The Quaternary Structure of the Saccharomyces cerevisiae Succinate Dehydrogenase

Abstract

Succinate dehydrogenases and fumarate reductases are complex mitochondrial or bacterial respiratory chain proteins with remarkably similar structures and functions. Succinate dehydrogenase oxidizes succinate and reduces ubiquinone using a flavin adenine dinucle- otide cofactor and iron-sulfur clusters to transport elec- trons.Amodelof the quaternary structure of the tetrameric Saccharomyces cerevisiae succinate dehydrogenase was constructed based on the crystal structures of the Esche- richia coli succinate dehydrogenase, the E. coli fumarate reductase, and the Wolinella succinogenes fumarate reduc- tase. One FAD and three iron-sulfur clusters were docked into the Sdh1p and Sdh2p catalytic dimer.Oneb-typeheme and two ubiquinone or inhibitor analog molecules were docked into the Sdh3p and Sdh4p membrane dimer. The model is consistent with numerous experimental observa- tions. The calculated free energies of inhibitor binding are in excellent agreement with the experimentally deter- mined inhibitory constants. Functionally important resi- dues identified by mutagenesis of the SDH3 and SDH4 genes are located near the two proposed quinone-binding sites, which are separated by the heme. The proximal qui- none-binding site, located nearest the catalytic dimer, has a considerably more polar environment than the distal site. Alternative low energy conformations of the membrane subunits were explored in a molecular dynamics simula- tion of the dimer embedded in a phospholipid bilayer. The simulation offers insight into why Sdh4p Cys-78 may be serving as the second axial ligand for the heme instead of a histidine residue.Wediscuss the possible roles ofhemeand of the two quinone-binding sites in electron transport. Succinate