Difference between revisions of "Sandbox"

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−
* '''Description:''' 2-isopropylmalate synthase <br/><br/>
+
* '''Description:''' 3-isopropylmalate dehydratase (small 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'''
−
|''leuA''
+
|''leuD''
 
|-
 
|-
 
|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''' || 2-isopropylmalate synthase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 3-isopropylmalate dehydratase (small subunit)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of leucine
 
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of leucine
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.657  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 4.582  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1554 bp, 518 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 597 bp, 199 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[leuB]]'', ''[[ilvC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysoA]]'', ''[[leuC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14788&#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:CAB14785&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:leuA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:leuD_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:''' BSU28280
+
* '''Locus tag:''' BSU28250
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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* '''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+BG11948]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11950]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + 3-methyl-2-oxobutanoate + H<sub>2</sub>O = (2S)-2-isopropylmalate + CoA (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmaleate + H<sub>2</sub>O (according to Swiss-Prot)  
  
−
* '''Protein family:''' LeuA type 1 subfamily (according to Swiss-Prot)
+
* '''Protein family:''' LeuD type 1 subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot),  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94565 P94565]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94568 P94568]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28280]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28250]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.13 2.3.3.13]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.33 4.2.1.33]
  
 
=== Additional information===
 
=== Additional information===
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=References=
 
=References=
  
−
<pubmed>12107147 18763711, </pubmed>
+
<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]
 
# 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]
 
# 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]
−
# 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]
 
 
# 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 13:21, 8 June 2009

  • Description: 3-isopropylmalate dehydratase (small subunit)

Gene name leuD
Synonyms
Essential no
Product 3-isopropylmalate dehydratase (small subunit)
Function biosynthesis of leucine
MW, pI 22 kDa, 4.582
Gene length, protein length 597 bp, 199 aa
Immediate neighbours ysoA, leuC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
LeuD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU28250

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmaleate + H2O (according to Swiss-Prot)
  • Protein family: LeuD type 1 subfamily (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

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

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: subject to Clp-dependent proteolysis upon glucose starvation PubMed

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. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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