title: The structures of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase before and after NAD+ and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family.
abstract: D-3-Hydroxybutyrate dehydrogenase, which catalyzes the reversible reaction between D-3-hydroxybutyrate and acetoacetate, has been classified into the short-chain dehydrogenase/reductase family and is a useful marker in the assay of diabetes mellitus and/or ketoacidosis. The enzyme from Alcaligenes faecalis was crystallized in the apo form and in the holo form with acetate as a substrate analogue. The crystal structures of both forms were determined at 2.2 angstroms resolution. The enzyme is a tetramer composed of four subunits assembled with noncrystallographic 222 point symmetry. Each subunit has two domains. The principal domain adopts the Rossmann fold essential for nucleotide binding, which is a common feature of the SDR family. NAD+ is bound in a large cleft in the domain. The pyrophosphate group of NAD+ is covered by the small additional domain, which is supported by two extended arms allowing domain movement. In the catalytic site, a water molecule is trapped by the catalytic Tyr155 and Ser142 residues in the vicinity of the bound NAD+ and acetate. The substrate analogue acetate is bound above the nicotinamide plane. A substrate (D-3-hydroxybutylate) bound model can reasonably be constructed by adding two C atoms into the void space between the water O atom and the methyl group of the acetate, suggesting a substrate-bound state before enzymatic reaction occurs. Based on these structural features, a reaction mechanism has been proposed.
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: 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: Masaru
authors.initials: M
authors.lastname: Tsunoda
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Amano
authors.forename: Takeshi
authors.initials: T
authors.lastname: Sekiguchi
authors.forename: Akio
authors.initials: A
authors.lastname: Takénaka
mesh_terms: D000085:Acetates / Q000737:chemistry* / Q000378:metabolism; D042481:Alcaligenes faecalis / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D006884:Hydroxybutyrate Dehydrogenase / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009243:NAD / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D000085:Acetates; D001426:Bacterial Proteins; D009243:NAD; D006884:Hydroxybutyrate Dehydrogenase