Difference between revisions of "Icd"

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* '''Domains:'''  
 
* '''Domains:'''  
  
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* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], ''in vitro'' phosphorylated by [[PrkC]] on Thr-138, Thr-147, and Thr-396 {{PubMed|20389117}}
+
* '''Modification:'''  
 +
** phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 +
** ''in vitro'' phosphorylated by [[PrkC]] on Thr-138, Thr-147, and Thr-396 {{PubMed|20389117}}
  
−
* '''Cofactor(s):''' Mg2+, Mn2+
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* '''Cofactor(s):''' Mg2+, Mn2+, NADP+  
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
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=== Additional information===
 
=== Additional information===
−
This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
+
* This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
 +
* extensive information on the structure and enzymatic properties of Icd can be found at [http://www.proteopedia.org/wiki/index.php/Isocitrate_dehydrogenase Proteopedia]
  
 
=Expression and regulation=
 
=Expression and regulation=

Revision as of 10:45, 19 February 2011

  • Description: isocitrate dehydrogenase

Gene name icd
Synonyms citC
Essential no
Product isocitrate dehydrogenase
Function TCA cycle
Metabolic function and regulation of this protein in SubtiPathways:
Central C-metabolism
MW, pI 46 kDa, 4.833
Gene length, protein length 1269 bp, 423 aa
Immediate neighbours mdh, citZ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Icd context.gif
This image was kindly provided by SubtiList







Categories containing this gene/protein

carbon core metabolism, membrane proteins, phosphoproteins

This gene is a member of the following regulons

CcpA regulon, CcpC regulon

The gene

Basic information

  • Locus tag: BSU29130

Phenotypes of a mutant

    • reduced ability to sporulate PubMed
    • growth and sporulation defects of the mutant could be partially bypassed by deletion of the major citrate synthase gene (citZ) PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH (according to Swiss-Prot)
  • Protein family: isocitrate and isopropylmalate dehydrogenases family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information: Reversible Michaelis-Menten PubMed
  • Domains:
  • Modification:
  • Cofactor(s): Mg2+, Mn2+, NADP+
  • Effectors of protein activity:
    • Inhibited by glyoxylate, oxaloacetate and oxalomalate PubMed
      • Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor PubMed
  • Localization: attached to the membrane PubMed

Database entries

  • KEGG entry: [3]

Additional information

  • This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ PubMed
  • extensive information on the structure and enzymatic properties of Icd can be found at Proteopedia

Expression and regulation

  • Regulatory mechanism:
    • CcpA: transcription repression, CcpC: transcription repression PubMed
    • CcpC: transcription repression (molecular inducer: citrate) PubMed
  • Additional information:

Biological materials

  • Mutant: GP666 (spc), GP672 (erm), available in Stülke lab
  • Expression vector:
    • pGP1121 (N-terminal Strep-tag, for SPINE, purification from B. subtilis, in pGP380) (available in Stülke lab)
    • for expression, purification in E. coli with N-terminal His-tag, in pWH844: pGP931, available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

Labs working on this gene/protein

Linc Sonenshein, Tufts University, Boston, MA, USA Homepage

Your additional remarks

References

Frederik M Meyer, Jan Gerwig, Elke Hammer, Christina Herzberg, Fabian M Commichau, Uwe Völker, Jörg Stülke
Physical interactions between tricarboxylic acid cycle enzymes in Bacillus subtilis: evidence for a metabolon.
Metab Eng: 2011, 13(1);18-27
[PubMed:20933603] [WorldCat.org] [DOI] (I p)

Nico Pietack, Dörte Becher, Sebastian R Schmidl, Milton H Saier, Michael Hecker, Fabian M Commichau, Jörg Stülke
In vitro phosphorylation of key metabolic enzymes from Bacillus subtilis: PrkC phosphorylates enzymes from different branches of basic metabolism.
J Mol Microbiol Biotechnol: 2010, 18(3);129-40
[PubMed:20389117] [WorldCat.org] [DOI] (I p)

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

Christine Eymann, Dörte Becher, Jörg Bernhardt, Katrin Gronau, Anja Klutzny, Michael Hecker
Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis.
Proteomics: 2007, 7(19);3509-26
[PubMed:17726680] [WorldCat.org] [DOI] (P p)

Alain Lévine, Françoise Vannier, Cédric Absalon, Lauriane Kuhn, Peter Jackson, Elaine Scrivener, Valérie Labas, Joëlle Vinh, Patrick Courtney, Jérôme Garin, Simone J Séror
Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes.
Proteomics: 2006, 6(7);2157-73
[PubMed:16493705] [WorldCat.org] [DOI] (P p)

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

Satinder K Singh, Stephen P Miller, Antony Dean, Leonard J Banaszak, David C LaPorte
Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/phosphatase.
J Biol Chem: 2002, 277(9);7567-73
[PubMed:11751849] [WorldCat.org] [DOI] (P p)

S K Singh, K Matsuno, D C LaPorte, L J Banaszak
Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase.
J Biol Chem: 2001, 276(28);26154-63
[PubMed:11290745] [WorldCat.org] [DOI] (P p)

C Jourlin-Castelli, N Mani, M M Nakano, A L Sonenshein
CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis.
J Mol Biol: 2000, 295(4);865-78
[PubMed:10656796] [WorldCat.org] [DOI] (P p)

K Matsuno, T Blais, A W Serio, T Conway, T M Henkin, A L Sonenshein
Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis.
J Bacteriol: 1999, 181(11);3382-91
[PubMed:10348849] [WorldCat.org] [DOI] (P p)

S Jin, P A Levin, K Matsuno, A D Grossman, A L Sonenshein
Deletion of the Bacillus subtilis isocitrate dehydrogenase gene causes a block at stage I of sporulation.
J Bacteriol: 1997, 179(15);4725-32
[PubMed:9244258] [WorldCat.org] [DOI] (P p)

R F Ramaley, M O Hudock
Purification and properties of isocitrate dehydrogenase (NADP) from Thermus aquaticus YT-1, Bacillus subtilis-168 and Chlamydomonas reinhardti-Y-2.
Biochim Biophys Acta: 1973, 315(1);22-36
[PubMed:4147570] [WorldCat.org] [DOI] (P p)

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