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TitleStructural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5.
Journal, issue, pagesNat Chem Biol, Vol. 20, Issue 2, Page 190-200, Year 2024
Publish dateAug 24, 2023
AuthorsLaura A Hehl / Daniel Horn-Ghetko / J Rajan Prabu / Ronnald Vollrath / D Tung Vu / David A Pérez Berrocal / Monique P C Mulder / Gerbrand J van der Heden van Noort / Brenda A Schulman /
PubMed AbstractUbiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron ...Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
External linksNat Chem Biol / PubMed:37620400 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 8.3 Å
Structure data

16355

8c06

EMDB-16355, PDB-8c06:
Structure of Dimeric HECT E3 Ubiquitin Ligase UBR5
Method: EM (single particle) / Resolution: 2.7 Å

16356

8c07

EMDB-16356, PDB-8c07:
Structure of HECT E3 UBR5 forming K48 linked Ubiquitin chains
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-16865: Tetrameric HECT E3 Ubiquitin Ligase UBR5
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-16866: Cryo-EM map of ubiquitin-VME bound HECT E3 ligase UBR5
Method: EM (single particle) / Resolution: 5.3 Å

EMDB-16867: Ubiquitin transfer from E2 to E3: UBE2D2-ubiquitin linked to HECT E3 ligase UBR5
Method: EM (single particle) / Resolution: 7.3 Å

EMDB-17466: Cryo-EM map of HECT E3 ligase UBR5 forming K48 linked ubiquitin chains
Method: EM (single particle) / Resolution: 8.3 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SY8:
5-azanylpentan-2-one

Source
  • homo sapiens (human)
KeywordsLIGASE / E3 ligase / UBR5 / Ubiquitination / UBQ / Ubiquitin / HECT / K48 / UBQ-chain / polyubiquitylation

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