Structural basis for regulation of poly‐SUMO chain by a SUMO‐like domain of Nip45

Abstract

Post-translational modification by small ubiquitin-like modifier (SUMO) provides an important regulatory mechanism in diverse cellular processes. Modification of SUMO has been shown to target proteins involved in systems ranging from DNA repair pathways to the ubiquitin-proteasome degradation system by the action of SUMO-targeted ubiquitin ligases (STUbLs). STUbLs recognize target proteins modified with a poly-SUMO chain through their SUMO-interacting motifs (SIMs). STUbLs are also associated with RENi family proteins, which commonly have two SUMO-like domains (SLD1 and SLD2) at their C terminus. We have determined the crystal structures of SLD2 of mouse RENi protein, Nip45, in a free form and in complex with a mouse E2 sumoylation enzyme, Ubc9. While Nip45 SLD2 shares a beta-grasp fold with SUMO, the SIM interaction surface conserved in SUMO paralogues does not exist in SLD2. Biochemical data indicates that neither tandem SLDs or SLD2 of Nip45 bind to either tandem SIMs from either mouse STUbL, RNF4 or to those from SUMO-binding proteins, whose interactions with SUMO have been well characterized. On the other hand, Nip45 SLD2 binds to Ubc9 in an almost identical manner to that of SUMO and thereby inhibits elongation of poly-SUMO chains. This finding highlights a possible role of the RENi proteins in the modulation of Ubc9-mediated poly-SUMO formation.

Identification of a molecular recognition feature in the E1A oncoprotein that binds the SUMO conjugase UBC9 and likely interferes with polySUMOylation

“…The only other proteins known to interact with the N-terminus of UBC9 are the Rad60 family members. These proteins bind UBC9 by large integral SUMO-like domains, which adopt a b-grasp fold similar to SUMO; these interactions promote cellular responses to genotoxic stress (Prudden et al, 2009;Sekiyama et al, 2009). Our discovery that the short linear MoRF EVIDLT in E1A recapitulates this interaction is unprecedented.…”

SUMO conjugation – a mechanistic view

“…All of these proteins share two tandem SUMO-like domains (SLD1 and SLD2). Structural and biochemical analysis of RENi SLDs revealed that these domains are unable to bind to class I SIMs but SLD2 interacts with the backside of Ubc9 by mimicking the β-sheet required for this class II SUMO interaction (136,137). Of note, RENi proteins also contain a conserved SIM in their N-termini and bind to SUMO, but they are themselves inefficient sumoylation substrates (138)(139)(140).…”

DNA Repair and Global Sumoylation Are Regulated by Distinct Ubc9 Noncovalent Complexes

“…Structure-based in vitro studies have suggested a role for a noncovalent complex formed by Ubc9 and SUMO (Ubc9:SUMO) in SUMO polymerization; however, in vivo evidence for such a function is lacking (9,15,22,48). It is also unclear whether the observed binding of Rad60 SLD2 to Ubc9 (39) antagonizes SUMO chain formation by disrupting the Ubc9:SUMO complex (42). In addition, whether the major SUMO E3 ligase Pli1 and its homologs Siz1/Siz2 of budding yeast and PIAS (protein inhibitor of activated STAT)-type ligases of higher eukaryotes (51) play a key role in forming SUMO chains remains unanswered.…”