› 3blv

X-ray diffraction
3.2Å resolution

Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits

Released:
DOI: 10.2210/pdb3blv/pdb
PDB entry 3blv coloured by chain, front view.
PDB entry 3blv coloured by chain, side view.
PDB entry 3blv coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Allosteric motions in structures of yeast NAD+-specific isocitrate dehydrogenase.
Taylor AB, Hu G, Hart PJ, McAlister-Henn L
J Biol Chem 283 10872-80 (2008)
PMID: 18256028

Function and Biology Details

Reaction catalysed: 
Isocitrate + NAD(+) = 2-oxoglutarate + CO(2) + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero octamer
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151181 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 354 amino acids
Theoretical weight: 39.1 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P28834 (Residues: 12-360; Coverage: 97%)
Gene names: IDH1, N2690, YNL037C
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase
Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 354 amino acids
Theoretical weight: 37.98 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P28241 (Residues: 16-369; Coverage: 96%)
Gene names: IDH2, O3326, YOR136W, YOR3326W
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

1 bound ligand:
Ligand FLC 4 x FLC
1 modified residue:
Ligand MSE 40 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 256.899Å b: 112.949Å c: 125.616Å
α: 90° β: 106.67° γ: 90°
R-values:
R R work R free
0.224 0.221 0.265
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Consequences of Oxidative Stress on Plant Glycolytic and Respiratory Metabolism.
Dumont et al. (2019)
1 more

8 mentions without citation

Ligand binding and structural changes associated with allostery in yeast NAD(+)-specific isocitrate dehydrogenase.
McAlister-Henn L. (2012)
7 more