [[Stülke]] lab
* GP703 (''gapA''::''cat'' ''gapB''::''spec''), available in [[Stülke]] lab
* GM1501 (under p(spac) control), available in [[Stephane Aymerich]] lab

* '''Expression vector:'''
** pGP1424 (expression in ''B. subtilis'', in [[pBQ200]]) (available in [[Stülke]] lab)
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Stülke]] lab

=Labs working on this gene/protein=

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

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

=Your additional remarks=

=References=

<pubmed> 12850135,19193632, 18673455 , 17726680,16479537,12622823,12359717,10799476,17505547,11489127,12123463,17218307,12634343,17142398,17114254,10559165 </pubmed>

[[Category:Protein-coding genes]]

GapA

2010-03-19T08:22:36Z

Npietac:

* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[cggR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15399]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33940

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
** This reaction is part of the glycolysis.

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''

* '''Modification:'''
** Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed2]
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]

* '''Cofactor(s):''' NAD+ (do not accept NADP+) [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''
** GapA-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** GapA-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1GD1 1GD1] (from ''Geobacillus stearothermophilus'')
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09124 P09124]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]

=== Additional information===

GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[cggR]]-[[gapA]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (10 fold) ([[CggR]]) {{PubMed|12850135,12622823}}

* '''Regulatory mechanism:'''
** [[CggR]]: transcription repression {{PubMed|11489127}}

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:'''
** GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).
** The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed|11489127}} The processing event requires the [[Rny|RNase Y]] {{PubMed|19193632}}.

=Biological materials =

* GP592 (''gapA''::''cat''), available in [[Stülke]] lab
* GP597 (''gapA''::''erm''), available in [[Stülke]] lab
* GP703 (''gapA''::''cat'' ''gapB''::''spec''), available in [[Stülke]] lab
* '''Mutant:''' essential, GM1501 (under p(spac) control), available in [[Stephane Aymerich]] lab

* '''Expression vector:'''
** pGP1424 (expression in ''B. subtilis'', in [[pBQ200]]) (available in [[Stülke]] lab)
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Stülke]] lab

=Labs working on this gene/protein=

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

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

=Your additional remarks=

=References=

<pubmed> 12850135,19193632, 18673455 , 17726680,16479537,12622823,12359717,10799476,17505547,11489127,12123463,17218307,12634343,17142398,17114254,10559165 </pubmed>

[[Category:Protein-coding genes]]

Pgm

2010-03-19T08:21:54Z

Npietac:

* '''Description:''' phosphoglycerate mutase, glycolytic / gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgm''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis / gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[eno]]'', ''[[tpi]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15396]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgm_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33910

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate (according to Swiss-Prot)

* '''Protein family:''' BPG-independent phosphoglycerate mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/33963 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mn2+

* '''Effectors of protein activity:'''
** Inhibited by diverse divalent heavy-metal ions, EDTA and 2,3-butanedione [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]
** 2,3-Diphosphoglycerate has NO role on this enzyme regulation [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EJJ 1EJJ] (Geobacillus stearothermophilus, complex with 3-phosphoglycerate), [http://www.rcsb.org/pdb/explore.do?structureId=1EQJ 1EQJ] (Geobacillus stearothermophilus, complex with 2-phosphoglycerate), ''Geobacillus stearothermophilus'', complex with 2-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=16359 NCBI], ''Geobacillus stearothermophilus'', complex with 3-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=15578 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39773 P39773]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33910]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1 5.4.2.1]]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =
* '''Mutant:'''
* GP593 (''pgm''::''cat''), available in [[Stülke]] lab
* GP598 (''pgm''::''erm''), available in [[Stülke]] lab
* GP698 (''pgm''-''eno''::cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1425 (expression of ''pgm'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP1101 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

[[Jedrzejas|Mark J. Jedrzejas]], Research Center Oakland, CA, USA [http://www.chori.org/Principal_Investigators/Jedrzejas_Mark_J/jedrzejas_research.html Homepage]

=Your additional remarks=

=References=

<pubmed>11514674,17085493,10764795,8215434,10747010,11712498,9830105,10388626,8636019,11827481,16479537, 12850135,17726680,17505547, 8021172,11489127, 10388626,10747010, 10764795, 11712498, 12729763, 17085493, 17218307 33963 </pubmed>

