Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes  <br/><br/>
+
* '''Description:''' 2-oxoglutarate dehydrogenase (E1 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'''
−
|''pdhD''
+
|''odhA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citL ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citK ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || dihydrolipoamide dehydrogenase E3 subunit<br/> of both pyruvate dehydrogenase and 2-oxoglutarate<br/> dehydrogenase complexes
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase (E1 subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle, enzyme in TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.76  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 105 kDa, 5.871  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1410 bp, 470 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2823 bp, 941 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhC]]'', ''[[slp]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojO]], [[odhB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13334&#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:CAB13829&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhD_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:odhA_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 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 40:
  
 
===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/pdhABCD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10210]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10272]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]], [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]], [[OdhA]]-[[OdhB]]-[[PdhD]]
+
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]],  
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 78: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')
+
* '''Structure:'''
  
−
* '''Swiss prot entry:'''  
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14610]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19370]
  
−
* '''E.C. number:''' 1.8.1.4
+
* '''E.C. number:''' 1.2.4.2
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 90:
 
=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 (2.0 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
* '''Regulation:''' constitutive
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 102: Line 102:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP671 (spc), GP665 (aphA3), GP684 (cat), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 120:
 
=References=
 
=References=
  
−
# 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]
 
−
# 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 00:07, 28 April 2009

  • Description: 2-oxoglutarate dehydrogenase (E1 subunit)

Gene name odhA
Synonyms citK
Essential no
Product 2-oxoglutarate dehydrogenase (E1 subunit)
Function TCA cycle
MW, pI 105 kDa, 5.871
Gene length, protein length 2823 bp, 941 aa
Immediate neighbours yojO, odhB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
OdhA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

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:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 1.2.4.2

Additional information

Expression and regulation

  • Regulation: constitutive
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant: GP671 (spc), GP665 (aphA3), GP684 (cat), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=62524"