3VDR

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

Replaces:  3EEW

Summary for 3VDR

• Entry DOI: 10.2210/pdb3vdr/pdb
• Related: 2YZ7 2ZEA 3VDQ
• Descriptor: D-3-hydroxybutyrate dehydrogenase, CALCIUM ION, CHLORIDE ION, ... (8 entities in total)
• Functional Keywords: nad dependent enzymes, ketone bodies, oxidoreductase
• Biological source: Alcaligenes faecalis
• Total number of polymer chains: 4
• Total formula weight: 114802.53

Authors

Hoque, M.M.,Shimizu, S.,Juan, E.C.M.,Sato, Y.,Hossain, M.T.,Yamamoto, T.,Imamura, S.,Amano, H.,Suzuki, K.,Sekiguchi, T.,Tsunoda, M.,Takenaka, A. (deposition date: 2012-01-06, release date: 2012-02-08, Last modification date: 2023-11-08)

Primary citation

Hoque, M.M.,Shimizu, S.,Juan, E.C.M.,Sato, Y.,Hossain, M.T.,Yamamoto, T.,Imamura, S.,Suzuki, K.,Amano, H.,Sekiguchi, T.,Tsunoda, M.,Takenaka, A.
Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
Acta Crystallogr.,Sect.F, 65:331-335, 2009

PubMed Abstract: D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis catalyzes the reversible conversion between D-3-hydroxybutyrate and acetoacetate. The enzyme was crystallized in the presence of the substrate D-3-hydroxybutyrate and the cofactor NAD(+) at the optimum pH for the catalytic reaction. The structure, which was solved by X-ray crystallography, is isomorphous to that of the complex with the substrate analogue acetate. The product as well as the substrate molecule are accommodated well in the catalytic site. Their binding geometries suggest that the reversible reactions occur by shuttle movements of a hydrogen negative ion from the C3 atom of the substrate to the C4 atom of NAD(+) and from the C4 atom of NADH to the C3 atom of the product. The reaction might be further coupled to the withdrawal of a proton from the hydroxyl group of the substrate by the ionized Tyr155 residue. These structural features strongly support the previously proposed reaction mechanism of D-3-hydroxybutyrate dehydrogenase, which was based on the acetate-bound complex structure.

PubMed: 19342772
DOI: 10.1107/S1744309109008537

Experimental method

X-RAY DIFFRACTION (3 Å)