TY - JOUR
T1 - XOTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis
AU - Mevissen, Tycho E.T.
AU - Hospenthal, Manuela K.
AU - Geurink, Paul P.
AU - Elliott, Paul R.
AU - Akutsu, Masato
AU - Arnaudo, Nadia
AU - Ekkebus, Reggy
AU - Kulathu, Yogesh
AU - Wauer, Tobias
AU - El Oualid, Farid
AU - Freund, Stefan M.V.
AU - Ovaa, Huib
AU - Komander, David
N1 - Funding Information:
We would like to thank E. Bennett (University of California, San Diego) for sharing unpublished mass spectrometry data, K. Bianchi and P. Meier (the Institute of Cancer Research, London) for the RIP1 purification protocol, T. Mund (Medical Research Council [MRC] Laboratory of Molecular Biology) for providing GST-tagged NEDD4 and E6AP, and members of the D.K. lab for reagents and helpful discussions. This work was supported by the MRC (U105192732 to D.K.), the European Research Council (309756 to D.K.), the European Molecular Biology Organization Young Investigator program (to D.K.), the Lister Institute for Preventive Medicine (to D.K.), the Netherlands Organization for Scientific Research (700.58.011 to H.O.), and the Marie Curie Initial Training Network UPStream (to T.E.T.M.). Crystallographic data were collected at the European Synchrotron Radiation Facility at beam lines ID23-1 and ID29 and at the Diamond Light Source beam lines I-03 and I-04. H.O. and F.E. are cofounders of UbiQ Bio BV.
PY - 2013/7/3
Y1 - 2013/7/3
N2 - 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.
AB - 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.
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U2 - 10.1016/j.cell.2013.05.046
DO - 10.1016/j.cell.2013.05.046
M3 - Article
C2 - 23827681
AN - SCOPUS:84878832998
SN - 0092-8674
VL - 154
SP - 169
JO - Cell
JF - Cell
IS - 1
ER -