title: Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46.
abstract: Protein ubiquitination patterns are an important component of cellular signaling. The WD-repeat protein WDR48 (USP1-associated factor UAF-1) stimulates activity of ubiquitin-specific proteases USP1, USP12, and USP46. To understand how WDR48 exerts its effect on the USP scaffold, we determined structures of the ternary WDR48:USP46:ubiquitin complex. WDR48 interacts with the USP46 fingers subdomain via a relatively small, highly polar surface on the top center of the WDR48 β propeller. In addition, WDR48 has a novel ancillary domain and a C-terminal SUMO-like domain encircling the USP46-bound ubiquitin. Mutation of residues involved in the WDR48:USP46 interaction abrogated both binding and deubiquitinase activity of the complex. An analogous mutation in USP1 similarly blocked WDR48-dependent activation. Our data suggest a possible mechanism of deubiquitinase stimulation via stabilization and prolonged residence time of substrate. The unprecedented mode of interaction between the USP fingers domain and the WD-repeat β propeller serves as a prototypical example for this family of deubiquitinases.
authors.affiliation: Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Jianping
authors.initials: J
authors.lastname: Yin
authors.affiliation: Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Allyn J
authors.initials: AJ
authors.lastname: Schoeffler
authors.affiliation: Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Katherine
authors.initials: K
authors.lastname: Wickliffe
authors.affiliation: Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Kim
authors.initials: K
authors.lastname: Newton
authors.affiliation: Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Starovasnik
authors.affiliation: Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: dueber.erin@gene.com.
authors.forename: Erin C
authors.initials: EC
authors.lastname: Dueber
authors.affiliation: Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: harris.seth@gene.com.
authors.forename: Seth F
authors.initials: SF
authors.lastname: Harris
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D010450:Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D009687:Nuclear Proteins
chemical_list: D010450:Endopeptidases; D047908:Intracellular Signaling Peptides and Proteins; D011506:Proteins; C562185:ubiquitin-specific peptidase 46, human; C526165:WDR48 protein, human; D009687:Nuclear Proteins