Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) <br/><br/>
+
* '''Description:''' 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''pdhC''
+
|''odhB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citM ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase <br/>(dihydrolipoamide acetyltransferase E2 subunit)  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase complex
 +
(dihydrolipoamide transsuccinylase, E2 subunit)  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.855  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.859  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1326 bp, 442 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1251 bp, 417 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhB]]'', ''[[pdhD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[odhA]], [[yocS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13333&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13828&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhC_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:odhB_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
Line 29: Line 32:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/><br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 39: Line 42:
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10209]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10273]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 75:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]], [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
+
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]],  
  
 
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
 
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
Line 78: Line 81:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PDE 2PDE] (peripheral subunit binding domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1LAC 1LAC] (lipoyl domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1B5S 1B5S] (catalytic domain (residues 184-425) , ''Geobacillus stearothermophilus'')
+
* '''Structure:'''
−
* '''Swiss prot entry:'''  
+
 
 +
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14600]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19360]
  
−
* '''E.C. number:''' 2.3.1.12
+
* '''E.C. number:''' 2.3.1.61
  
 
=== Additional information===
 
=== Additional information===
Line 89: Line 93:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
+
* '''Operon:''' ''[[odhA]]''-''[[odhB]]''
  
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' expression activated by glucose (1.9 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  constitutive
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 114: Line 118:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Arthur Aronson]], Purdue University, West Lafayette, USA [http://wwwdev.gradschool.purdue.edu/PULSe/faculty.cfm?fid=5&range=0 homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 124:
  
 
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
# Gao et al. (2002) The E1beta and E2 subunits of the ''Bacillus subtilis'' pyruvate dehydrogenase complex are involved in regulation of sporulation.''J. Bacteriol.'' '''184:''' 2780-2788. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Kobayashi et al. (2003) Essential ''Bacillus subtilis'' genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 00:06, 28 April 2009

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

Gene name odhB
Synonyms citM
Essential yes PubMed
Product 2-oxoglutarate dehydrogenase complex

(dihydrolipoamide transsuccinylase, E2 subunit)

Function TCA cycle
MW, pI 45 kDa, 4.859
Gene length, protein length 1251 bp, 417 aa
Immediate neighbours odhA, yocS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
OdhB context.gif
This image was kindly provided by SubtiList







The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: membrane associated PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 2.3.1.61

Additional information

Expression and regulation

  • Regulation: repressed by glucose (2.4-fold) (CcpA) PubMed, constitutive
  • Regulatory mechanism: CcpA: transcription repression
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  3. Kobayashi et al. (2003) Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=62521"