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PMID: 23827681 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis.

Cell ·Vol. 154 ·No. 1 ·2013-07-03 ·Pages 169-84

Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D

Abstract

Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1' and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates.

MeSH Terms
Catalysis Catalytic Domain Crystallography, X-Ray Endopeptidases/chemistry,genetics,metabolism Female Humans Models, Molecular Ovarian Neoplasms/enzymology,metabolism Protein Structure, Tertiary Thiolester Hydrolases/chemistry,metabolism Ubiquitination Ubiquitins/metabolism
Chemicals
Ubiquitins YOD1 protein, human Thiolester Hydrolases Endopeptidases
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Mevissen Tycho E T
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
Hospenthal Manuela K
Geurink Paul P
Elliott Paul R
Akutsu Masato
Arnaudo Nadia
Ekkebus Reggy
Kulathu Yogesh
Wauer Tobias
El Oualid Farid
Freund Stefan M V
Ovaa Huib
Komander David
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Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
DOI
10.1016/j.cell.2013.05.046
Published
2013-07-03
Pages
169-84
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC3705208
Subset
IM
Grants
European Research Council · 309756 · International
Medical Research Council · MC_U105192732 · United Kingdom
Medical Research Council · U105192732 · United Kingdom
Databases
PDB
4BOP, 4BOQ, 4BOS, 4BOU, 4BOZ
External Links
PubMed source DOI: 10.1016/j.cell.2013.05.046 PMC Full Text View journal details
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