Icd

• 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 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]

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:
  • phosphorylated PubMed, PubMed
  • in vitro phosphorylated by PrkC on Thr-138, Thr-147, and Thr-396 PubMed

• 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

• Interactions:
  • homodimer PubMed
  • CitZ-Mdh-Icd (this is the core of the TCA cycle metabolon) PubMed
  • GltA-Icd PubMed
  • OdhB-Icd PubMed

• Localization: attached to the membrane PubMed

Database entries

• Structure: 1HQS

• UniProt: P39126

• KEGG entry: [3]

• E.C. number: 1.1.1.42

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

• Operon:
  • citZ-icd-mdh PubMed
  • icd-mdh PubMed

• Sigma factor:
  • citZ: SigA PubMed
  • icd: SigA PubMed

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

• 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

• Antibody: available in Linc Sonenshein lab

Labs working on this gene/protein

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