title: A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis.
abstract: Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. However, this intermediate is not found in the thiamine-dependent catalysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and was structurally determined at 1.34 Å resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring nitrogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 Å. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Haigang
authors.initials: H
authors.lastname: Song
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Dong
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Qin
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Yaozong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Yueru
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Wan
authors.initials: W
authors.lastname: Chan
authors.affiliation: Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Guo
mesh_terms: D002384:Catalysis; D003653:Decarboxylation; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D011771:Pyruvate Oxidase / Q000737:chemistry*; D013831:Thiamine / Q000737:chemistry*; D013835:Thiamine Pyrophosphate / Q000737:chemistry*; D014812:Vitamin K / Q000096:biosynthesis*
chemical_list: D029968:Escherichia coli Proteins; D014812:Vitamin K; C534108:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase, E coli; D011771:Pyruvate Oxidase; D013835:Thiamine Pyrophosphate; D013831:Thiamine