title: Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
abstract: D-serine is an endogenous coagonist for the N-methyl-D-aspartate receptor and is involved in excitatory neurotransmission in the brain. Mammalian pyridoxal 5'-phosphate-dependent serine racemase, which is localized in the mammalian brain, catalyzes the racemization of L-serine to yield D-serine and vice versa. The enzyme also catalyzes the dehydration of D- and L-serine. Both reactions are enhanced by Mg.ATP in vivo. We have determined the structures of the following three forms of the mammalian enzyme homolog from Schizosaccharomyces pombe: the wild-type enzyme, the wild-type enzyme in the complex with an ATP analog, and the modified enzyme in the complex with serine at 1.7, 1.9, and 2.2 A resolution, respectively. On binding of the substrate, the small domain rotates toward the large domain to close the active site. The ATP binding site was identified at the domain and the subunit interface. Computer graphics models of the wild-type enzyme complexed with L-serine and D-serine provided an insight into the catalytic mechanisms of both reactions. Lys-57 and Ser-82 located on the protein and solvent sides, respectively, with respect to the cofactor plane, are acid-base catalysts that shuttle protons to the substrate. The modified enzyme, which has a unique "lysino-D-alanyl" residue at the active site, also exhibits catalytic activities. The crystal-soaking experiment showed that the substrate serine was actually trapped in the active site of the modified enzyme, suggesting that the lysino-D-alanyl residue acts as a catalytic base in the same manner as inherent Lys-57 of the wild-type enzyme.
authors.affiliation: Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Goto
authors.forename: Takae
authors.initials: T
authors.lastname: Yamauchi
authors.forename: Nobuo
authors.initials: N
authors.lastname: Kamiya
authors.forename: Ikuko
authors.initials: I
authors.lastname: Miyahara
authors.forename: Tohru
authors.initials: T
authors.lastname: Yoshimura
authors.forename: Hisaaki
authors.initials: H
authors.lastname: Mihara
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Kurihara
authors.forename: Ken
authors.initials: K
authors.lastname: Hirotsu
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Esaki
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D000818:Animals; D002384:Catalysis; D020134:Catalytic Domain / Q000502:physiology; D008322:Mammals; D017434:Protein Structure, Tertiary / Q000502:physiology; D019998:Racemases and Epimerases / Q000737:chemistry* / Q000378:metabolism; D012568:Schizosaccharomyces / Q000201:enzymology*; D029702:Schizosaccharomyces pombe Proteins / Q000737:chemistry* / Q000378:metabolism; D012694:Serine / Q000737:chemistry* / Q000378:metabolism; D040681:Structural Homology, Protein; D000099300:Serine Racemase
chemical_list: D000255:Adenosine Triphosphate; D019998:Racemases and Epimerases; D029702:Schizosaccharomyces pombe Proteins; D012694:Serine; D000099300:Serine Racemase