Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution

The crystal structure of brewers' yeast pyruvate decarboxylase, a thiamin diphosphate dependent alpha-keto acid decarboxylase, has been determined to 2.4-A resolution. The homotetrameric assembly contains two dimers, exhibiting strong intermonomer interactions within each dimer but more limited ones between dimers. Each monomeric subunit is partitioned into three structural domains, all folding according to a mixed alpha/beta motif. Two of these domains are associated with cofactor binding, while the other is associated with substrate activation. The catalytic centers containing both thiamin diphosphate and Mg(II) are located deep in the intermonomer interface within each dimer. Amino acids important in cofactor binding and likely to participate in catalysis and substrate activation are identified.