Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination.

Publication Type:

Journal Article

Authors:

Tang, Xiaojing; Orlicky, Stephen; Lin, Zhenyuan; Willems, Andrew; Neculai, Dante; Ceccarelli, Derek; Mercurio, Frank; Shilton, Brian H; Sicheri, Frank; Tyers, Mike

Source:

Cell, Volume 129, Issue 6, p.1165-76 (2007)

Keywords:

Amino Acid Sequence, Binding Sites, Catalytic Domain, Cell Cycle Proteins, Dimerization, F-Box Proteins, Models, Molecular, Molecular Conformation, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sequence Homology, Amino Acid, SKP Cullin F-Box Protein Ligases, Ubiquitin, Ubiquitin-Protein Ligases

Abstract:

<p>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(Cdc4) toward the CDK inhibitor Sic1 and other substrates. SCF(Cdc4) dimerization has little effect on the affinity for Sic1 but markedly stimulates ubiquitin conjugation. A model of the dimeric holo-SCF(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 A within and 102 A 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.</p>