On the unique structural organization of the Saccharomyces cerevisiae pyruvate dehydrogenase complex

Dihydrolipoamide acyltransferase (E₂), a catalytic and structural component of the three functional classes of multienzyme complexes that catalyze the oxidative decarboxylation of α-keto acids, forms the central core to which the other components attach. We have determined the structures of the truncated 60-mer core dihydrolipoamide acetyltransferase (tE₂) of the Saccharomyces cerevisiae pyruvate dehydrogenase complex and complexes of the tE₂ core associated with a truncated binding protein (tBP), intact binding protein (BP), and the BP associated with its dihydrolipoamide dehydrogenase (BP·E₃). The tE₂ core is a pentagonal dodecahedron consisting of 20 cone- shaped trimers interconnected by 30 bridges. Previous studies have given rise to the generally accepted belief that the other components are bound on the outside of the E₂ scaffold. However, this investigation shows that the 12 large openings in the tE₂ core permit the entrance of tBP, BP, and BP·E₃ into a large central cavity where the BP component apparently binds near the tip of the tE₂ trimer. The bone-shaped E₃ molecule is anchored inside the central cavity through its interaction with BP. One end of E₃ has its catalytic site within the surface of the scaffold for interaction with other external catalytic domains. Though tE₂ has 60 potential binding sites, it binds only about 30 copies of tBP, 15 of BP, and 12 of BP·E₃. Thus, E₂ is unusual in that the stoichiometry and arrangement of the tBP, BP, and E₃-BP components are determined by the geometric constraints of the underlying scaffold.