title: Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination.
abstract: 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.
authors.affiliation: Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada M5G 1X5.
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Tang
authors.forename: Stephen
authors.initials: S
authors.lastname: Orlicky
authors.forename: Zhenyuan
authors.initials: Z
authors.lastname: Lin
authors.forename: Andrew
authors.initials: A
authors.lastname: Willems
authors.forename: Dante
authors.initials: D
authors.lastname: Neculai
authors.forename: Derek
authors.initials: D
authors.lastname: Ceccarelli
authors.forename: Frank
authors.initials: F
authors.lastname: Mercurio
authors.forename: Brian H
authors.initials: BH
authors.lastname: Shilton
authors.forename: Frank
authors.initials: F
authors.lastname: Sicheri
authors.forename: Mike
authors.initials: M
authors.lastname: Tyers
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D018797:Cell Cycle Proteins / Q000378:metabolism*; D019281:Dimerization; D044783:F-Box Proteins; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D044843:SKP Cullin F-Box Protein Ligases / Q000737:chemistry* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D025801:Ubiquitin / Q000737:chemistry*; D044767:Ubiquitin-Protein Ligases / Q000378:metabolism*
chemical_list: C080443:CDC4 protein, S cerevisiae; D018797:Cell Cycle Proteins; D044783:F-Box Proteins; D029701:Saccharomyces cerevisiae Proteins; D025801:Ubiquitin; D044843:SKP Cullin F-Box Protein Ligases; D044767:Ubiquitin-Protein Ligases