› 3vdr

X-ray diffraction
3Å resolution

Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)

Released:
DOI: 10.2210/pdb3vdr/pdb
PDB entry 3vdr coloured by chain, front view.
PDB entry 3vdr coloured by chain, side view.
PDB entry 3vdr coloured by chain, top view.
Source organism: Alcaligenes faecalis
Primary publication:
Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
Hoque MM, Shimizu S, Juan EC, Sato Y, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Amano H, Sekiguchi T, Tsunoda M, Takénaka A
Acta Crystallogr Sect F Struct Biol Cryst Commun 65 331-5 (2009)
PMID: 19342772

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 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 260 amino acids
Theoretical weight: 27.12 KDa
Source organism: Alcaligenes faecalis
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 NAI 4 x NAI

Cofactor: Ligand NAD 4 x NAD
4 bound ligands:
Ligand CA 2 x CA
Ligand CL 3 x CL
Ligand 3HR 4 x 3HR
Ligand AAE 4 x AAE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P41212
Unit cell:
a: 91.1Å b: 91.1Å c: 262Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.176 0.241

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)