title: An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains.
abstract: Eight different types of ubiquitin linkages are present in eukaryotic cells that regulate diverse biological processes. Proteins that mediate specific assembly and disassembly of atypical Lys6, Lys27, Lys29 and Lys33 linkages are mainly unknown. We here reveal how the human ovarian tumor (OTU) domain deubiquitinase (DUB) TRABID specifically hydrolyzes both Lys29- and Lys33-linked diubiquitin. A crystal structure of the extended catalytic domain reveals an unpredicted ankyrin repeat domain that precedes an A20-like catalytic core. NMR analysis identifies the ankyrin domain as a new ubiquitin-binding fold, which we have termed AnkUBD, and DUB assays in vitro and in vivo show that this domain is crucial for TRABID efficiency and linkage specificity. Our data are consistent with AnkUBD functioning as an enzymatic S1' ubiquitin-binding site, which orients a ubiquitin chain so that Lys29 and Lys33 linkages are cleaved preferentially.
authors.affiliation: Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
authors.forename: Julien D F
authors.initials: JD
authors.lastname: Licchesi
authors.forename: Juliusz
authors.initials: J
authors.lastname: Mieszczanek
authors.forename: Tycho E T
authors.initials: TE
authors.lastname: Mevissen
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Rutherford
authors.forename: Masato
authors.initials: M
authors.lastname: Akutsu
authors.forename: Satpal
authors.initials: S
authors.lastname: Virdee
authors.forename: Farid
authors.initials: F
authors.lastname: El Oualid
authors.forename: Jason W
authors.initials: JW
authors.lastname: Chin
authors.forename: Huib
authors.initials: H
authors.lastname: Ovaa
authors.forename: Mariann
authors.initials: M
authors.lastname: Bienz
authors.forename: David
authors.initials: D
authors.lastname: Komander
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017089:Ankyrin Repeat; D001665:Binding Sites / Q000235:genetics; D015153:Blotting, Western; D019556:COS Cells; D020134:Catalytic Domain; D002522:Chlorocebus aethiops; D018360:Crystallography, X-Ray; D010450:Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D036681:Fluorescence Recovery After Photobleaching; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D057809:HEK293 Cells; D006801:Humans; D008239:Lysine / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D018613:Microscopy, Confocal; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D025801:Ubiquitin / Q000378:metabolism*; D043222:Ubiquitin Thiolesterase / Q000378:metabolism
chemical_list: D025801:Ubiquitin; D049452:Green Fluorescent Proteins; D010450:Endopeptidases; C570449:ZRANB1 protein, human; D043222:Ubiquitin Thiolesterase; D008239:Lysine