title: Molecular basis of the general base catalysis of an α/β-hydrolase catalytic triad.
abstract: The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change in the catalysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical α/β-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of half of the α-helical cap domain, which causes extensive structural changes in the α/β-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche conformation to form the functional triad. NMR analysis shows that the inactive open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couples formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the nucleophilicity of the triad, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.
authors.affiliation: From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and.
authors.forename: Yueru
authors.initials: Y
authors.lastname: Sun
authors.affiliation: From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and.
authors.forename: Shuhui
authors.initials: S
authors.lastname: Yin
authors.affiliation: From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and.
authors.forename: Yitao
authors.initials: Y
authors.lastname: Feng
authors.affiliation: State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
authors.forename: Jiahai
authors.initials: J
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and Division of Life Sciences, and.
authors.forename: Changdong
authors.initials: C
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and Division of Life Sciences, and.
authors.forename: Guang
authors.initials: G
authors.lastname: Zhu
authors.affiliation: From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and chguo@ust.hk.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Guo
mesh_terms: D001224:Aspartic Acid / Q000378:metabolism; D002384:Catalysis; D018360:Crystallography, X-Ray; D004789:Enzyme Activation / Q000502:physiology; D004926:Escherichia coli / Q000201:enzymology*; D006639:Histidine / Q000378:metabolism; D006860:Hydrogen Bonding; D016297:Mutagenesis, Site-Directed; D007652:Oxo-Acid-Lyases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012694:Serine / Q000378:metabolism; D013329:Structure-Activity Relationship; D014812:Vitamin K / Q000096:biosynthesis
chemical_list: D014812:Vitamin K; D001224:Aspartic Acid; D012694:Serine; D006639:Histidine; C060510:2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase; D007652:Oxo-Acid-Lyases
keywords: Crystal Structure; Enzyme Mechanisms; Hydrolases; Open-Closed Conformational Change; Protein Conformation; Vitamin K
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