ZnF-UBP domains regulate deubiquitinase activity by relieving ubiquitin product inhibition

Most ubiquitin specific protease (USP) deubiquitinases (DUBs) combine non-selective catalytic domains with one or multiple exo-domains that contribute substrate specificity and localisation, but are generally poorly characterised. Zinc-Finger UBP (ZnF-UBP) domains exist in 12 USP DUBs, yet their function is unclear. We here comprehensively analyse human ZnF-UBP domains, and reveal that 8 of 14 bind ubiquitin (Ub), via an unattached Ub C-terminal GlyGly motif. We focus on USP16, a nucleosome DUB with activity for Ub and Ub-like modifiers, and show that whilte its ZnF-UBP domain can bind substrates, it is also a crucial contributor to enzyme kinetics. Slow Ub release from the catalytic domain after cleavage causes product inhibition, which is overcome in cis by ZnF-UBP-mediated product release. Interestingly, supplying a high affinity product-capturing ZnF-UBP domain in trans, activates USP16 and other USP enzymes. Our data shows the importance of product inhibition as a regulatory mechanism in DUBs, and exemplifies the unappreciated role of exo-domains in regulating DUB function beyond substrate binding.