Mechanism, specificity and structure of the deubiquitinases

Removal of ubiquitin from modified proteins is an important process to regulate the ubiquitin system. Roughly 100 dedicated enzymes for this purpose, the deubiquitinases, exist in human cells and are intricately involved in a wide variety of cellular processes, although many enzymes remain unstudied to date. The deubiquitinases consist of five enzyme families that contain USP, OTU, UCH, Josephin, or JAMM/MPN+ domains providing catalytic activity. We now understand the catalytic mechanisms of all deubiquitinase families from structural work and more importantly, have obtained insight into an unanticipated variety of ways to exercise specificity. It emerges that deubiquitinases exploit the entire complexity of the ubiquitin system by recognizing their substrates, particular ubiquitin chain linkages and even the position within a ubiquitin chain. This chapter describes the mechanisms of deubiquitination and the different layers of deubiquitinase specificity. The individual deubiquitinase families are discussed with a focus on structure, regulation and specificity features for selected enzymes.