› 2d4a

X-ray diffraction
2.87Å resolution

Structure of the malate dehydrogenase from Aeropyrum pernix

Released:
DOI: 10.2210/pdb2d4a/pdb
PDB entry 2d4a coloured by chain, front view.
PDB entry 2d4a coloured by chain, side view.
PDB entry 2d4a coloured by chain, top view.
Source organism: Aeropyrum pernix
Primary publication:
Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.
Kawakami R, Sakuraba H, Goda S, Tsuge H, Ohshima T
Biochim Biophys Acta 1794 1496-504 (2009)
PMID: 19555779

Function and Biology Details

Reaction catalysed: 
(S)-malate + NAD(P)(+) = oxaloacetate + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195487 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Malate dehydrogenase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 308 amino acids
Theoretical weight: 33.53 KDa
Source organism: Aeropyrum pernix
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YEA1 (Residues: 1-308; Coverage: 100%)
Gene names: APE_0672.1, mdh
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P212121
Unit cell:
a: 78.168Å b: 84.012Å c: 216.148Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.205 0.24
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

Expression and identification of a thermostable malate dehydrogenase from multicellular prokaryote Streptomyces avermitilis MA-4680.
Wang et al. (2011)
3 more

1 mention without citation

An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range.
Matthews et al. (2023)