Difference between revisions of "Sandbox"

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* '''Description:''' undecaprenyl pyrophosphate phosphatase, bacitracin resistance <br/><br/>
+
* '''Description:''' pyruvate dehydrogenase (E1 alpha 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'''
−
|''bcrC''
+
|''pdhA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywoA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''aceA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || undecaprenyl pyrophosphate phosphatase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase (E1 alpha subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance to bacitracin and oxidative stress
+
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 9.455  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.837  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 579 bp, 193 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1113 bp, 371 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nrgB]]'', ''[[ywnJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykyA]]'', ''[[pdhB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywoA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywoA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ywoA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhA_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 ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 +
 +
''pdhA'' is essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12488]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10207]
  
 
=== Additional information===
 
=== Additional information===
Line 71: Line 75:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 77: Line 81:
 
=== 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'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36530]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14580]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 1.2.4.1
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''bcrC''
+
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
  
−
* '''Sigma factor:''' [[SigM]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed], [[SigI]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 PubMed]
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' expression activated by glucose (3.34) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
+
* '''Regulation:''' expression activated by glucose (3.43) [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:'''  
Line 118: Line 122:
  
 
=References=
 
=References=
−
 
+
hier steht Paper
−
hier kommt Ppaer rein
+
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
−
# Jervis et al. 2007. SigM-responsive genes of ''Bacillus subtilis'' and their promoters. J. Bacteriol. 189: 4534-4538. [http://www.ncbi.nlm.nih.gov/sites/entrez/17434969 PubMed]
 
−
# Tseng, C. L., and Shaw, G. C. (2008) Genetic evidence for the actin homolog gene ''mreBH'' and the bacitracin resistance gene ''bcrC'' as targets of the alternative sigma factor SigI of ''Bacillus subtilis''. ''J. Bacteriol.'' '''190:''' 1561-1567. [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 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 18:06, 1 April 2009

  • Description: pyruvate dehydrogenase (E1 alpha subunit)

Gene name pdhA
Synonyms aceA
Essential yes
Product pyruvate dehydrogenase (E1 alpha subunit)
Function links glycolysis and TCA cycle
MW, pI 41 kDa, 5.837
Gene length, protein length 1113 bp, 371 aa
Immediate neighbours ykyA, pdhB
Gene sequence (+200bp) Protein sequence
Genetic context
PdhA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

pdhA is 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:

Database entries

  • Structure: 1W88 (E1 in complex with subunit binding domain of E2, Geobacillus stearothermophilus)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 1.2.4.1

Additional information

Expression and regulation

  • Regulation: expression activated by glucose (3.43) 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

hier steht Paper

  1. Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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