Difference between revisions of "Sandbox"

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−
* '''Description:''' purine nucleoside transporter <br/><br/>
+
* '''Description:''' 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, 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'''
−
|''nupG''
+
|''odhB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxjA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citM ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || purine nucleoside transporter
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase complex
 +
(dihydrolipoamide transsuccinylase, E2 subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || purine uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 7.757  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.859  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1191 bp, 397 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1251 bp, 417 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxjB]]'', ''[[yxiT]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[odhA]], [[yocS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15928&#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:CAB13828&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yxjA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:odhB_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 31: Line 32:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/><br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 38:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU39020
+
* '''Locus tag:''' BSU19360
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
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/odhAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11150]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10273]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 57:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine (according to Swiss-Prot)
  
−
* '''Protein family:''' SLC28A transporter family (according to Swiss-Prot)
+
* '''Protein family:''' sodium:bile acid symporter family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 75:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]]
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
+
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 83:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42312 P42312]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P16263 P16263]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39020]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19360]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.61 2.3.1.61] 1
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''nupG''
+
* '''Operon:''' ''[[odhA]]''-''[[odhB]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  constitutive
−
** expression activated by glucose (4.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
 
−
** repressed by hypoxanthine and guanine, [[PurR]]-independent, [[G-box]][http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
 
  
−
* '''Regulatory mechanism:''' [[G-box]]: transcriptional termination/ antitermination [[riboswitch]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 122: Line 123:
 
=References=
 
=References=
  
−
<pubmed>12850135 18763711 12923093, </pubmed>
+
<pubmed>12850135 18763711 12682299, </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]
 
# 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]
 
# 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]
−
# Johansen et al. (2003) Definition of a second ''Bacillus subtilis pur'' regulon comprising the ''pur'' and ''xpt-pbuX'' operons plus ''pbuG'', ''nupG'' (''yxjA''), and ''pbuE'' (''ydhL''). ''J. Bacteriol.'' '''185:''' 5200-5209. [http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
+
# Kobayashi et al. (2003) Essential ''Bacillus subtilis'' genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. [http://www.ncbi.nlm.nih.gov/pubmed/12682299 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 13:27, 8 June 2009

  • Description: 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit)

Gene name odhB
Synonyms citM
Essential yes PubMed
Product 2-oxoglutarate dehydrogenase complex

(dihydrolipoamide transsuccinylase, E2 subunit)

Function TCA cycle
MW, pI 45 kDa, 4.859
Gene length, protein length 1251 bp, 417 aa
Immediate neighbours odhA, yocS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
OdhB context.gif
This image was kindly provided by SubtiList







The gene

Basic information

  • Locus tag: BSU19360

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine (according to Swiss-Prot)
  • Protein family: sodium:bile acid symporter family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cell membrane (according to Swiss-Prot), membrane associated PubMed

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: repressed by glucose (2.4-fold) (CcpA) PubMed, constitutive
  • Regulatory mechanism: CcpA: transcription repression
  • 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

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)

K Kobayashi, S D Ehrlich, A Albertini, G Amati, K K Andersen, M Arnaud, K Asai, S Ashikaga, S Aymerich, P Bessieres, F Boland, S C Brignell, S Bron, K Bunai, J Chapuis, L C Christiansen, A Danchin, M Débarbouille, E Dervyn, E Deuerling, K Devine, S K Devine, O Dreesen, J Errington, S Fillinger, S J Foster, Y Fujita, A Galizzi, R Gardan, C Eschevins, T Fukushima, K Haga, C R Harwood, M Hecker, D Hosoya, M F Hullo, H Kakeshita, D Karamata, Y Kasahara, F Kawamura, K Koga, P Koski, R Kuwana, D Imamura, M Ishimaru, S Ishikawa, I Ishio, D Le Coq, A Masson, C Mauël, R Meima, R P Mellado, A Moir, S Moriya, E Nagakawa, H Nanamiya, S Nakai, P Nygaard, M Ogura, T Ohanan, M O'Reilly, M O'Rourke, Z Pragai, H M Pooley, G Rapoport, J P Rawlins, L A Rivas, C Rivolta, A Sadaie, Y Sadaie, M Sarvas, T Sato, H H Saxild, E Scanlan, W Schumann, J F M L Seegers, J Sekiguchi, A Sekowska, S J Séror, M Simon, P Stragier, R Studer, H Takamatsu, T Tanaka, M Takeuchi, H B Thomaides, V Vagner, J M van Dijl, K Watabe, A Wipat, H Yamamoto, M Yamamoto, Y Yamamoto, K Yamane, K Yata, K Yoshida, H Yoshikawa, U Zuber, N Ogasawara
Essential Bacillus subtilis genes.
Proc Natl Acad Sci U S A: 2003, 100(8);4678-83
[PubMed:12682299] [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. Kobayashi et al. (2003) Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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