OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function

Abstract

SUMMARY Ubiquitylation entails the concerted action of E1, E2 and E3 enzymes. We recently reported that OTUB1, a deubiquitylase, inhibits the DNA damage response independently of its isopeptidase activity. OTUB1 does so by blocking ubiquitin transfer by UBC13, the cognate E2 enzyme for RNF168. OTUB1 also inhibits E2s of the UBE2D and UBE2E families. Here we elucidate the structural mechanism by which OTUB1 binds E2s to inhibit ubiquitin transfer. OTUB1 recognizes ubiquitin-charged E2s through contacts with both donor ubiquitin and the E2 enzyme. Surprisingly, free ubiquitin associates with the canonical distal ubiquitin-binding site on OTUB1 to promote formation of the inhibited E2 complex. Lys48 of donor ubiquitin lies near the OTUB1 catalytic site and the C-terminus of free ubiquitin, a configuration that mimics the products of Lys48-linked ubiquitin chain cleavage. OTUB1 therefore co-opts Lys48-linked ubiquitin chain recognition to suppress ubiquitin conjugation and the DNA damage response.

Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity

“…Recognition mechanisms of specific Ub linkages by JAMM and OTU family DUBs have been extensively studied [28][29][30][31] . Structures of DUB catalytic domains in complex with their cognate Ub chains highlight common features of the enzymes' substrate-selection strategies, despite the lack of substantial sequence or structure similarities.…”

Layers of DUB regulation

“…OTUB1 can noncatalytically interfere with polyubiquitin synthesis by specifically inhibiting E2 enzyme Ubc13 linked to ubiquitin at its active site (charged E2) [57,58]. Conversely, a subset of charged and uncharged E2s, including UbcH5B, stimulate Lys48-linked polyubiquitin hydrolysis by OTUB1 by increasing substrate affinity [59].…”

RING E3-Catalyzed E2 Self-Ubiquitination Attenuates the Activity of Ube2E Ubiquitin-Conjugating Enzymes

“…Quite a few of such regulatory mechanisms that control activities of various E3 ligases [18,19] and affect their substrate recognitions have been deciphered. On the other hand, the existence of diverse mechanisms that regulate E2 activity is appreciated only recently [20][21][22].…”