Icd

• Description: isocitrate dehydrogenase
  
  

Gene name	icd
Synonyms	citC
Essential	no
Product	isocitrate dehydrogenase
Function	TCA cycle
Gene expression levels in SubtiExpress: icd
Interactions involving this protein in SubtInteract: Icd
Metabolic function and regulation of this protein in SubtiPathways: icd
MW, pI	46 kDa, 4.833
Gene length, protein length	1269 bp, 423 aa
Immediate neighbours	mdh, citZ
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

carbon core metabolism, membrane proteins, phosphoproteins, most abundant proteins

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

• BsubCyc: BSU29130

• 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
  • specific activity: 1.64 µmol min^-1 (mg protein)^-1 PubMed

• Domains:

• Modification:
  • phosphorylated on Arg-180 PubMed
  • phosphorylated PubMed, PubMed
  • in vitro phosphorylated by PrkC on Thr-138, Thr-147, and Thr-396 PubMed

• Cofactors: 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
  • Mdh-Icd PubMed
  • GltA-Icd PubMed
  • OdhB-Icd PubMed

• Localization: attached to the membrane PubMed

Database entries

• BsubCyc: BSU29130

• 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

• Expression browser: icd 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:
  • belongs to the 100 most abundant proteins PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 37100 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 77080 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 41324 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 16631 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 32135 PubMed

Biological materials

• Mutant: GP666 (spc), GP672 (erm), available in Jörg Stülke's lab
  • 1A1000 ( icd::spec), PubMed, available at BGSC
  • 1A999 ( icd::spec), PubMed, available at BGSC
  • GP790 (citZ-icd-mdh::kan), available in Jörg Stülke's lab

• Expression vector:
  • pGP1121 (N-terminal Strep-tag, for SPINE, purification from B. subtilis, in pGP380) (available in Jörg Stülke's lab)

• lacZ fusion:

• GFP fusion:

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab

• Antibody: available in Linc Sonenshein's lab

Labs working on this gene/protein

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