Difference between revisions of "Sandbox"

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−
* '''Description:''' xanthine transport in/out via proton symport <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'''
−
|''pbuX''
+
|''pdhC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypaQ ''
+
|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''' || xanthine permease
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase <br/>(dihydrolipoamide acetyltransferase E2 subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || xanthine uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 8.793  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.855  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1314 bp, 438 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1326 bp, 442 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bcsA]]'', ''[[xpt]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhB]]'', ''[[pdhD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14123&#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:CAB13333&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pbuX_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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU22060
+
* '''Locus tag:''' BSU14600
  
 
===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/xpt-pbuX.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11080]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10209]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' lipoyl-binding domain (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylated (Ser/Thr/Tyr) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
  
−
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
+
* '''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:''' [http://www.uniprot.org/uniprot/P21883 P21883]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42086 P42086]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14600]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22060]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.12 2.3.1.12] 2
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[xpt]]-[[pbuX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9098051 PubMed]
+
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expression activated by glucose (1.9 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−
** repressed in the presence of adenine or adenosine ([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11591660 PubMed]
 
−
** induced in the absence of guanine ([[G-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12787499 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[G-box]]: transcription termination/ antitermination  ([[riboswitch]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9098051 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12787499 PubMed2]
 
−
** [[PurR]]: transcription repression (molecular inducer: PRPP) [http://www.ncbi.nlm.nih.gov/sites/entrez/11591660 PubMed]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=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 121:
 
=References=
 
=References=
  
−
<pubmed>18763711, </pubmed>
+
<pubmed>12850135 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]
+
# 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]
 +
# 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 13:28, 8 June 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
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PdhC context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU14600

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: Acetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine (according to Swiss-Prot)
  • Protein family: lipoyl-binding domain (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated (Ser/Thr/Tyr) PubMed
  • 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: P21883
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: expression activated by glucose (1.9 fold) PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Arthur Aronson, Purdue University, West Lafayette, USA homepage

Your additional remarks

References

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

  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. 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
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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