Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations

Abstract

Thiamin diphosphate (ThDP), the vitamin B1 coenzyme is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/carbene/C2-carbanion of the thiazolium ring and the C2α-carbanion/enamine, once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of several intermediates which are stable under acidic conditions, solid-state NMR and circular dichroism detection of the states of ionization and tautomerization of the 4'-aminopyrimidine moiety of ThDP in some of the intermediates. These methods also enabled in some cases determination of the rate-limiting step in the complex series of steps. This review is an update of a review with the same title published by the authors in 2005 in this Journal. Much progress has been made in the intervening decade in the identification of the intermediates and their application to gain additional mechanistic insight.

Keywords: 1-Deoxy-d-xylulose-5 phosphate synthase; 1′,4′-imino tautomer; 2-oxoglutarate dehydrogenase complex; Benzaldehyde lyase; Benzoylformate decarboxylase; C2-ylide/C2-carbanion/C2-carbene; C2α-carbanion or enamine; C2α-hydroxyethylthiamin diphosphate; C2α-lactylthiamin diphosphate; Circular dichroism; Glyoxylate carboligase; Pyruvate dehydrogenase complex; Thiamin diphosphate; Yeast pyruvate decarboxylase.