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TitleStructural basis for E4 enzyme Ufd2-catalyzed K48/K29 branched ubiquitin chains.
Journal, issue, pagesNat Chem Biol, Vol. 22, Issue 2, Page 239-248, Year 2026
Publish dateAug 15, 2025
AuthorsZebin Tong / Xiangwei Wu / Hongyi Cai / Shidian Wu / Tianyi Zhang / Zhiheng Deng / Ziyu Xu / Rujing Yuan / Huasong Ai / Lei Liu / Man Pan /
PubMed AbstractE4 enzymes amplify and remodel ubiquitin chain signals beyond the conventional E1-E2-E3 cascade. The first identified E4 enzyme Ufd2 preferentially catalyzes K48/K29 branched ubiquitin chains, yet ...E4 enzymes amplify and remodel ubiquitin chain signals beyond the conventional E1-E2-E3 cascade. The first identified E4 enzyme Ufd2 preferentially catalyzes K48/K29 branched ubiquitin chains, yet the structural mechanism remains unknown. Here, we combined chemical biology and cryo-electron microscopy to visualize stable intermediates in Ufd2 loading ubiquitin at K48 of proximal ubiquitin on K29-linked di- and triubiquitin. Our data reveal that the core region of Ufd2 functions as an unprecedented K29 diubiquitin binding domain, interacting extensively with proximal and distal ubiquitin, which orients the K48 site of proximal ubiquitin toward the active site of Ubc4, facilitating K48/K29 branched ubiquitin chain formation. We also identified a unique dimeric conformation where dimerized Ufd2 and Ubc4 stabilize each other's distal ubiquitin during branching on K29 triubiquitin. Our findings provide mechanistic insights into the assembly of K48/K29 branched ubiquitin chains by the E4 enzyme Ufd2 and highlight the spatial cooperation among multiple pairs of ubiquitin-related enzymes on longer ubiquitin chains.
External linksNat Chem Biol / PubMed:40817136
MethodsEM (single particle)
Resolution4.14 - 7.84 Å
Structure data

62353

9khs

EMDB-62353, PDB-9khs:
Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation)
Method: EM (single particle) / Resolution: 4.31 Å

62354

9kht

EMDB-62354, PDB-9kht:
cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation)
Method: EM (single particle) / Resolution: 4.85 Å

62355

9m7o

EMDB-62355: cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (monomeric conformation)
PDB-9m7o: Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation)
Method: EM (single particle) / Resolution: 4.14 Å

EMDB-62356: cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (dimeric conformation)
Method: EM (single particle) / Resolution: 7.84 Å

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • homo sapiens (human)
  • Saccharomyces cerevisiae (brewer's yeast)
KeywordsLIGASE / E4 enzyme / Ub ligase / Ufd2 / Ubc4 / Branching / K48/29 / branch Ub chains

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