Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional regulator of extracellular enzyme genes <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'''
|''senS''
+
|''odhA''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|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''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase (E1 subunit)
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of extracellular enzyme genes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 10.551 
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 216 bp, 72 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 105 kDa, 5.871 
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygaK]]'', ''[[katA]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2823 bp, 941 aa
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12709&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojO]], [[odhB]]''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:senS_context.gif]]
+
|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: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>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
* '''Locus tag:''' BSU08810
+
* '''Locus tag:''' BSU19370
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 45:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/senS.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10747]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10272]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 56:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO<sub>2</sub> (according to Swiss-Prot)
  
* '''Protein family:'''
+
* '''Protein family:''' 2-oxoacid dehydrogenase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
* '''Interactions:'''
+
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]]
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21344 P21344]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P23129 P23129]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08810]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19370]
  
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.4.2 1.2.4.2]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:'''  
+
* '''Operon:''' ''[[odhA]]''-''[[odhB]]''
  
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]
  
* '''Regulation:'''  
+
* '''Regulation:''' constitutive
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
* '''Mutant:'''
+
* '''Mutant:''' GP671 (spc), GP665 (aphA3), GP684 (cat), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 118: Line 122:
 
=References=
 
=References=
  
<pubmed>1479343,, </pubmed>
+
<pubmed>2500417,,1508153, </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 09:04, 13 June 2009

  • Description: 2-oxoglutarate dehydrogenase (E1 subunit)

Gene name odhA
Synonyms citK
Essential no
Product 2-oxoglutarate dehydrogenase (E1 subunit)
Function TCA cycle
Metabolic function and regulation of this protein in SubtiPathways:
Central C-metabolism
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

  • Locus tag: BSU19370

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2 (according to Swiss-Prot)
  • Protein family: 2-oxoacid dehydrogenase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]

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

O Resnekov, L Melin, P Carlsson, M Mannerlöv, A von Gabain, L Hederstedt
Organization and regulation of the Bacillus subtilis odhAB operon, which encodes two of the subenzymes of the 2-oxoglutarate dehydrogenase complex.
Mol Gen Genet: 1992, 234(2);285-96
[PubMed:1508153] [WorldCat.org] [DOI] (P p)

P Carlsson, L Hederstedt
Genetic characterization of Bacillus subtilis odhA and odhB, encoding 2-oxoglutarate dehydrogenase and dihydrolipoamide transsuccinylase, respectively.
J Bacteriol: 1989, 171(7);3667-72
[PubMed:2500417] [WorldCat.org] [DOI] (P p)

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