[[Category:Protein-coding genes]]

Pgm

2010-03-19T08:20:57Z

Npietac:

* '''Description:''' phosphoglycerate mutase, glycolytic / gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgm''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis / gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[eno]]'', ''[[tpi]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15396]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgm_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33910

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate (according to Swiss-Prot)

* '''Protein family:''' BPG-independent phosphoglycerate mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/33963 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mn2+

* '''Effectors of protein activity:'''
** Inhibited by diverse divalent heavy-metal ions, EDTA and 2,3-butanedione [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]
** 2,3-Diphosphoglycerate has NO role on this enzyme regulation [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EJJ 1EJJ] (Geobacillus stearothermophilus, complex with 3-phosphoglycerate), [http://www.rcsb.org/pdb/explore.do?structureId=1EQJ 1EQJ] (Geobacillus stearothermophilus, complex with 2-phosphoglycerate), ''Geobacillus stearothermophilus'', complex with 2-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=16359 NCBI], ''Geobacillus stearothermophilus'', complex with 3-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=15578 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39773 P39773]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33910]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1 5.4.2.1]]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =
* GP593 (''pgm''::''cat'')
* GP598 (''pgm''::''erm'')
* '''Mutant:''' GP698 (''pgm''-''eno''::cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1425 (expression of ''pgm'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP1101 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

[[Jedrzejas|Mark J. Jedrzejas]], Research Center Oakland, CA, USA [http://www.chori.org/Principal_Investigators/Jedrzejas_Mark_J/jedrzejas_research.html Homepage]

=Your additional remarks=

=References=

<pubmed>11514674,17085493,10764795,8215434,10747010,11712498,9830105,10388626,8636019,11827481,16479537, 12850135,17726680,17505547, 8021172,11489127, 10388626,10747010, 10764795, 11712498, 12729763, 17085493, 17218307 33963 </pubmed>

[[Category:Protein-coding genes]]

FbaA

2010-03-19T08:17:44Z

Npietac:

* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywjH]]'', ''[[spo0F]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15729]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:fbaA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37120

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate (according to Swiss-Prot)

* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot)
* '''Paralogous protein(s):''' [[FbaB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Domains:'''
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)

* '''Modification:''' phosphorylation on Thr-212 and Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):''' Zn2+ (Metalloenzyme)

* '''Effectors of protein activity:'''
** Inhibited by alpha-ketoglutarate, oxaloacetate and pyruvate [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2fjk 2FJK] (from ''Thermus caldophilus'') {{PubMed|16843441}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P13243 P13243]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13]

=== Additional information===

Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution

=Expression and regulation=

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

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP591 (''fbaA''::''cat'')
* GP596 (''fbaA''::''erm'')

* '''Expression vector:'''
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1423, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP88, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP395, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP601 (in [[pAC6]])

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307, 15125960, 24624 16843441 11489127</pubmed>

[[Category:Protein-coding genes]]

PfkA

2010-03-19T08:17:19Z

Npietac:

* '''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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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''' || ''[[pyk]]'', ''[[accA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pfkA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29190

===Phenotypes of a mutant ===

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

=== 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 (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation (Reversible) [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]

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

* '''Modification:'''

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by citrate, PEP (Hill Coefficient 3) and Ca2+ (competes with Mg2+) in ''B. licheniformes'' [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed].
** Inhibited by ATP (competitively) and f6p (non-competitively) in ''G. stearothermophillus'' [http://www.ncbi.nlm.nih.gov/pubmed/8136379 PubMed]
** Activated by GDP and ADP in lower concentrations (1mM); above that inhibition, competing with the ATP for the binding site (in ''G. stearothermophillus'') [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]

* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MTO 1MTO] (mutant, complex with fructose-6-phosphate, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=4PFK 4PFK] (Geobacillus stearothermophilus), ''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]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34529 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 2.7.1.11]

=== Additional information===
PfkA is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

=Expression and regulation=
* '''Operon:''' ''[[pfkA]]-[[pyk]]-[[ytzA]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:'''
** twofold induced by glucose {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP590 (''pfkA''::''cat'')
* GP595 (''pfkA''::''erm'')

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP87, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP393, available in [[Stülke]] lab
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1422, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed> 16479537,19193632, 11489127, 8136379, 7873536 4269800 </pubmed>

[[Category:Protein-coding genes]]

GapA

2010-03-19T08:16:16Z

Npietac:

* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[cggR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15399]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33940

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
** This reaction is part of the glycolysis.

