Difference between revisions of "Sandbox"

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−
* '''Description:''' citrate synthase <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'''
−
|''citZ''
+
|''icd''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
+
|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''' || citrate synthase II
+
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
 
|-
 
|-
 
|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:citZ_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
+
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 44: Line 44:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' acetyl-CoA + oxaloacetate ---> citrate, the reaction is irreversible
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 65: Line 65:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' inhibited by ATP [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
+
* '''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+BSU29140]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]
  
−
* '''E.C. number:''' 4.1.3.7
+
* '''E.C. number:''' 1.1.1.42
  
 
=== Additional information===
 
=== Additional information===
Line 89: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''
+
* '''Operon:'''  
 +
**''[[citZ]]-[[icd]]-[[mdh]]''
 +
**''[[icd]]-[[mdh]]''
  
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
+
* '''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, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 101: Line 103:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab  
+
* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 114: Line 116:
  
 
=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]
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 122:
  
 
# 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]
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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]
−
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 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]
−
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 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]
−
# Jin S, Sonenshein AL  (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 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 18:19, 15 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
Hier soll was neues rein
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
  • 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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