The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes

Abstract

The three-dimensional reconstruction of the bovine kidney pyruvate dehydrogenase complex (Mr≈ 7.8 × 10 6) comprising about 22 molecules of pyruvate dehydrogenase (E 1) and about 6 molecules of dihydrolipoamide dehydrogenase (E 3) with its binding protein associated with the 60-subunit dihydrolipoamide acetyltransferase (E 2) core provides considerable insight into the structural and functional organization of the largest multienzyme complex known. The structure shows that potentially 60 centers for acetyl-CoA synthesis are organized in sets of three at each of the 20 vertices of the pentagonal dodecahedral core. These centers consist of three E 1 molecules bound to one E 2 trimer adjacent to an E 3 molecule in each of 12 pentagonal openings. The E 1 components are anchored to the E 1-binding domain of the E 2 subunits through an ≈50-Å-long linker. Three of these linkers emanate from the outside edges of the triangular base of the E 2 trimer and form a cage around its base that may shelter the lipoyl domains and the E 1 and E 2 active sites. The docking of the atomic structures of E 1 and the E 1 binding and lipoyl domains of E 2 in the electron microscopy map gives a good fit and indicates that the E 1 active site is ≈95 Å above the base of the trimer. We propose that the lipoyl domains and its tether (swinging arm) rotate about the E 1-binding domain of E 2,which is centrally located 45–50 Å from the E 1, E 2, and E 3 active sites, and that the highly flexible breathing core augments the transfer of intermediates between active sites.