Difference between revisions of "Sandbox"

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* '''Description:''' isocitrate dehydrogenase <br/><br/>
+
* '''Description:''' malate 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'''
−
|''icd''
+
|''mdh''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
 
|-
 
|-
 
|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:icd_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 38:
  
 
===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 ===
Line 44: Line 43:
 
* '''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+BG10856]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]
  
 
=== Additional information===
 
=== Additional information===
Line 65: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 73: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]
  
−
* '''E.C. number:''' 1.1.1.42
+
* '''E.C. number:''' 1.1.1.37
  
 
=== Additional information===
 
=== Additional information===
−
 
−
=Expression and regulation=
 
  
 
* '''Operon:'''  
 
* '''Operon:'''  
Line 95: Line 92:
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''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]])
+
* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
−
''[[icd]]'': constitutive  
+
''[[mdh]]'': constitutive  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression
 +
 
 +
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 103: Line 102:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab
+
* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab  
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 121: Line 120:
 
=References=
 
=References=
  
−
# 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]
+
# 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]
−
# 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 18:19, 15 April 2009

  • Description: malate dehydrogenase

Gene name mdh
Synonyms citH
Essential no
Product malate dehydrogenase
Function TCA cycle
MW, pI 33 kDa, 4.727
Gene length, protein length 936 bp, 312 aa
Immediate neighbours icd, phoP
Hier soll was neues rein
Genetic context
Mdh 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: membrane associated PubMed

Database entries

  • Structure: 1EMD (E.coli)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 1.1.1.37

Additional information

  • Regulation: citZ: catabolite repression (CcpA), repression by glucose + glutamate (CcpC)

mdh: constitutive

  • Regulatory mechanism: CcpA: transcription repression, CcpC: transcription repression


  • Additional information:

Biological materials

  • Mutant: GP719 (spc), 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. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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