Difference between revisions of "Sandbox"

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−
* '''Description:''' anti-anti-SigB, antagonist of RsbW <br/><br/>
+
* '''Description:''' succinate dehydrogenase (flavoprotein 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'''
−
|''rsbV''
+
|''sdhA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citF ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-anti-SigB
+
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (flavoprotein subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of SigB activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.698  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 5.714  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 327 bp, 109 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1758 bp, 586 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbU]]'', ''[[rsbW]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhC]], [[sdhB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rsbV_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sdhA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rsbV_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sdhA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rsbV_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhA_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 42: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10733]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10352]
  
 
=== Additional information===
 
=== Additional information===
Line 65: Line 67:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-52 AND Ser-56 OR Thr-57 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 71: Line 73:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RsbW]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8144446 PubMed]
+
* '''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+BSU04710]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28440]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 1.3.99.1
  
 
=== Additional information===
 
=== Additional information===
Line 89: Line 91:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]''
  
−
* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]  
+
* '''Sigma factor:''' [[SigA]]  
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
* '''Regulation:''' constitutive
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 122:
  
 
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
−
# Petersohn et al. (2001) Global Analysis of the General Stress Response of ''Bacillus subtilis''. ''J Bacteriol.'' '''183:''' 5617-5631 [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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]
+
# 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]# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 +
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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 16:11, 31 March 2009

  • Description: succinate dehydrogenase (flavoprotein subunit)

Gene name sdhA
Synonyms citF
Essential no
Product succinate dehydrogenase (flavoprotein subunit)
Function TCA cycle
MW, pI 65 kDa, 5.714
Gene length, protein length 1758 bp, 586 aa
Immediate neighbours sdhC, sdhB
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
SdhA 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:
  • 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

  • Sigma factor: SigA
  • Regulation: constitutive
  • Regulatory mechanism:
  • 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. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  2. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  3. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  4. Levine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. PubMed
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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