Organization of the Cores of the Mammalian Pyruvate Dehydrogenase Complex Formed by E2 and E2 Plus the E3-binding Protein and Their Capacities to Bind the E1 and E3 Components

The subunits of the dihydrolipoyl acetyltransferase (E2) component of mammalian pyruvate dehydrogenase complex can form a 60-mer via association of the C-terminal I domain of E2 at the vertices of a dodecahedron. Exterior to this inner core structure, E2 has a pyruvate dehydrogenase component (E1)-binding domain followed by two lipoyl domains, all connected by mobile linker regions. The assembled core structure of mammalian pyruvate dehydrogenase complex also includes the dihydrolipoyl dehydrogenase (E3) -binding protein (E3BP) that binds the I domain of E2 by its C-terminal I′ domain. E3BP similarly has linker regions connecting an E3-binding domain and a lipoyl domain. The composition of E2-E3BP was thought to be 60 E2 plus ∼12 E3BP. We have prepared homogenous human components. E2 and E2-E3BP have S_20,w values of 36 S and 31.8 S, respectively. Equilibrium sedimentation and small angle x-ray scattering studies indicate that E2-E3BP has lower total mass than E2, and small angle x-ray scattering showed that E3 binds to E2-E3BP outside the central dodecahedron. In the presence of saturating levels of E1, E2 bound ∼60 E1 and maximally sedimented 64.4 ± 1.5 S faster than E2, whereas E1-saturated E2-E3BP maximally sedimented 49.5 ± 1.4 S faster than E2-E3BP. Based on the impact on sedimentation rates by bound E1, we estimate fewer E1 (∼12) were bound by E2-E3BP than by E2. The findings of a smaller E2-E3BP mass and a lower capacity to bind E1 support the smaller E3BP substituting for E2 subunits rather than adding to the 60-mer. We describe a substitution model in which 12 I′ domains of E3BP replace 12 I domains of E2 by forming 6 dimer edges that are symmetrically located in the dodecahedron structure. Twelve E3 dimers were bound per E2₄₈-E3BP₁₂ mass, which is consistent with this model.