› 5zi4

X-ray diffraction
2.1Å resolution

MDH3 wild type, nad-oaa-form

Released:
DOI: 10.2210/pdb5zi4/pdb
PDB entry 5zi4 coloured by chain, front view.
PDB entry 5zi4 coloured by chain, side view.
PDB entry 5zi4 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae.
Moriyama S, Nishio K, Mizushima T
Acta Crystallogr F Struct Biol Commun 74 617-624 (2018)
PMID: 30279312

Function and Biology Details

Reaction catalysed: 
(S)-malate + NAD(+) = oxaloacetate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152297 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Malate dehydrogenase, peroxisomal Chains: A, B
Molecule details ›
Chains: A, B
Length: 345 amino acids
Theoretical weight: 37.38 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P32419 (Residues: 1-343; Coverage: 100%)
Gene names: D2468, MDH3, YDL078C
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
1 bound ligand:
Ligand OAA 2 x OAA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 57.218Å b: 86.658Å c: 135.05Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.196 0.266
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The Role of Yeasts and Lactic Acid Bacteria on the Metabolism of Organic Acids during Winemaking.
Mendes Ferreira et al. (2020)
3 other articles

1 mention without citation

Structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae.
Moriyama et al. (2018)