Summary Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage.
Graphical Abstract
Highlights • DUB profiling identifies ZUFSP/ZUP1 as distinct DUB class that cleaves K63 chains • High-resolution crystal structure reveals mechanisms of Ub recognition and catalysis • Ub binding UBZ and ZHA domains identified in ZUFSP are essential for DUB activity • ZUFSP prevents genome instability and promotes cellular survival following DNA damage
Kwasna et al. discover ZUFSP/ZUP1 as a new deubiquitinase class specific at cleaving K63-linked polyubiquitin. They identify two ubiquitin binding domains in ZUFSP that are essential for enzyme activity. ZUFSP is a predominantly nuclear DUB with important roles in maintaining genome stability.