› 2qfx

X-ray diffraction
2.7Å resolution

Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with NADPH, a-ketoglutarate and Ca(2+)

Released:
DOI: 10.2210/pdb2qfx/pdb
PDB entry 2qfx coloured by chain, front view.
PDB entry 2qfx coloured by chain, side view.
PDB entry 2qfx coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.
Peng Y, Zhong C, Huang W, Ding J
Protein Sci 17 1542-54 (2008)
PMID: 18552125

Function and Biology Details

Reaction catalysed: 
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149482 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate dehydrogenase [NADP], mitochondrial Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 427 amino acids
Theoretical weight: 48.14 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P21954 (Residues: 16-428; Coverage: 97%)
Gene names: IDP1, YDL066W
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments


Cofactor: Ligand NDP 6 x NDP
2 bound ligands:
Ligand CA 6 x CA
Ligand AKG 6 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P2
Unit cell:
a: 113.415Å b: 99.63Å c: 129.95Å
α: 90° β: 111.21° γ: 90°
R-values:
R R work R free
0.217 0.217 0.285
Expression system: Escherichia coli

Quick links

Citations

22 citation in other articles

Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation.
Wang et al. (2013)
21 more

5 mentions without citation

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.
Peng et al. (2008)
4 more