Difference between revisions of "Sandbox"

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−
* '''Description:''' similar to enoyl CoA hydratase <br/><br/>
+
* '''Description:''' isocitrate dehydrogenase <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'''
−
|''yhaR''
+
|''icd''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 6.355  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 765 bp, 255 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhaS]]'', ''[[yhaQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yhaR_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/icd_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yhaR_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/icd_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yhaR_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 32: Line 30:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 41: Line 39:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12994]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]
  
 
=== Additional information===
 
=== Additional information===
Line 67: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 75: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09880]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 1.1.1.42
  
 
=== Additional information===
 
=== Additional information===
Line 92: Line 91:
  
 
* '''Operon:'''  
 
* '''Operon:'''  
 +
**''[[citZ]]-[[icd]]-[[mdh]]''
 +
**''[[icd]]-[[mdh]]''
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]
−
 
 
−
* '''Regulation:''' repressed by glucose (17-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
 
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulation:''' repressed by glucose (2.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
 +
''[[icd]]'': constitutive
 +
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 122: Line 123:
  
 
# 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]
 
# 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]
 +
# Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. [http://www.ncbi.nlm.nih.gov/sites/entrez/10348849 PubMed]
 +
# Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. [http://www.ncbi.nlm.nih.gov/sites/entrez/11751849 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]
 +
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 +
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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 10:00, 6 April 2009

  • Description: isocitrate dehydrogenase

Gene name icd
Synonyms citC
Essential no
Product isocitrate dehydrogenase
Function TCA cycle
MW, pI 46 kDa, 4.833
Gene length, protein length 1269 bp, 423 aa
Immediate neighbours citZ, mdh
Gene sequence (+200bp) Protein sequence
Genetic context
Icd context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

reduced ability to sporulate PubMed

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:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: attached to the membrane PubMed

Database entries

  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 1.1.1.42

Additional information

Expression and regulation

  • Regulation: repressed by glucose (2.2-fold) (CcpA) PubMed, citZ: catabolite repression (CcpA), repression by glucose + glutamate (CcpC)

icd: constitutive

  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression
  • Additional information:

Biological materials

  • Mutant: GP666 (spc), GP672 (erm), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

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. Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. PubMed
  3. Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. PubMed
  4. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  5. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  6. Levine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. PubMed
  7. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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