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''

* '''Modification:'''
** Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed2]
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]

* '''Cofactor(s):''' NAD+ (do not accept NADP+) [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''
** GapA-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** GapA-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1GD1 1GD1] (from ''Geobacillus stearothermophilus'')
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09124 P09124]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]

=== Additional information===

GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[cggR]]-[[gapA]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (10 fold) ([[CggR]]) {{PubMed|12850135,12622823}}

* '''Regulatory mechanism:'''
** [[CggR]]: transcription repression {{PubMed|11489127}}

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:'''
** GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).
** The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed|11489127}} The processing event requires the [[Rny|RNase Y]] {{PubMed|19193632}}.

=Biological materials =

* GP592 (''gapA''::''cat'')
* GP597 (''gapA''::''erm'')
* GP703 (''gapA''::''cat'' ''gapB''::''spec'')
* '''Mutant:''' essential, GM1501 (under p(spac) control), available in [[Stephane Aymerich]] lab

* '''Expression vector:'''
** pGP1424 (expression in ''B. subtilis'', in [[pBQ200]]) (available in [[Stülke]] lab)
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Stülke]] lab

=Labs working on this gene/protein=

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

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

=Your additional remarks=

=References=

<pubmed> 12850135,19193632, 18673455 , 17726680,16479537,12622823,12359717,10799476,17505547,11489127,12123463,17218307,12634343,17142398,17114254,10559165 </pubmed>

[[Category:Protein-coding genes]]

FbaA

2010-03-19T08:10:52Z

Npietac:

* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywjH]]'', ''[[spo0F]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15729]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:fbaA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37120

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate (according to Swiss-Prot)

* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot)
* '''Paralogous protein(s):''' [[FbaB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Domains:'''
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)

* '''Modification:''' phosphorylation on Thr-212 and Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):''' Zn2+ (Metalloenzyme)

* '''Effectors of protein activity:'''
** Inhibited by alpha-ketoglutarate, oxaloacetate and pyruvate [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2fjk 2FJK] (from ''Thermus caldophilus'') {{PubMed|16843441}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P13243 P13243]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13]

=== Additional information===

Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution

=Expression and regulation=

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

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP591 (''fbaA''::''cat'')
* GP596 (''fbaA''::''ery'')

* '''Expression vector:'''
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1423, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP88, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP395, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP601 (in [[pAC6]])

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307, 15125960, 24624 16843441 11489127</pubmed>

[[Category:Protein-coding genes]]

PfkA

2010-03-19T08:07:15Z

Npietac:

* '''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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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''' || ''[[pyk]]'', ''[[accA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pfkA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29190

===Phenotypes of a mutant ===

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

=== 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 (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation (Reversible) [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]

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

* '''Modification:'''

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by citrate, PEP (Hill Coefficient 3) and Ca2+ (competes with Mg2+) in ''B. licheniformes'' [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed].
** Inhibited by ATP (competitively) and f6p (non-competitively) in ''G. stearothermophillus'' [http://www.ncbi.nlm.nih.gov/pubmed/8136379 PubMed]
** Activated by GDP and ADP in lower concentrations (1mM); above that inhibition, competing with the ATP for the binding site (in ''G. stearothermophillus'') [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]

* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MTO 1MTO] (mutant, complex with fructose-6-phosphate, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=4PFK 4PFK] (Geobacillus stearothermophilus), ''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]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34529 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 2.7.1.11]

=== Additional information===
PfkA is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

=Expression and regulation=
* '''Operon:''' ''[[pfkA]]-[[pyk]]-[[ytzA]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:'''
** twofold induced by glucose {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP590 (''pfkA''::''cat'')
* GP595 (''pfkA''::''ery'')

