Difference between revisions of "Sandbox"

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* '''Description:''' seryl-tRNA-synthetase <br/><br/>
+
* '''Description:''' citrate synthase <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'''
−
|''serS''
+
|''citZ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || seryl-tRNA-synthetase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.193  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1275 bp, 425 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdxT]]'', ''[[trnSL-Ser1]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11789&#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:CAB14874&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:serS_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
+
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serS.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10077]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' acetyl-CoA + oxaloacetate ---> citrate, the reaction is irreversible
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' inhibited by ATP [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed]
  
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:'''http://www.uniprot.org/uniprot/O34991 O34991
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00130]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 4.1.3.7
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''serS'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' induced in the presence of serine [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
  
−
* '''Regulatory mechanism:''' antitermination by a ''[[trnD-Ser]]-''dependent RNA switch [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 112: Line 111:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:'''
+
* '''Antibody:''' available in [[Linc Sonenshein]] lab
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 +
 +
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 +
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 124:
 
=References=
 
=References=
  
−
# Condon et al. (1996) Aminoacyl-tRNA synthetase gene regulation in ''Bacillus subtilis''.
+
# 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]
−
''Biochimie'' '''78:''' 381-389. [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 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]
 +
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
 +
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
 +
# Jin S, Sonenshein AL  (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 22:35, 1 May 2009

  • Description: citrate synthase

Gene name citZ
Synonyms citA2
Essential no
Product citrate synthase II
Function TCA cycle
MW, pI 41 kDa, 5.451
Gene length, protein length 1116 bp, 372 aa
Immediate neighbours ytwI, icd
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CitZ context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

glutamate auxotrophy and a defect in sporulation PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: acetyl-CoA + oxaloacetate ---> citrate, the reaction is irreversible
  • Protein family:

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Ser-284 PubMed
  • Cofactor(s):
  • Effectors of protein activity: inhibited by ATP PubMed
  • Interactions:
  • Localization:

Database entries

  • KEGG entry: [3]
  • E.C. number: 4.1.3.7

Additional information

Expression and regulation

  • Regulation: repressed by glucose (6.7-fold) (CcpA) PubMed, catabolite repression (CcpA), repression by glucose + glutamate (CcpC) PubMed, repression under anaerobic conditions PubMed
  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression, CcpC: transcription repression PubMed
  • Additional information:

Biological materials

  • Mutant: GP678 (erm), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:

Labs working on this gene/protein

Linc Sonenshein, Tufts University, Boston, MA, USA Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

  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. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  3. Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of Bacillus subtilis Krebs cycle genes. Mol Microbiol 45:179-190. PubMed
  4. Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of Bacillus subtilis Krebs cycle genes. J Bacteriol. 180: 3304-3311. PubMed
  5. Jin S, Sonenshein AL (1994) Identification of two distinct Bacillus subtilis citrate synthase genes J Bacteriol. 176: 4669-4679. PubMed
  6. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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