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Role of zinc ion for catalytic activity in d-serine dehydratase from Saccharomyces cerevisiae.

Abstract
d-Serine dehydratase from Saccharomyces cerevisiae (DsdSC) is a fold-type III pyridoxal 5'-phosphate-dependent enzyme catalyzing d-serine dehydration. The enzyme contains 1 mol Zn(2+) in its active site and shows a unique zinc dependence. The Zn(2+) is essential for the d-serine dehydration, but not for the α,β-elimination of β-Cl-d-alanine catalyzed as a side-reaction. The fact that dehydration of d-threonine and d-allo-threonine, also catalyzed by DsdSC, is likewise Zn(2+) dependent indicates that Zn(2+) is indispensable for the elimination of hydroxyl group, regardless of the stereochemistry of C(β) . Removal of Zn(2+) results in a less polar active site without changing the gross conformation of DsdSC. (1) H NMR determined the rates of α-hydrogen abstraction and hydroxyl group elimination of d-serine in (2) H(2) O to be 9.7 and 8.5 s(-1) , respectively, while the removal of Zn(2+) abolished both reactions. Mutation of Cys400 or His398 within the Zn(2+) binding sites to Ala endowed DsdSC with similar properties to those of the Zn(2+) -depleted wild-type enzyme: the mutants lost the reactivity toward d-serine and d-threonine but retained that toward β-Cl-d-alanine. (1) H NMR analysis also revealed that both α-hydrogen abstraction and hydroxyl group elimination from d-serine were severely hampered in the C400A mutant. Our data suggest that DsdSC catalyzes the α-hydrogen abstraction and hydroxyl group elimination in a concerted fashion.
AuthorsTomokazu Ito, Kazushi Koga, Hisashi Hemmi, Tohru Yoshimura
JournalThe FEBS journal (FEBS J) Vol. 279 Issue 4 Pg. 612-24 (Feb 2012) ISSN: 1742-4658 [Electronic] England
PMID22176976 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
Copyright© 2011 The Authors Journal compilation © 2011 FEBS.
Chemical References
  • Hydroxides
  • Saccharomyces cerevisiae Proteins
  • Water
  • Serine
  • Hydrogen
  • hydroxide ion
  • Hydro-Lyases
  • D-serine dehydratase
  • Zinc
Topics
  • Amino Acid Substitution
  • Binding Sites (genetics)
  • Biocatalysis (drug effects)
  • Catalytic Domain (genetics)
  • Hydro-Lyases (chemistry, genetics, metabolism)
  • Hydrogen (chemistry, metabolism)
  • Hydroxides (chemistry, metabolism)
  • Kinetics
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Mutation
  • Protein Structure, Tertiary
  • Saccharomyces cerevisiae (enzymology, genetics)
  • Saccharomyces cerevisiae Proteins (chemistry, genetics, metabolism)
  • Serine (chemistry, genetics, metabolism)
  • Spectrometry, Fluorescence
  • Water (chemistry, metabolism)
  • Zinc (chemistry, metabolism, pharmacology)

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