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP87, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP393, available in [[Stülke]] lab
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1422, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed> 16479537,19193632, 11489127, 8136379, 7873536 4269800 </pubmed>

[[Category:Protein-coding genes]]

PfkA

2010-03-19T08:06:43Z

Npietac:

* '''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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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''' || ''[[pyk]]'', ''[[accA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pfkA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29190

===Phenotypes of a mutant ===

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

=== 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 (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation (Reversible) [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]

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

* '''Modification:'''

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by citrate, PEP (Hill Coefficient 3) and Ca2+ (competes with Mg2+) in ''B. licheniformes'' [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed].
** Inhibited by ATP (competitively) and f6p (non-competitively) in ''G. stearothermophillus'' [http://www.ncbi.nlm.nih.gov/pubmed/8136379 PubMed]
** Activated by GDP and ADP in lower concentrations (1mM); above that inhibition, competing with the ATP for the binding site (in ''G. stearothermophillus'') [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]

* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MTO 1MTO] (mutant, complex with fructose-6-phosphate, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=4PFK 4PFK] (Geobacillus stearothermophilus), ''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]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34529 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 2.7.1.11]

=== Additional information===
PfkA is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

=Expression and regulation=
* '''Operon:''' ''[[pfkA]]-[[pyk]]-[[ytzA]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:'''
** twofold induced by glucose {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
* GP590 (''pfkA''::''cat'')
* GP595 (''pfkA''::''mls'')

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP87, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP393, available in [[Stülke]] lab
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1422, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed> 16479537,19193632, 11489127, 8136379, 7873536 4269800 </pubmed>

[[Category:Protein-coding genes]]

Pgi

2010-03-18T22:00:44Z

Npietac:

* '''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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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''' || ''[[yugM]]'', ''[[yugK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15124]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pgi_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31350

===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 (according to Swiss-Prot) D-glucose 6-phosphate = D-fructose 6-phosphate

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/7400125 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Thr-39 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:''' competitively inhibited by 6-phosphogluconate (in ''B.caldotenax, B.stearothermophilus'') [http://www.ncbi.nlm.nih.gov/pubmed/7400125 PubMed]

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0Z 1B0Z] (''Geobacillus stearothermophilus''), [http://www.proteopedia.org/wiki/index.php/2pgi 2PGI] (''Geobacillus stearothermophilus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80860 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 5.3.1.9]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pgi]]-[[yugM]]-[[yugN]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP508 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* pGP398 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab

* '''lacZ fusion:''' pGP510 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

[http://www.ncbi.nlm.nih.gov/pubmed/17218307,19052382,4214896,11489127,4275311,11491085,17218307 PubMed]

<pubmed>17218307 19052382 4214896 11489127 4275311 11491085 17218307, </pubmed>

[[Category:Protein-coding genes]]

Pgi

2010-03-18T22:00:06Z

Npietac:

* '''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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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''' || ''[[yugM]]'', ''[[yugK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15124]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:pgi_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31350

===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 (according to Swiss-Prot) D-glucose 6-phosphate = D-fructose 6-phosphate

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/7400125 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Thr-39 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:''' competitively inhibited by 6-phosphogluconate (in ''B.caldotenax, B.stearothermophilus'') [http://www.ncbi.nlm.nih.gov/pubmed/7400125 PubMed]

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0Z 1B0Z] (''Geobacillus stearothermophilus''), [http://www.proteopedia.org/wiki/index.php/2pgi 2PGI] (''Geobacillus stearothermophilus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80860 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 5.3.1.9]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[pgi]]-[[yugM]]-[[yugN]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP508 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* '''pGP398 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab

* '''lacZ fusion:''' pGP510 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

[http://www.ncbi.nlm.nih.gov/pubmed/17218307,19052382,4214896,11489127,4275311,11491085,17218307 PubMed]

<pubmed>17218307 19052382 4214896 11489127 4275311 11491085 17218307, </pubmed>

[[Category:Protein-coding genes]]

Eno

2010-03-18T21:55:06Z

Npietac:

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''eno''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:eno_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33900

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H2O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Domains:'''
** substrate binding domain (366–369)

* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3ES8 3ES8] (from ''Oceanobacillus iheyensis'', complex with Mg(2+) and malate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]

=== Additional information===
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
* [[universally conserved protein]]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP698 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1426 (expression of ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP399 (expression of ''eno'' from ''E. coli'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab

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

* '''Antibody:''' available in [[Stülke]] lab

=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=

<pubmed> 17726680, 17218307, 12850135 , 19193632 , 11489127, 8021172, 17505547, 25885 15003462 </pubmed>

[[Category:Protein-coding genes]]

Pgm

2010-03-18T21:52:35Z

Npietac:

* '''Description:''' phosphoglycerate mutase, glycolytic / gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgm''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis / gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[eno]]'', ''[[tpi]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15396]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgm_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33910

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate (according to Swiss-Prot)

* '''Protein family:''' BPG-independent phosphoglycerate mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/33963 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mn2+

* '''Effectors of protein activity:'''
** Inhibited by diverse divalent heavy-metal ions, EDTA and 2,3-butanedione [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]
** 2,3-Diphosphoglycerate has NO role on this enzyme regulation [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EJJ 1EJJ] (Geobacillus stearothermophilus, complex with 3-phosphoglycerate), [http://www.rcsb.org/pdb/explore.do?structureId=1EQJ 1EQJ] (Geobacillus stearothermophilus, complex with 2-phosphoglycerate), ''Geobacillus stearothermophilus'', complex with 2-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=16359 NCBI], ''Geobacillus stearothermophilus'', complex with 3-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=15578 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39773 P39773]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33910]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1 5.4.2.1]]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP698 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1425 (expression of ''pgm'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP1101 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

[[Jedrzejas|Mark J. Jedrzejas]], Research Center Oakland, CA, USA [http://www.chori.org/Principal_Investigators/Jedrzejas_Mark_J/jedrzejas_research.html Homepage]

=Your additional remarks=

=References=

<pubmed>11514674,17085493,10764795,8215434,10747010,11712498,9830105,10388626,8636019,11827481,16479537, 12850135,17726680,17505547, 8021172,11489127, 10388626,10747010, 10764795, 11712498, 12729763, 17085493, 17218307 33963 </pubmed>

[[Category:Protein-coding genes]]

Pgm

2010-03-18T21:51:19Z

Npietac:

* '''Description:''' phosphoglycerate mutase, glycolytic / gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgm''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis / gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[eno]]'', ''[[tpi]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15396]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgm_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33910

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate (according to Swiss-Prot)

* '''Protein family:''' BPG-independent phosphoglycerate mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/33963 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mn2+

* '''Effectors of protein activity:'''
** Inhibited by diverse divalent heavy-metal ions, EDTA and 2,3-butanedione [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]
** 2,3-Diphosphoglycerate has NO role on this enzyme regulation [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EJJ 1EJJ] (Geobacillus stearothermophilus, complex with 3-phosphoglycerate), [http://www.rcsb.org/pdb/explore.do?structureId=1EQJ 1EQJ] (Geobacillus stearothermophilus, complex with 2-phosphoglycerate), ''Geobacillus stearothermophilus'', complex with 2-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=16359 NCBI], ''Geobacillus stearothermophilus'', complex with 3-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=15578 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39773 P39773]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33910]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1 5.4.2.1]]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP698 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1101 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression of ''pgm'' and ''eno'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP1425 (expression of ''pgm'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

[[Jedrzejas|Mark J. Jedrzejas]], Research Center Oakland, CA, USA [http://www.chori.org/Principal_Investigators/Jedrzejas_Mark_J/jedrzejas_research.html Homepage]

=Your additional remarks=

=References=

<pubmed>11514674,17085493,10764795,8215434,10747010,11712498,9830105,10388626,8636019,11827481,16479537, 12850135,17726680,17505547, 8021172,11489127, 10388626,10747010, 10764795, 11712498, 12729763, 17085493, 17218307 33963 </pubmed>

[[Category:Protein-coding genes]]

GapA

2010-03-18T21:47:44Z

Npietac:

* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[cggR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15399]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33940

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
** This reaction is part of the glycolysis.

