The human UBR5 (also known as EDD) is a single polypeptide chain HECT-type E3 ubiquitin ligase essential for embryonic development in mammals. Although widely expressed, UBR5 is markedly amplified and overexpressed in breast, ovarian, prostate, gastric and pancreatic cancers. Dysregulated UBR5 functions like an oncoprotein to promote cancer growth and metastasis, making UBR5 a potential target for therapeutics. Unexpectedly, we found that human UBR5 assembles a dimer and a tetramer in solution. We determined the dimer structure at 2.8 Å and the tetramer structure at 3.5 Å average resolution. UBR5 is a crescent shaped molecule with a seven-bladed β-propeller and two small β-barrel domains (SBB1/2) at the N-terminal region, a catalytic HECT domain at the C-terminus, and an extended helical scaffold and an N-degron-recognizing UBR box in the middle. The dimer is assembled as a stable head-to-tail dimer via extensive interactions in the middle helical scaffold region. The tetramer is assembled via SBB2-SBB2 interaction from two face-to-face dimers, forming a large cage with all four catalytic HECT domains facing the central cavity. Importantly, the N-terminal region of one subunit and the HECT of the other form an intermolecular jaw in the dimer. Using enzymatic and cellular assays, we showed that the jaw-lining residues are important for function, suggesting that the intermolar jaw functions to recruit ubiquitin loaded E2 to UBR5 for the transthiolation reaction. Further work is needed to understand how oligomerization regulates the UBR5 ligase activity. This work provides a framework for structure-based anticancer drug development against the distinctive HECT E3 ligase and contributes to a growing appreciation of E3 ligase diversity.

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Yta7 is a novel chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes and unfolds histone H3 to promote nucleosome disassembly for DNA replication. By cryo-EM analysis, we here show that Yta7 assembles a three-tiered hexamer ring with a top spiral, a middle AAA1-tier, and a bottom AAA2-tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix termed BRD- interacting motif (BIM) of the largely disordered N-terminal region, and they together assemble the spiral structure on top of the hexamer to engage the nucleosome. We found that the Yta7 BRD lacks key residues involved in acetylated peptide recognition, and as such, it is a noncanonical BRD that does not distinguish the H3 acetylation state, consistent with its role in general DNA replication. Upon nucleosome binding, the BRD/BIM spiral transitions into a flat ring to allow threading of the histone H3 tail into the AAA+ chamber. The H3 peptide is stabilized by the AAA1 pore loops 1 and 2 that spiral around the peptide. Therefore, Yta7 unfolds the nucleosome by pulling on the H3 peptide in a rotary staircase mechanism. Our study sheds light on the nucleosome recognition and unfolding mechanism of Yta7.