Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' succinate dehydrogenase(cytochrome b558 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'''
−
|''yslB''
+
|''sdhC''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.68  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.831  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 444 bp, 148 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhC]]'', ''[[lysC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]], [[sdhA]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yslB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhC_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 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yslB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11236]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]
  
 
=== Additional information===
 
=== Additional information===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28460]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28450]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 1.3.99.1
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''yslB''
+
* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' expression activated by glucose (5.4 fold) [[CcpA]] [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
* '''Regulation:''' constitutive
 +
 
 +
* '''Regulatory mechanism:''' [[FsrA]]: translational repression [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
  
−
* '''Regulatory mechanism:''' [[CcpA]]: mechanism unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP516 (spc), available in [[Stülke]] lab
+
* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 118: Line 119:
 
=References=
 
=References=
  
−
# 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]
+
# 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]
 +
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [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 18:23, 15 April 2009

  • Description: succinate dehydrogenase(cytochrome b558 subunit)

Gene name sdhC
Synonyms
Essential no
Product succinate dehydrogenase (cytochrome b558 subunit)
Function TCA cycle
MW, pI 22 kDa, 9.831
Gene length, protein length 606 bp, 202 aa
Immediate neighbours yslB, sdhA
Hier soll was neues rein
Genetic context
SdhC 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:
  • Interactions:
  • Localization: membrane protein PubMed

Database entries

  • Structure: 1NEK (E. coli)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 1.3.99.1

Additional information

Expression and regulation

  • Regulation: constitutive
  • Regulatory mechanism: FsrA: translational repression PubMed


  • Additional information:

Biological materials

  • Mutant: GP743 (sdhCA, 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. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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