The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes
The three-dimensional reconstruction of the bovine kidney pyruvate dehydrogenase complex (Mr ≈ 7.8 × 106) comprising about 22 molecules of pyruvate dehydrogenase (E1) and about 6 molecules of dihydrolipoamide dehydrogenase (E3) with its binding protein associated with the 60-subunit dihydrolipoamide acetyltransferase (E2) 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 E1 molecules bound to one E2 trimer adjacent to an E3 molecule in each of 12 pentagonal openings. The E1 components are anchored to the E1-binding domain of the E2 subunits through an ≈50-Å-long linker. Three of these linkers emanate from the outside edges of the triangular base of the E2 trimer and form a cage around its base that may shelter the lipoyl domains and the E1 and E2 active sites. The docking of the atomic structures of E1 and the E1 binding and lipoyl domains of E2 in the electron microscopy map gives a good fit and indicates that the E1 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 E1-binding domain of E2, which is centrally located 45-50 Å from the E1, E2, and E3 active sites, and that the highly flexible breathing core augments the transfer of intermediates between active sites.