Pyruvate Decarboxylase: A Molecular Modeling Study of Pyruvate Decarboxylation and Acyloin Formation

Using crystal structure data for the pyruvate decarboxylase from Saccharomyces uvarum (which is nearly identical with the enzyme from Saccharomyces cerevisiae), molecular modeling studies have been carried out to investigate the mode of action of the enzyme. Each step of the decarboxylation mechanism can be explained by assuming that the 4‘-amino group of thiamin diphosphate (TDP) acts as a general acid and, in its deprotonated form, as a general base. The carboxyl group of Glu 477 plays a key role in both pyruvate decarboxylation and acyloin formation. In the first case it interacts with the carboxylate group of pyruvate to stabilize the incipient dianion formed by attack of the thiazolium carbanion on pyruvate. In the second case, it interacts with the developing alkoxide anion arising from attack on acetaldehyde or benzaldehyde by the carbanion−enamine intermediate. These studies have permitted the assignment of configuration to all of the key intermediates in the catalytic process. Thus the carbanion−...