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''

* '''Modification:'''
** Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed2]
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]

* '''Cofactor(s):''' NAD+ (do not accept NADP+) [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''
** GapA-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** GapA-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1GD1 1GD1] (from ''Geobacillus stearothermophilus'')
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09124 P09124]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]

=== Additional information===

GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[cggR]]-[[gapA]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (10 fold) ([[CggR]]) {{PubMed|12850135,12622823}}

* '''Regulatory mechanism:'''
** [[CggR]]: transcription repression {{PubMed|11489127}}

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:'''
** GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).
** The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed|11489127}} The processing event requires the [[Rny|RNase Y]] {{PubMed|19193632}}.

=Biological materials =

* '''Mutant:''' essential, GM1501 (under p(spac) control), available in [[Stephane Aymerich]] lab

* '''Expression vector:'''
** pGP1424 (expression in ''B. subtilis'', in [[pBQ200]]) (available in [[Stülke]] lab)
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Stülke]] lab

=Labs working on this gene/protein=

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

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

=Your additional remarks=

=References=

<pubmed> 12850135,19193632, 18673455 , 17726680,16479537,12622823,12359717,10799476,17505547,11489127,12123463,17218307,12634343,17142398,17114254,10559165 </pubmed>

[[Category:Protein-coding genes]]

FbaA

2010-03-18T21:44:50Z

Npietac:

* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywjH]]'', ''[[spo0F]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15729]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:fbaA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37120

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate (according to Swiss-Prot)

* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot)
* '''Paralogous protein(s):''' [[FbaB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Domains:'''
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)

* '''Modification:''' phosphorylation on Thr-212 and Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):''' Zn2+ (Metalloenzyme)

* '''Effectors of protein activity:'''
** Inhibited by alpha-ketoglutarate, oxaloacetate and pyruvate [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.proteopedia.org/wiki/index.php/2fjk 2FJK] (from ''Thermus caldophilus'') {{PubMed|16843441}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P13243 P13243]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13]

=== Additional information===

Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution

=Expression and regulation=

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

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1423, available in [[Stülke]] lab
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP88, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP395, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP601 (in [[pAC6]])

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307, 15125960, 24624 16843441 11489127</pubmed>

[[Category:Protein-coding genes]]

PfkA

2010-03-18T21:42:35Z

Npietac:

* '''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
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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''' || ''[[pyk]]'', ''[[accA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pfkA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29190

===Phenotypes of a mutant ===

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

=== 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 (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation (Reversible) [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]

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

* '''Modification:'''

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by citrate, PEP (Hill Coefficient 3) and Ca2+ (competes with Mg2+) in ''B. licheniformes'' [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed].
** Inhibited by ATP (competitively) and f6p (non-competitively) in ''G. stearothermophillus'' [http://www.ncbi.nlm.nih.gov/pubmed/8136379 PubMed]
** Activated by GDP and ADP in lower concentrations (1mM); above that inhibition, competing with the ATP for the binding site (in ''G. stearothermophillus'') [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]

* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MTO 1MTO] (mutant, complex with fructose-6-phosphate, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=4PFK 4PFK] (Geobacillus stearothermophilus), ''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]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34529 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 2.7.1.11]

=== Additional information===
PfkA is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

=Expression and regulation=
* '''Operon:''' ''[[pfkA]]-[[pyk]]-[[ytzA]]'' {{PubMed|11489127}}

* '''Sigma factor:'''

* '''Regulation:'''
** twofold induced by glucose {{PubMed|11489127}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP87, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP393, available in [[Stülke]] lab
** for expression in ''B. subtilis'', in [[pBQ200]]: pGP1422, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed> 16479537,19193632, 11489127, 8136379, 7873536 4269800 </pubmed>

[[Category:Protein-coding genes]]

PtsH

2010-03-18T21:36:07Z

Npietac:

* '''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 transport and carbon catabolite repression
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|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]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13263]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ptsH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU13900

===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 HPr + protein EIIA N(tau)-phospho-L-histidine (according to Swiss-Prot) Protein HPr N(pi)-phospho-L-histidine + protein EIIA = protein [[PtsH|HPr]] + protein EIIA N(tau)-phospho-L-histidine

