title: Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney.
abstract: D-serine is a physiological co-agonist of the N-methyl-D-aspartate receptor. It regulates excitatory neurotransmission, which is important for higher brain functions in vertebrates. In mammalian brains, D-amino acid oxidase degrades D-serine. However, we have found recently that in chicken brains the oxidase is not expressed and instead a D-serine dehydratase degrades D-serine. The primary structure of the enzyme shows significant similarities to those of metal-activated D-threonine aldolases, which are fold-type III pyridoxal 5'-phosphate (PLP)-dependent enzymes, suggesting that it is a novel class of D-serine dehydratase. In the present study, we characterized the chicken enzyme biochemically and also by x-ray crystallography. The enzyme activity on D-serine decreased 20-fold by EDTA treatment and recovered nearly completely by the addition of Zn(2+). None of the reaction products that would be expected from side reactions of the PLP-D-serine Schiff base were detected during the >6000 catalytic cycles of dehydration, indicating high reaction specificity. We have determined the first crystal structure of the D-serine dehydratase at 1.9 Å resolution. In the active site pocket, a zinc ion that coordinates His(347) and Cys(349) is located near the PLP-Lys(45) Schiff base. A theoretical model of the enzyme-D-serine complex suggested that the hydroxyl group of D-serine directly coordinates the zinc ion, and that the ε-NH(2) group of Lys(45) is a short distance from the substrate Cα atom. The α-proton abstraction from D-serine by Lys(45) and the elimination of the hydroxyl group seem to occur with the assistance of the zinc ion, resulting in the strict reaction specificity.
authors.affiliation: Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Ohtsu, Shiga 520-2192, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Tanaka
authors.forename: Miki
authors.initials: M
authors.lastname: Senda
authors.forename: Nagarajan
authors.initials: N
authors.lastname: Venugopalan
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yamamoto
authors.forename: Toshiya
authors.initials: T
authors.lastname: Senda
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Ishida
authors.forename: Kihachiro
authors.initials: K
authors.lastname: Horiike
mesh_terms: D000818:Animals; D002384:Catalysis; D002645:Chickens; D018360:Crystallography, X-Ray; D006836:Hydro-Lyases / Q000737:chemistry* / Q000378:metabolism; D007668:Kidney / Q000201:enzymology*; D013056:Spectrophotometry, Ultraviolet; D015032:Zinc / Q000737:chemistry*
chemical_list: D006836:Hydro-Lyases; C101950:D-serine dehydratase; D015032:Zinc