› 2d4v

X-ray diffraction
1.9Å resolution

Crystal structure of NAD dependent isocitrate dehydrogenase from Acidithiobacillus thiooxidans

Released:
DOI: 10.2210/pdb2d4v/pdb
PDB entry 2d4v coloured by chain, front view.
PDB entry 2d4v coloured by chain, side view.
PDB entry 2d4v coloured by chain, top view.
Source organism: Acidithiobacillus thiooxidans
Primary publication:
Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity.
Imada K, Tamura T, Takenaka R, Kobayashi I, Namba K, Inagaki K
Proteins 70 63-71 (2008)
PMID: 17634983

Function and Biology Details

Reaction catalysed: 
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184482 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate dehydrogenase [NADP] Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 429 amino acids
Theoretical weight: 46.27 KDa
Source organism: Acidithiobacillus thiooxidans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8GAX0 (Residues: 1-429; Coverage: 100%)
Gene name: icd
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
1 bound ligand:
Ligand FLC 4 x FLC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P43212
Unit cell:
a: 125.981Å b: 125.981Å c: 267.774Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.179 0.203
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

Novel type II and monomeric NAD+ specific isocitrate dehydrogenases: phylogenetic affinity, enzymatic characterization, and evolutionary implication.
Wang et al. (2015)
4 more

9 mentions without citation

Induced fit and the catalytic mechanism of isocitrate dehydrogenase.
Gonçalves et al. (2012)
8 more