Suprafacial Orientation of the SCF[superscript Cdc4] Dimer Accommodates Multiple Geometries for Substrate Ubiquitination

SCF ubiquitin ligases recruit substrates for degradation via F box protein adaptor subunits. WD40 repeat F box proteins, such as Cdc4 and {beta}-TrCP, contain a conserved dimerization motif called the D domain. Here, we report that the D domain protomers of yeast Cdc4 and human {beta}-TrCP form a superhelical homotypic dimer. Disruption of the D domain compromises the activity of yeast SCF{sup Cdc4} toward the CDK inhibitor Sic1 and other substrates. SCF{sup Cdc4} dimerization has little effect on the affinity for Sic1 but markedly stimulates ubiquitin conjugation. A model of the dimeric holo-SCF{sup Cdc4} complex based on small-angle X-ray scatter measurements reveals a suprafacial configuration, in which substrate-binding sites and E2 catalytic sites lie in the same plane with a separation of 64 {angstrom} within and 102 {angstrom} between each SCF monomer. This spatial variability may accommodate diverse acceptor lysine geometries in both substrates and the elongating ubiquitin chain and thereby increase catalytic efficiency.