Difference between revisions of "Sandbox"

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−
* '''Description:''' acetolactate synthase (large subunit) <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'''
−
|''ilvB''
+
|''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''' || acetolactate synthase (large subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate, 2-acetolactate)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of branched-chain amino acids
 
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of branched-chain amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.178  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 5.37  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1722 bp, 574 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1026 bp, 342 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ilvH]]'', ''[[ysnD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[leuA]]'', ''[[ilvH]]''
 
|-
 
|-
 
|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:ilvB_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>
 
|-
 
|-
Line 43: Line 43:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ilvBHC-leuABCD.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ilvBHC-leuABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10670]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10672]
  
 
=== Additional information===
 
=== Additional information===
Line 80: Line 80:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28310]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28290]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 86: Line 86:
 
=== Additional information===
 
=== Additional information===
  
−
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
 
=Expression and regulation=
 
=Expression and regulation=
  
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* '''[[Sigma factor]]:''' [[SigA]]
 
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''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 (CcpA) [http://www.ncbi.nlm.ntnrih.gov/sites/entrez/12193635 PubMed], during growth repressed under nitrogen limiting conditions ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15547269 PubMed]
+
* '''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]
  
−
* '''Regulatory mechanism:''' glucose regulation: [[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed], [[TnrA]]: transcription repession [http://www.ncbi.nlm.nih.gov/sites/entrez/15547269 PubMed], repression by BCAA: tRNA-controlled RNA switch (T-box) that mediates termination/antitermination, transcription repression by [[CodY]]  
+
* '''Regulatory mechanism:''' 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, transcription repression by [[CodY]]  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 119:
  
 
# 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]
 
# 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]
−
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
−
# Grandoni, J. A., S. A. Zahler, and J. M. Calvo. 1992. Transcriptional regulation of the ilv-leu operon of Bacillus subtilis. J. Bacteriol. 174:3212-3219. [http://www.ncbi.nlm.nih.gov/sites/entrez/1577690 PubMed]
 
−
# Ludwig, H., Meinken, C., Matin, A. & Stülke, J. (2002) Insufficient expression of the ilv-leu operon encoding enzymes of branched-chain amino acids biosynthesis limits growth of a ''Bacillus subtilis ccpA'' mutant. J. Bacteriol. 184: 5174-5178. [http://www.ncbi.nlm.nih.gov/sites/entrez/12193635 PubMed]
 
−
# Shivers RP, Sonenshein AL: Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol 2005, 56:1549-1559. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916605 PubMed]
 
−
# Tojo S, Satomura T, Morisaki K, Deutscher J, Hirooka K, Fujita Y: Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA. Mol Microbiol 2005, 56:1560-1573. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916606 PubMed]
 
−
# Tojo S, Satomura T, Morisaki K, Yoshida KI, Hirooka K, Fujita Y: Negative transcriptional regulation of the ''ilv-leu'' operon for biosynthesis of branched-chain amino acids through the ''Bacillus subtilis'' global regulator TnrA. J Bacteriol 2004, 186:7971-7979. [http://www.ncbi.nlm.nih.gov/sites/entrez/15547269 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 18:24, 15 April 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
Hier soll was neues rein
Genetic context
IlvC 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:

Database entries

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

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
  • Regulatory mechanism: glucose regulation: CcpA PubMed, repression by BCAA: tRNA-controlled RNA switch (T-box) that mediates termination/antitermination, transcription repression by CodY
  • 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

  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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