SubtiWiki - User contributions [en]

Pgm

2009-07-09T18:05:37Z

MArnold: /* Biological materials */

* '''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''' || ''[[tpi]]'', ''[[eno]]''
|-
|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]

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

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

* '''Regulation:''' expression activated by glucose (7.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar

''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''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 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>

Pgm

2009-07-07T09:47:01Z

MArnold: /* Biological materials */

* '''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''' || ''[[tpi]]'', ''[[eno]]''
|-
|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]

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

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

* '''Regulation:''' expression activated by glucose (7.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar

''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP1101 (N-terminal His-tag, in [[pWH844]]), pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), pGP1500 (expression in ''B. subtilis'', in [[pBQ200]]), pGP1502 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[pUT18]]), pGP1503 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[pUT18C]]), pGP1504 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[p25-N]]), pGP1505 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[pKT25]]), 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>

Eno

2009-07-07T09:46:18Z

MArnold: /* Biological materials */

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme 

{| 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''' || ''[[pgm]]'', ''[[yvgK]]''
|-
|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)

* '''Swiss prot entry:''' [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===
There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP563 (N-terminal His-tag, in [[pWH844]]), pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), pGP1500 (expression 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 </pubmed>

Tpi

2009-07-07T09:45:30Z

MArnold: /* Biological materials */

* '''Description:''' triose phosphate isomerase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tpi''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate 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''' || 26,9 kDa, 4.79
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15397]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:tpi_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:''' BSU33920

===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+BG10897]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1BTM 1BTM] (complex with 2-phosphoglycolic acid, Geobacillus stearothermophilus), complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P27876 P27876]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33920]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1] 5.3.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP700 (cat), available in [[Stülke]] lab

* '''Expression vector:''' pGP394 (N-terminal His-tag, in [[pWH844]]), pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), pGP1511 (expression 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=

=Your additional remarks=

=References=

<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 </pubmed>

Pgk

2009-07-07T09:44:46Z

MArnold: /* Biological materials */

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

{| 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''' || ''[[gapA]]'', ''[[tpi]]''
|-
|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]

* '''Swiss prot entry:''' [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]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': induced by sugar [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP1102 (N-terminal His-tag, in [[pWH844]]), pGP95 (N-terminal Strep-tag, in [[pGP172]]), pGP91 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]), 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 </pubmed>

Tpi

2009-07-07T09:42:39Z

MArnold: /* Biological materials */

* '''Description:''' triose phosphate isomerase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tpi''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate 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''' || 26,9 kDa, 4.79
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15397]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:tpi_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:''' BSU33920

===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+BG10897]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1BTM 1BTM] (complex with 2-phosphoglycolic acid, Geobacillus stearothermophilus), complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P27876 P27876]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33920]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1] 5.3.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP700 (cat), available in [[Stülke]] lab

* '''Expression vector:''' pGP394 (N-terminal His-tag, in [[pWH844]]), pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), pGP1511 (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=

=Your additional remarks=

=References=

<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 </pubmed>

Pgm

2009-07-07T09:39:58Z

MArnold: /* Biological materials */

* '''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''' || ''[[tpi]]'', ''[[eno]]''
|-
|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]

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

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

* '''Regulation:''' expression activated by glucose (7.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar

''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP1101 (N-terminal His-tag, in [[pWH844]]), pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), pGP1500 (in [[pBQ200]]), pGP1502 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[pUT18]]), pGP1503 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[pUT18C]]), pGP1504 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[p25-N]]), pGP1505 (Pgm-S62A, for [[BACTH]], expression in B. subtilis, in [[pKT25]]), 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>

Eno

2009-07-07T09:33:55Z

MArnold: /* Biological materials */

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme 

{| 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''' || ''[[pgm]]'', ''[[yvgK]]''
|-
|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)

* '''Swiss prot entry:''' [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===
There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP563 (N-terminal His-tag, in [[pWH844]]), pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), pGP1500 (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 </pubmed>

Pgm

2009-07-07T09:32:38Z

MArnold: /* Biological materials */

* '''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''' || ''[[tpi]]'', ''[[eno]]''
|-
|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]

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

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

* '''Regulation:''' expression activated by glucose (7.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar

''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP1101 (N-terminal His-tag, in [[pWH844]]), pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), pGP1500 (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>

Tpi

2009-07-07T09:13:14Z

MArnold: /* Biological materials */

* '''Description:''' triose phosphate isomerase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tpi''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate 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''' || 26,9 kDa, 4.79
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15397]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:tpi_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:''' BSU33920

===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+BG10897]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1BTM 1BTM] (complex with 2-phosphoglycolic acid, Geobacillus stearothermophilus), complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P27876 P27876]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33920]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1] 5.3.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP700 (cat), available in [[Stülke]] lab

* '''Expression vector:''' pGP394 (N-terminal His-tag, in [[pWH844]]), pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 </pubmed>

Pgk

2009-07-07T09:11:55Z

MArnold: /* Biological materials */

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

{| 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''' || ''[[gapA]]'', ''[[tpi]]''
|-
|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]

* '''Swiss prot entry:''' [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]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': induced by sugar [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP1102 (N-terminal His-tag, in [[pWH844]]), pGP95 (N-terminal Strep-tag, in [[pGP172]]), pGP91 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]), 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 </pubmed>

Eno

2009-07-07T09:10:32Z

MArnold: /* Biological materials */

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme 

{| 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''' || ''[[pgm]]'', ''[[yvgK]]''
|-
|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)

* '''Swiss prot entry:''' [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===
There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

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

* '''Regulation:''' expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP563 (N-terminal His-tag, in [[pWH844]]), pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), 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 </pubmed>

Pgm

2009-07-07T09:09:02Z

MArnold: /* Biological materials */

* '''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''' || ''[[tpi]]'', ''[[eno]]''
|-
|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]

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

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

* '''Regulation:''' expression activated by glucose (7.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar

''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

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

* '''Expression vector:''' pGP1101 (N-terminal His-tag, in [[pWH844]]), pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), 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>