title: The differential modulation of USP activity by internal regulatory domains, interactors and eight ubiquitin chain types.
abstract: Ubiquitin-specific proteases (USPs) are papain-like isopeptidases with variable inter- and intramolecular regulatory domains. To understand the effect of these domains on USP activity, we have analyzed the enzyme kinetics of 12 USPs in the presence and absence of modulators using synthetic reagents. This revealed variations of several orders of magnitude in both the catalytic turnover (k(cat)) and ubiquitin (Ub) binding (K(M)) between USPs. Further activity modulation by intramolecular domains affects both the k(cat) and K(M), whereas the intermolecular activators UAF1 and GMPS mainly increase the k(cat). Also, we provide the first comprehensive analysis comparing Ub chain preference. USPs can hydrolyze all linkages and show modest Ub-chain preferences, although some show a lack of activity toward linear di-Ub. This comprehensive kinetic analysis highlights the variability within the USP family.
authors.affiliation: Division of Biochemistry and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Alex C
authors.initials: AC
authors.lastname: Faesen
authors.forename: Mark P A
authors.initials: MP
authors.lastname: Luna-Vargas
authors.forename: Paul P
authors.initials: PP
authors.lastname: Geurink
authors.forename: Marcello
authors.initials: M
authors.lastname: Clerici
authors.forename: Remco
authors.initials: R
authors.lastname: Merkx
authors.forename: Willem J
authors.initials: WJ
authors.lastname: van Dijk
authors.forename: Dharjath S
authors.initials: DS
authors.lastname: Hameed
authors.forename: Farid
authors.initials: F
authors.lastname: El Oualid
authors.forename: Huib
authors.initials: H
authors.lastname: Ovaa
authors.forename: Titia K
authors.initials: TK
authors.lastname: Sixma
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D010450:Endopeptidases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006157:Guanosine Monophosphate / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D009687:Nuclear Proteins / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013873:Thionucleotides / Q000378:metabolism; D025801:Ubiquitin / Q000737:chemistry / Q000378:metabolism*; D064570:Ubiquitin-Specific Proteases
chemical_list: D010450:Endopeptidases; D006157:Guanosine Monophosphate; D009687:Nuclear Proteins; D011994:Recombinant Proteins; D013873:Thionucleotides; D025801:Ubiquitin; D064570:Ubiquitin-Specific Proteases; C526165:WDR48 protein, human; C066524:guanosine 5'-monophosphorothioate