title: Reaction mechanism of Zn2+-dependent d-serine dehydratase: role of a conserved tyrosine residue interacting with pyridine ring nitrogen of pyridoxal 5'-phosphate.
abstract: d-Serine dehydratase from Saccharomyces cerevisiae (Dsd1p) is a pyridoxal 5'-phosphate (PLP)- and Zn(2+)-dependent enzyme that catalyzes the dehydration of d-serine to yield pyruvate and ammonia. Dsd1p uses the Tyr residue (Y203) to interact with the pyridine nitrogen of PLP, which is a unique feature of PLP enzymes. To investigate the role of Y203 in catalysis, a series of Y203 mutants was constructed and studied. Mutant enzymes possessing a non-polar or a basic residue instead of Y203 (Y203F, A, S and R) exhibited substantial levels of catalytic activity, and among these, the Y203F mutant had the least impact on catalytic activity. The Y203D exhibited a 10(5)-fold decrease in enzyme activity, and unlike wild-type enzyme, the mutant enzyme favoured the Cα reprotonation before hydroxyl group protonation. Our data show that the Y203 does not participate in the protonation of the pyridine nitrogen (N1) of PLP, and Dsd1p uses the cofactor in an N1-unprotonated state. The unprotonated N1 promotes elimination of the leaving group and evades Cα reprotonation before hydroxyl group protonation.
authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Tomokazu
authors.initials: T
authors.lastname: Ito
authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Mai
authors.initials: M
authors.lastname: Matsuoka
authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Kazushi
authors.initials: K
authors.lastname: Koga
authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Hisashi
authors.initials: H
authors.lastname: Hemmi
authors.affiliation: Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furou-Chou, Chikusa, Nagoya, Aichi 464-8601, Japan yosimura@agr.nagoya-u.ac.jp.
authors.forename: Tohru
authors.initials: T
authors.lastname: Yoshimura
mesh_terms: D001665:Binding Sites / Q000235:genetics; D055162:Biocatalysis; D020134:Catalytic Domain; D006836:Hydro-Lyases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D015394:Molecular Structure; D020125:Mutation, Missense; D009584:Nitrogen / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins; D011725:Pyridines / Q000737:chemistry / Q000378:metabolism*; D011732:Pyridoxal Phosphate / Q000737:chemistry / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012694:Serine / Q000737:chemistry / Q000378:metabolism; D013053:Spectrophotometry; D014443:Tyrosine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015032:Zinc / Q000378:metabolism* / Q000494:pharmacology
chemical_list: D011506:Proteins; D011725:Pyridines; D029701:Saccharomyces cerevisiae Proteins; D014443:Tyrosine; D012694:Serine; D011732:Pyridoxal Phosphate; D006836:Hydro-Lyases; C101950:D-serine dehydratase; D015032:Zinc; D009584:Nitrogen; C023666:pyridine
keywords: d-serine; d-serine dehydratase; pyridine nitrogen; pyridoxal 5′-phosphate; reaction mechanism