{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Ward SJ"],"funding":["Ministry of Education and Culture | Direktorat Jenderal Pendidikan Tinggi (DIKTI) (Ministry of Research, Technology and Higher Education)","Biotechnology and Biological Sciences Research Council"],"pagination":["17362-17374"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6231127"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["293(45)"],"pubmed_abstract":["Ubiquitin-specific protease 15 (USP15) regulates important cellular processes, including transforming growth factor β (TGF-β) signaling, mitophagy, mRNA processing, and innate immune responses; however, structural information on USP15's catalytic domain is currently unavailable. Here, we determined crystal structures of the USP15 catalytic core domain, revealing a canonical USP fold, including a finger, palm, and thumb region. Unlike for the structure of paralog USP4, the catalytic triad is in an inactive configuration with the catalytic cysteine ∼10 Å apart from the catalytic histidine. This conformation is atypical, and a similar misaligned catalytic triad has so far been observed only for USP7, although USP15 and USP7 are differently regulated. Moreover, we found that the active-site loops are flexible, resulting in a largely open ubiquitin tail-binding channel. Comparison of the USP15 and USP4 structures points to a possible activation mechanism. Sequence differences between these two USPs mainly map to the S1' region likely to confer specificity, whereas the S1 ubiquitin-binding pocket is highly conserved. Isothermal titration calorimetry monoubiquitin- and linear diubiquitin-binding experiments showed significant differences in their thermodynamic profiles, with USP15 displaying a lower affinity for monoubiquitin than USP4. Moreover, we report that USP15 is weakly inhibited by the antineoplastic agent mitoxantrone <i>in vitro</i> A USP15-mitoxantrone complex structure disclosed that the anthracenedione interacts with the S1' binding site. Our results reveal first insights into USP15's catalytic domain structure, conformational changes, differences between paralogs, and small-molecule interactions and establish a framework for cellular probe and inhibitor development."],"journal":["The Journal of biological chemistry"],"pubmed_title":["The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel."],"pmcid":["PMC6231127"],"funding_grant_id":["DIKTI scholarship","DTP studentship","1488397","BB/H012656/1","1803618"],"pubmed_authors":["Indrayudha P","Ward SJ","Caulton SG","Gratton HE","Maurer SK","Michavila C","Emsley J","Mukhopadhyay R","Dreveny I"],"additional_accession":[]},"is_claimable":false,"name":"The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel.","description":"Ubiquitin-specific protease 15 (USP15) regulates important cellular processes, including transforming growth factor β (TGF-β) signaling, mitophagy, mRNA processing, and innate immune responses; however, structural information on USP15's catalytic domain is currently unavailable. Here, we determined crystal structures of the USP15 catalytic core domain, revealing a canonical USP fold, including a finger, palm, and thumb region. Unlike for the structure of paralog USP4, the catalytic triad is in an inactive configuration with the catalytic cysteine ∼10 Å apart from the catalytic histidine. This conformation is atypical, and a similar misaligned catalytic triad has so far been observed only for USP7, although USP15 and USP7 are differently regulated. Moreover, we found that the active-site loops are flexible, resulting in a largely open ubiquitin tail-binding channel. Comparison of the USP15 and USP4 structures points to a possible activation mechanism. Sequence differences between these two USPs mainly map to the S1' region likely to confer specificity, whereas the S1 ubiquitin-binding pocket is highly conserved. Isothermal titration calorimetry monoubiquitin- and linear diubiquitin-binding experiments showed significant differences in their thermodynamic profiles, with USP15 displaying a lower affinity for monoubiquitin than USP4. Moreover, we report that USP15 is weakly inhibited by the antineoplastic agent mitoxantrone <i>in vitro</i> A USP15-mitoxantrone complex structure disclosed that the anthracenedione interacts with the S1' binding site. Our results reveal first insights into USP15's catalytic domain structure, conformational changes, differences between paralogs, and small-molecule interactions and establish a framework for cellular probe and inhibitor development.","dates":{"release":"2018-01-01T00:00:00Z","publication":"2018 Nov","modification":"2026-05-06T06:21:43.142Z","creation":"2019-03-27T00:07:18Z"},"accession":"S-EPMC6231127","cross_references":{"pubmed":["30228188"],"doi":["10.1074/jbc.RA118.003857"]}}