* '''Protein family:''' HPr domain (according to Swiss-Prot) HPr family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' HPr Domain (2–88)

* '''Modification:'''
** transient phosphorylation by [[PtsI |Enzyme I]] of the PTS on His-15
** regulatory phosphorylation on Ser-46 by [[HprK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2507315 PubMed]
** weak phosphorylation on Ser-12 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
** an extensive study on ''in vivo'' HPr phosphorylation can be found in Singh et al. (2008) [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]

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

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

* '''Interactions:''' [[PtsH|HPr]]-[[LicT]], [[PtsH|HPr]]-[[SacY]], [[PtsH|HPr]]-[[SacT]], [[PtsH|HPr]]-[[GlcT]], [[PtsH|HPr]]-[[GlpK]], [[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]], [[PtsH|HPr(Ser-46)-P]]-[[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], [[PtsH|HPr(His)-P]]-[[YesS]] {{PubMed|19651770}}, [[PtsH|HPr]]-[[PtsG]] {{PubMed|8418852}}

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1KKM 1KKM] (complex of L. casei HprK with B. subtilis HPr-Ser-P), [http://www.rcsb.org/pdb/explore.do?structureId=1KKL 1KKL] (complex of Lactobacillus casei HprK with B. subtilis HPr), [http://www.rcsb.org/pdb/explore.do?structureId=2HID 2HID] (NMR)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P08877 P08877]

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

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[ptsG]]-[[ptsH]]-[[ptsI]]'' {{PubMed|11902727}}
**''[[ptsH]]-[[ptsI]]'' {{PubMed|11902727}}

* '''[[Sigma factor]]:'''
** ''[[ptsG]]'': [[SigA]] {{PubMed|11902727}}
** ''[[ptsH]]'': [[SigA]] {{PubMed|11902727}}

* '''Regulation:'''
** expression activated by glucose (2 fold) ([[GlcT]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** the ''[[ptsH]]'' promoter is constitutive {{PubMed|11902727}}
** subject to negative stringent control upon amino acid limitation (due to control of'' [[ptsG]]'' transcription initiation) {{PubMed|20081037}}

* '''Regulatory mechanism:'''
** ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent [[RNA switch]] {{PubMed|9765562}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' MZ303 (cat), GP507 ptsH1 (S46A), GP506 (ptsH-H15A), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP438 (with N-terminal Strep-tag, in [[pGP172]]), available in [[Stülke]] lab
** pAG2 (His-tag), available in [[Anne Galinier]] lab
** pGP371(expression / purification of HPr-S46A, with His-tag from ''E. coli'', in [[pWH844]]), available in [[Stülke]] lab
** pGP1415(HPr, expression in ''B. subtilis'', from [[pBQ200]]), available in [[Stülke]] lab
** pGP1416(HPr-H15A, expression in ''B. subtilis'', from [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Stülke]] lab

=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=

<pubmed>16519689,,12850135 17218307 16519689 17142398 12359875 1577686 9162046 11929549 9336834 7803390, 7623661, 2846556, 8169206, 9973552, 15126459, 10048041, 12169607, 9622354, 10217795, 17693724, 18757537 , 9202047 , 7592487, 15369672 , 14527945, 2507315 8580838 19651770 8418852 1303754 1549615 20081037 </pubmed>

[[Category:Protein-coding genes]]

YabT

2010-03-18T21:26:36Z

Npietac:

* '''Description:''' similar to Ser/Thr kinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yabT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 9.943
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1014 bp, 338 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yabS]]'', ''[[tilS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11842]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yabT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00660

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10129]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + a protein = ADP + a phosphoprotein (according to Swiss-Prot)

* '''Protein family:''' protein kinase domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37562 P37562]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00660]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:''' [[SigF]] {{PubMed|16497325}}

* '''Regulation:''' expressed early during sporulation in the forespore ([[SigF]]) {{PubMed|16497325}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP577 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP391, available in [[Stülke]] lab
** purification from ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP823, available in [[Stülke]] lab
** purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1408, available in [[Stülke]] lab

* '''lacZ fusion:'''
* translational lacZ fusion (in [[pAC7]]): pGP831, available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16497325,, </pubmed>

