Suprafacial orientation of the SCFCdc4 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(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.
Tang
Xiaojing
X
Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada M5G 1X5.
Orlicky
Stephen
S
Lin
Zhenyuan
Z
Willems
Andrew
A
Neculai
Dante
D
Ceccarelli
Derek
D
Mercurio
Frank
F
Shilton
Brian H
BH
Sicheri
Frank
F
Tyers
Mike
M
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*
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