Non-hydrolyzable Diubiquitin Probes Reveal Linkage-Specific Reactivity of Deubiquitylating Enzymes Mediated by S2 Pockets. Issue 4 (21st April 2016) - Flierman, Dennis
Summary: Ubiquitin chains are important post-translational modifications that control a large number of cellular processes. Chains can be formed via different linkages, which determines the type of signal they convey. Deubiquitylating enzymes (DUBs) regulate ubiquitylation status by trimming or removing chains from attached proteins. DUBs can contain several ubiquitin-binding pockets, which confer specificity toward differently linked chains. Most tools for monitoring DUB specificity target binding pockets on opposing sides of the active site; however, some DUBs contain additional pockets. Therefore, reagents targeting additional pockets are essential to fully understand linkage specificity. We report the development of active site-directed probes and fluorogenic substrates, based on non-hydrolyzable diubiquitin, that are equipped with a C-terminal warhead or a fluorogenic activity reporter moiety. We demonstrate that various DUBs in lysates display differential reactivity toward differently linked diubiquitin probes, as exemplified by the proteasome-associated DUB USP14. In addition, OTUD2 and OTUD3 show remarkable linkage-specific reactivity with our diubiquitin-based reagents. Graphical Abstract: Highlights: Protease-resistant diUb probes bind to DUB S1-S2 sites and react at the proximal end First kinetic assay showing proximal end cleavage by DUBs using diUb-based substrates OTUD3 binds K11-linked diUb and OTUD2 binds K11- and K33-linked diUb in S1-S2 pockets Kinetics suggest different mechanisms for polyUb cleavage by OTUD2 and OTUD3 Abstract : Deubiquitylating enzymes (DUBs) use multiple ubiquitin-binding pockets to disassemble polyubiquitin chains. Most tools probing DUB specificity target pockets adjacent to the active site. The protease-resistant diUb probes described here monitor linkage specificity of an additional S2 pocket and provide kinetics that explain polyubiquitin chain specificity.