Difference between revisions of "Sandbox"

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−
* '''Description:''' transcription activator of the ''[[gutB]]-[[gutP]]'' operon <br/><br/>
+
* '''Description:''' ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate, 2-acetolactate) <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'''
−
|''gutR''
+
|''ilvC''
 
|-
 
|-
 
|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''' || transcription activator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate, 2-acetolactate)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of glucitol utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of branched-chain amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 94 kDa, 6.113  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 5.37  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2487 bp, 829 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1026 bp, 342 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydjC]]'', ''[[gutB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[leuA]]'', ''[[ilvH]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12433&#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:CAB14789&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gutR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ilvC_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:''' BSU06140
+
* '''Locus tag:''' BSU28290
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gutR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ilvBHC-leuABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10178]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10672]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' (R)-2,3-dihydroxy-3-methylbutanoate + NADP<sup>+</sup> = (S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' ketol-acid reductoisomerase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39143 P39143]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37253 P37253]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06140]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28290]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.86 1.1.1.86]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuB]]-[[leuC]]-[[leuD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1577690 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1577690 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] ,  expressed in the absence of branched-chain amino acids (BCAA), expression is stimulated in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed], glucose regulation: [[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed], repression by BCAA: tRNA-controlled RNA switch (T-box) that mediates termination/antitermination
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>8195087 8195086 11118449, </pubmed>
+
<pubmed>12107147, </pubmed>
−
# Ye R, Rehemtulla SN, Wong SL. (1994) Glucitol induction in Bacillus subtilis is mediated by a regulatory factor, GutR. ''J Bacteriol.'' '''Jun;176(11):''' 3321-7. [http://www.ncbi.nlm.nih.gov/sites/entrez/8195087 PubMed]
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−
# Ye R, Wong SL. (1994) Transcriptional regulation of the Bacillus subtilis glucitol dehydrogenase gene. ''J Bacteriol.'' '''Jun;176(11):''' 3314-20. [http://www.ncbi.nlm.nih.gov/sites/entrez/8195086 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Poon KK, Chen CL, Wong SL. (2001) Roles of glucitol in the GutR-mediated transcription activation process in Bacillus subtilis: tight binding of GutR to tis binding site. ''J Biol Chem. '' '''Mar 30;276(13):''' 9620-5 [http://www.ncbi.nlm.nih.gov/sites/entrez/11118449 PubMed]
 

Revision as of 13:20, 8 June 2009

  • Description: ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate, 2-acetolactate)

Gene name ilvC
Synonyms
Essential no
Product ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate, 2-acetolactate)
Function biosynthesis of branched-chain amino acids
MW, pI 37 kDa, 5.37
Gene length, protein length 1026 bp, 342 aa
Immediate neighbours leuA, ilvH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
IlvC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU28290

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: (R)-2,3-dihydroxy-3-methylbutanoate + NADP+ = (S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH (according to Swiss-Prot)
  • Protein family: ketol-acid reductoisomerase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: repressed by casamino acids PubMed , expressed in the absence of branched-chain amino acids (BCAA), expression is stimulated in the presence of glucose PubMed, repressed by CodY PubMed
  • Regulatory mechanism: CodY: transcription repression PubMed, glucose regulation: CcpA PubMed, repression by BCAA: tRNA-controlled RNA switch (T-box) that mediates termination/antitermination
  • 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

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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