[[Category:Protein-coding genes]]

PrkD

2010-03-18T21:24:36Z

Npietac:

* '''Description:''' protein kinase D 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''prkD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybdM''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || protein kinase D
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 6.359
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 768 bp, 256 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybdL]]'', ''[[ybdN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11997]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ybdM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU02030

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12726]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + a protein = ADP + a phosphoprotein (according to Swiss-Prot)

* '''Protein family:''' protein kinase domain (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31435 O31435]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02030]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:''' [[SigG]] {{PubMed|15699190}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP578 (aphA3), available in the [[Stülke]] lab

* '''Expression vector:'''
** pGP390 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP821, available in [[Stülke]] lab
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP1407, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP830 (in [[pAC7]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

GlmM

2010-03-18T21:19:48Z

Npietac:

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' phosphohexose mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Stülke]] lab

**pGP1400: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab

**pGP1402: (cloning vector for glmM (GlmM S100A) in ''E. coli'', in [[pBlueskript KS]]), available in [[Stülke]] lab

**pGP1403: (expression of GlmM (S100A) in ''B. subtilis'' in [[pBQ200]]), available in [[Stülke]] lab

**pGP1405: (expression, purification of GlmM (S100A) in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2010-03-18T21:12:53Z

Npietac:

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' phosphohexose mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Stülke]] lab

**pGP1400: (expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2010-03-18T21:07:21Z

Npietac:

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' phosphohexose mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

**pGP400: (expression in ''B. subtilis'' in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2010-03-18T21:06:41Z

Npietac:

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' phosphohexose mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

**pGP400: (expression in ''B. subtilis',' in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2010-03-18T21:03:33Z

Npietac:

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' phosphohexose mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

**pGP400: expression in ''B. subtilis'' in [[pBQ200]]: , available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 </pubmed>

[[Category:Protein-coding genes]]

Eno

2010-03-18T20:59:35Z

Npietac:

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''eno''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:eno_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33900

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H2O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Domains:'''
** substrate binding domain (366–369)

* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3ES8 3ES8] (from ''Oceanobacillus iheyensis'', complex with Mg(2+) and malate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]

=== Additional information===
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
* [[universally conserved protein]]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP698 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP399 (expression of ''eno'' from ''E. coli'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab

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

* '''Antibody:''' available in [[Stülke]] lab

=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=

<pubmed> 17726680, 17218307, 12850135 , 19193632 , 11489127, 8021172, 17505547, 25885 15003462 </pubmed>

[[Category:Protein-coding genes]]

Eno

2010-03-18T20:58:28Z

Npietac:

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''eno''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:eno_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33900

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H2O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Domains:'''
** substrate binding domain (366–369)

* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3ES8 3ES8] (from ''Oceanobacillus iheyensis'', complex with Mg(2+) and malate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]

=== Additional information===
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
* [[universally conserved protein]]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP698 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
** pGP399 (expression of "eno" from ''E. coli'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab

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

* '''Antibody:''' available in [[Stülke]] lab

=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=

<pubmed> 17726680, 17218307, 12850135 , 19193632 , 11489127, 8021172, 17505547, 25885 15003462 </pubmed>

[[Category:Protein-coding genes]]

GlmM

2010-03-18T20:48:58Z

Npietac:

* '''Description:''' phosphoglucosamine mutase, required for cell wall synthesis 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''glmM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbT''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglucosamine mutase, required for cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 4.677
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1344 bp, 448 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbR]]'', ''[[glmS]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11953]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ybbT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU01770

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12704]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Alpha-D-glucosamine 1-phosphate = D-glucosamine 6-phosphate (according to Swiss-Prot)

* '''Protein family:''' phosphohexose mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-100 {{PubMed|17218307,17726680,20097688}}, this is an autophosphorylation {{PubMed|20097688}}

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34824 O34824]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01770]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.10 5.4.2.10]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

** for expression in ''B. subtilis'' in [[pBQ200]]: pGP400, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 17726680, 17218307, 8550580 , 10231382 , 10671448 20097688 </pubmed>

[[Category:Protein-coding genes]]