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TitleStructural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 4313, Year 2025
Publish dateMay 9, 2025
AuthorsXiangwei Wu / Huasong Ai / Junxiong Mao / Hongyi Cai / Lu-Jun Liang / Zebin Tong / Zhiheng Deng / Qingyun Zheng / Lei Liu / Man Pan /
PubMed AbstractThe K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ...The K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ubiquitination to K48-linked ubiquitin chains to augment polyubiquitination. How HECT-E3 ligase Ufd4 mediates the ubiquitination event remains unclear. Here, we biochemically determine that Ufd4 preferentially catalyses K29-linked ubiquitination on K48-linked ubiquitin chains to generate K29/K48-branched ubiquitin chains and capture structural snapshots of Ub transfer cascades for Ufd4-mediated ubiquitination. The N-terminal ARM region and HECT domain C-lobe of Ufd4 are identified and characterized as key structural elements that together recruit K48-linked diUb and orient Lys29 of its proximal Ub to the active cysteine of Ufd4 for K29-linked branched ubiquitination. These structures not only provide mechanistic insights into the architecture of the Ufd4 complex but also provide structural visualization of branched ubiquitin chain formation by a HECT-type E3 ligase.
External linksNat Commun / PubMed:40341121 / PubMed Central
MethodsEM (single particle)
Resolution3.31 - 3.63 Å
Structure data

35929

8j1p

EMDB-35929, PDB-8j1p:
Cryo-EM structure of Ufd4 in complex with K29/48 triUb
Method: EM (single particle) / Resolution: 3.31 Å

35931

8j1r

EMDB-35931, PDB-8j1r:
cryo-EM structures of Ufd4 in complex with Ubc4-Ub
Method: EM (single particle) / Resolution: 3.52 Å

62292

9ken

EMDB-62292, PDB-9ken:
cryo-EM structure of TRIP12 in complex with K29/48 branched-triUb
Method: EM (single particle) / Resolution: 3.63 Å

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • homo sapiens (human)
KeywordsLYASE / Ufd4 / HECT / E3 / K29/48 / LIGASE / Ubc4 / Ubc4-Ub / HECT-type E3 ligase / HECT E3 ligase / Branching

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