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A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis.

Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z
J Am Chem Soc 138 7244-7 (2016)
Related entries: 5ej4, 5ej5, 5ej6, 5ej7, 5ej9, 5eja

Cited: 6 times
EuropePMC logo PMID: 27213829

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.

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  1. Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations. Kříž K, Fanfrlík J, Lepšík M. Chemphyschem 19 2540-2548 (2018)
  2. Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode. Chen Y, Li TL, Lin X, Li X, Li XD, Guo Z. J Biol Chem 292 12296-12310 (2017)
  3. Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites. Fries A, Mazzaferro LS, Grüning B, Bisel P, Stibal K, Buchholz PCF, Pleiss J, Sprenger GA, Müller M. Chembiochem 20 1672-1677 (2019)
  4. Single-Turnover Kinetics Reveal a Distinct Mode of Thiamine Diphosphate-Dependent Catalysis in Vitamin K Biosynthesis. Qin M, Song H, Dai X, Chan CK, Chan W, Guo Z. Chembiochem 19 1514-1522 (2018)


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