Difference between revisions of "Sandbox"

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−
* '''Description:''' aliphatic sulfonate ABC transporter (permease) <br/><br/>
+
* '''Description:''' succinyl-CoA synthetase (beta 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'''
−
|''ssuC''
+
|''sucC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ygaM, yzeB ''
+
|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''' || aliphatic sulfonate ABC transporter (permease)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || sulfonate uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 10.481  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.846  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 828 bp, 276 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ssuA]]'', ''[[ssuD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12713&#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:CAB13482&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ssuC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sucC_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:''' BSU08850
+
* '''Locus tag:''' BSU16090
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10657]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)
  
−
* '''Protein family:''' ABC transmembrane type-1 domain (according to Swiss-Prot)
+
* '''Protein family:''' ATP-grasp domain (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40401 P40401]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80886 P80886]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08850]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16090]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ssuB]]-[[ssuA]]-[[ssuC]]-[[ssuD]]-[[ygaN]]''
+
* '''Operon:''' ''[[sucC]]''-''[[SucD]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed in the presence of cysteine ([[CymR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]
+
* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
  
−
* '''Regulatory mechanism:''' [[CymR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>9782504, </pubmed>
+
<pubmed>12850135 17218307, </pubmed>
−
# van der Ploeg JR, Cummings NJ, Leisinger T, Connerton IF. (1998) Bacillus subtilis genes for the utilization of sulfur from aliphatic sulfonates. ''Microbiology'' '''Sep;144(Pt9):''' 2555-61. [http://www.ncbi.nlm.nih.gov/sites/entrez/9782504 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]# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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 13:38, 8 June 2009

  • Description: succinyl-CoA synthetase (beta subunit)

Gene name sucC
Synonyms
Essential no
Product succinyl-CoA synthetase (beta subunit)
Function TCA cycle
MW, pI 41 kDa, 4.846
Gene length, protein length 1155 bp, 385 aa
Immediate neighbours ylqH, sucD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SucC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU16090

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)
  • Protein family: ATP-grasp domain (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Ser-220 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure: 1JKJ (E. coli)
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: repressed by glucose (2.7-fold) (CcpA) PubMed
  • 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

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P 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# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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