Cryo‐EM structure of the chain‐elongating E3 ubiquitin ligase UBR5

Abstract

UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain‐containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo‐EM structure of human UBR5, revealing an α‐solenoid scaffold with numerous protein–protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo‐EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein–protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.

Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1

“…Helical-repeat platforms also recur in the structures of UBR5 (refs. 10 , 11 , 47 , 48 , 50 ), Ufd4 (ref. 49 ) and AF2 predictions of additional human HECTs, such as HECTD1.…”

“… 45 , 46 ) and UBR5 (refs. 10 , 11 , 47 , 48 , 50 ). The dynamic nature of these regions may allow HECTs to recruit diverse substrates for modification within the constraints of an overall similar catalytic platform.…”

Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity

“…Supporting this idea, recent structural studies of HUWE1 have revealed three distinct substrate binding domains 106,107 , facilitating the recognition and ubiquitination of unbound nucleic acid binding proteins as well as ubiquitinated/PARylated substrates. Similarly, UBR5 was recently shown to bind and ubiquitinate unengaged transcription factors 87 , and has the ability to function as a ubiquitin chain elongating E4 90,91 . In combination with our findings in this study, these results indicate that HUWE1 and UBR5 are both important players in recognizing and degrading unengaged DNA- and RNA-binding proteins.…”

Deciphering the RNA-binding protein network during endosomal mRNA transport

“…However, we also observed clear differential recognition, such as MLLE PABC1 and MLLE UBR5 binding to PAM2 GW182 and PAM2L MKRN1 , respectively. Recent cryo-EM structural analyses revealed that UBR5 forms functional dimers and tetramers (27,28). Interestingly, MLLE UBR5 is inserted in the middle of the catalytic HECT domain essential for ubiquitin transfer (Fig.…”

“…This domain interacts with PAM2 sequences such as PAM2 PAIP , with high affinity (25). However, the biological function of its MLLE domain is currently unclear (26)(27)(28).…”