Difference between revisions of "Sandbox"

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* '''Description:''' hydroxyethylthiazole phosphate biosynthesis <br/><br/>
+
* '''Description:''' pyruvate dehydrogenase (dihydrolipoamide acetyltransferase 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'''
−
|''thiG''
+
|''pdhC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjbT ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of thiamine
+
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.718  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.855  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 768 bp, 256 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1326 bp, 442 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiS]]'', ''[[thiF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhB]]'', ''[[pdhD]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/thiG_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhC_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/thiG_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhC_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:thiG_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhC_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>
 
|-
 
|-
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===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]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tenAI-goxB-thiSGF-yjbV.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13149]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10209]
  
 
=== Additional information===
 
=== Additional information===
Line 65: Line 67:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 71: Line 73:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
  
−
* '''Localization:'''
+
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''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'')
−
 
+
* '''Swiss prot entry:'''  
−
* '''Swiss prot entry:'''
 
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11690]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14600]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 2.3.1.12
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expression activated by glucose (1.94) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]  weak induction by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 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]
−
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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]
 
# 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 17:05, 1 April 2009

  • Description: pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)

Gene name pdhC
Synonyms
Essential no
Product pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)
Function links glycolysis and TCA cycle
MW, pI 47 kDa, 4.855
Gene length, protein length 1326 bp, 442 aa
Immediate neighbours pdhB, pdhD
Gene sequence (+200bp) Protein sequence
Genetic context
PdhC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

defects in sporulation and unable to grow on glucose as single carbon source 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: 1W88 (E1 in complex with subunit binding domain of E2, Geobacillus stearothermophilus), 2PDE (peripheral subunit binding domain, Geobacillus stearothermophilus), 1LAC (lipoyl domain, Geobacillus stearothermophilus), 1B5S (catalytic domain (residues 184-425) , Geobacillus stearothermophilus)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 2.3.1.12

Additional information

Expression and regulation

  • Regulation: expression activated by glucose (1.94) PubMed weak induction by glucose PubMed
  • Regulatory mechanism:
  • 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. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. 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. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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