Ubc13: the Lys63 ubiquitin chain building machine

Abstract

Ubc13 is an ubiquitin E2 conjugating enzyme that participates with many different E3 ligases to form lysine 63-linked (Lys63) ubiquitin chains that are critical to signaling in inflammatory and DNA damage response pathways. Recent studies have suggested Ubc13 as a potential therapeutic target for intervention in various human diseases including several different cancers, alleviation of anti-cancer drug resistance, chronic inflammation, and viral infections. Understanding a potential therapeutic target from different angles is important to assess its usefulness and potential pitfalls. Here we present a global review of Ubc13 from its structure, function, and cellular activities, to its natural and chemical inhibition. The aim of this article is to review the literature that directly implicates Ubc13 in a biological function, and to integrate structural and mechanistic insights into the larger role of this critical E2 enzyme. We discuss observations of multiple Ubc13 structures that suggest a novel mechanism for activation of Ubc13 that involves conformational change of the active site loop.

Proteasome‐independent functions of lysine‐63 polyubiquitination in plants

“…Detailed insight into the mechanisms of K63-linked chain formation and extension arose from the crystal structure of human UBC13-UEV1-Ub complexes. The active site cysteine of UBC13 is covalently bound to a first donor Ub, whereas UEV1A binds non-covalently to a second acceptor Ub, presenting residue K63 for chain assembly (Hodge et al, 2016). The K63 chain extension mechanism also suggests that UBC13-UEV1A needs a priming ubiquitination event on the substrate protein to polymerize the K63-linked chain extension (Soss et al, 2011;Mattiroli et al, 2012).…”

Structural basis of generic versus specific E2–RING E3 interactions in protein ubiquitination

“…The poorly characterized RING E3 ligase ZNRF1 was found to tightly interact with UBE2N in cells, a broad‐specificity E2 that associates with many other E3s to build K63‐type Ub chains . ZNRF1 is known to bind UBE2Ds and UBE2W, but it appears to be specialized to interact with UBE2N in particular, with its binding affinity against UBE2N being ~50 nM . in vitro data suggest that ZNRF1 might inhibit UBE2N activity via binding it tightly .…”

“…75 ZNRF1 is known to bind UBE2Ds and UBE2W, but it appears to be specialized to interact with UBE2N in particular, with its binding affinity against UBE2N being~50 nM. 59,75 in vitro data suggest that ZNRF1 might inhibit UBE2N activity via binding it tightly. 59 The UBE2N:ZNRF1 complex structure illustrates the details of this astonishingly tight E2-E3 interaction and reveals that it is mediated by specialization of ZNRF1 within its canonical E2-E3 binding interface.…”

Reconstitution of the plant ubiquitination cascade in bacteria using a synthetic biology approach

“…E2s play key roles in Ub chain assembly and in determination of the lysine specificity of Ub chains (Ye and Rape, ; Sadowski et al ., ; Middleton and Day, ; Hodge et al ., ). Thus, the concerted actions of the E2s and E3s determine the substrate specificities, the types of Ub modification and even the ubiquitination site(s) on the substrate proteins, resulting in different specificities and destinies of the target proteins (VanDemark et al ., ; Petroski and Deshaies, ; Wickliffe et al ., ; Suryadinata et al ., ).…”