Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' membrane-embedded thiol-disulfide oxidoreductase <br/><br/>
+
* '''Description:''' transcriptional repressor of ''[[citZ]]'' and ''[[citB]]'' <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'''
−
|''ccdA''
+
|''ccpC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykuM ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || thiol-disulfide oxidoreductase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || cytochrome c synthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of tricarboxylic acid branch of the TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.667  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.932  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 705 bp, 235 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 879 bp, 293 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynzD]]'', ''[[yneI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuL]]'', ''[[ykuN]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13677&#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:CAB13287&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ccdA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ccpC_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU17930
+
* '''Locus tag:''' BSU14140
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccdA-yneIJ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11240]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13297]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' dsbD family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes controlled by CcpC ===
 +
 +
''[[citB]]'', ''[[citZ]]-[[icd]]-[[mdh]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 76:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 82:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P45706 P45706]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17930]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14140]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 113: Line 117:
  
 
=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]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 124:
 
=References=
 
=References=
  
−
<pubmed>9068642, </pubmed>
+
<pubmed>10656796 12591885 11985717 14636591, </pubmed>
−
# Schiött T, von Wachenfeldt C, Hederstedt L. (1997) Identification and characterization of the ccdA gene, required for cytochrome c synthesis in Bacillus subtilis. ''J Bacteriol.'' '''Mar;179(6):''' 1962-73. [http://www.ncbi.nlm.nih.gov/sites/entrez/9068642 PubMed]
+
# Jourlin-Castelli C, Mani N, Nakano MM, Sonenshein AL (2000) CcpC, a novel regulator of the LysR family required for glucose repression of the ''citB'' gene in ''Bacillus subtilis''. J Mol Biol 295:865-878. [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
 +
# Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the ''Bacillus subtilis'' aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
 +
# Kim HJ, Jourlin-Castelli C, Kim SI, Sonenshein AL (2002a) Regulation of the ''Bacillus subtilis ccpC'' gene by CcpA and CcpC. Mol Microbiol 43:399-410. [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 PubMed]
 +
# Kim SI, Jourlin-Castelli C, Wellington SR, Sonenshein AL (2003) Mechanism of repression by ''Bacillus subtilis'' CcpC, a LysR family regulator. J Mol Biol 334:609-624. [http://www.ncbi.nlm.nih.gov/sites/entrez/14636591 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 13:59, 8 June 2009

  • Description: transcriptional repressor of citZ and citB

Gene name ccpC
Synonyms ykuM
Essential no
Product transcriptional repressor
Function regulation of tricarboxylic acid branch of the TCA cycle
MW, pI 33 kDa, 5.932
Gene length, protein length 879 bp, 293 aa
Immediate neighbours ykuL, ykuN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CcpC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU14140

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):

Genes controlled by CcpC

citB, citZ-icd-mdh

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

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

Your additional remarks

References

Sam-In Kim, Cécile Jourlin-Castelli, Stephen R Wellington, Abraham L Sonenshein
Mechanism of repression by Bacillus subtilis CcpC, a LysR family regulator.
J Mol Biol: 2003, 334(4);609-24
[PubMed:14636591] [WorldCat.org] [DOI] (P p)

Hyun-Jin Kim, Sam-In Kim, Manoja Ratnayake-Lecamwasam, Kiyoshi Tachikawa, Abraham L Sonenshein, Mark Strauch
Complex regulation of the Bacillus subtilis aconitase gene.
J Bacteriol: 2003, 185(5);1672-80
[PubMed:12591885] [WorldCat.org] [DOI] (P p)

Hyun-Jin Kim, Cécile Jourlin-Castelli, Sam-In Kim, Abraham L Sonenshein
Regulation of the bacillus subtilis ccpC gene by ccpA and ccpC.
Mol Microbiol: 2002, 43(2);399-410
[PubMed:11985717] [WorldCat.org] [DOI] (P p)

C Jourlin-Castelli, N Mani, M M Nakano, A L Sonenshein
CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis.
J Mol Biol: 2000, 295(4);865-78
[PubMed:10656796] [WorldCat.org] [DOI] (P p)

  1. Jourlin-Castelli C, Mani N, Nakano MM, Sonenshein AL (2000) CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis. J Mol Biol 295:865-878. PubMed
  2. Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J. Bacteriol. 185:1672-1680. PubMed
  3. Kim HJ, Jourlin-Castelli C, Kim SI, Sonenshein AL (2002a) Regulation of the Bacillus subtilis ccpC gene by CcpA and CcpC. Mol Microbiol 43:399-410. PubMed
  4. Kim SI, Jourlin-Castelli C, Wellington SR, Sonenshein AL (2003) Mechanism of repression by Bacillus subtilis CcpC, a LysR family regulator. J Mol Biol 334:609-624. PubMed
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=89084"