› 5b4t

X-ray diffraction
1.19Å resolution

Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and a substrate D-3-hydroxybutyrate

Released:
DOI: 10.2210/pdb5b4t/pdb
PDB entry 5b4t coloured by chain, front view.
PDB entry 5b4t coloured by chain, side view.
PDB entry 5b4t coloured by chain, top view.
Source organism: Alcaligenes faecalis
Primary publication:
Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase.
Kanazawa H, Hoque MM, Tsunoda M, Suzuki K, Yamamoto T, Kawai G, Kondo J, Takénaka A
Acta Crystallogr F Struct Biol Commun 72 507-15 (2016)
PMID: 27380367

Function and Biology Details

Reaction catalysed: 
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112062 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-3-hydroxybutyrate dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 260 amino acids
Theoretical weight: 27.12 KDa
Source organism: Alcaligenes faecalis
Expression system: Escherichia coli
UniProt:
  • Canonical: D0VWQ0 (Residues: 1-260; Coverage: 100%)
Gene name: DF183_01165
Sequence domains: short chain dehydrogenase
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAD 1 x NAD
2 bound ligands:
Ligand 3HR 1 x 3HR
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P42212
Unit cell:
a: 62.78Å b: 62.78Å c: 119.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.157 0.173
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry.
Machado et al. (2020)
1 more

1 mention without citation

Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase.
Kanazawa et al. (2016)