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−enamine intermediate 5 is found to have the
E-configuration. The S-configuration is
imposed on the
2-(2-hydroxypropionyl)ethyl)thiamin diphosphate intermediate
4 by the chiral conformation induced in the
achiral
cofactor through its interactions with the protein. The
R-configuration is assigned to the
2-(1-hydroxyethyl)thiamin
diphosphate intermediate 6 arising through protonation of
the carbanion−enamine intermediate 5. The
tight
stereochemical control observed in acyloin formation from aromatic
aldehydes and pyruvate is explained, as is the
relaxed stereocontrol in acyloin formation from acetaldehyde and
pyruvate.