title: Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
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.
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan.
authors.forename: Md Mominul
authors.initials: MM
authors.lastname: Hoque
authors.forename: Satoru
authors.initials: S
authors.lastname: Shimizu
authors.forename: Ella Czarina Magat
authors.initials: EC
authors.lastname: Juan
authors.forename: Yoshiteru
authors.initials: Y
authors.lastname: Sato
authors.forename: Md Tofazzal
authors.initials: MT
authors.lastname: Hossain
authors.forename: Tamotsu
authors.initials: T
authors.lastname: Yamamoto
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Imamura
authors.forename: Kaoru
authors.initials: K
authors.lastname: Suzuki
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Amano
authors.forename: Takeshi
authors.initials: T
authors.lastname: Sekiguchi
authors.forename: Masaru
authors.initials: M
authors.lastname: Tsunoda
authors.forename: Akio
authors.initials: A
authors.lastname: Takénaka