IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-59569-6.html
   My bibliography  Save this article

Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination

Author

Listed:
  • Xiangwei Wu

    (Shanghai Jiao Tong University
    Tsinghua University)

  • Huasong Ai

    (Shanghai Jiao Tong University)

  • Junxiong Mao

    (Tsinghua University)

  • Hongyi Cai

    (Tsinghua University)

  • Lu-Jun Liang

    (Tsinghua University)

  • Zebin Tong

    (Tsinghua University)

  • Zhiheng Deng

    (Tsinghua University)

  • Qingyun Zheng

    (Shanghai Jiao Tong University)

  • Lei Liu

    (Tsinghua University)

  • Man Pan

    (Shanghai Jiao Tong University
    Zhengzhou)

Abstract

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.

Suggested Citation

  • Xiangwei Wu & Huasong Ai & Junxiong Mao & Hongyi Cai & Lu-Jun Liang & Zebin Tong & Zhiheng Deng & Qingyun Zheng & Lei Liu & Man Pan, 2025. "Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59569-6
    DOI: 10.1038/s41467-025-59569-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-59569-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-59569-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Kirby N. Swatek & Joanne L. Usher & Anja F. Kueck & Christina Gladkova & Tycho E. T. Mevissen & Jonathan N. Pruneda & Tim Skern & David Komander, 2019. "Insights into ubiquitin chain architecture using Ub-clipping," Nature, Nature, vol. 572(7770), pages 533-537, August.
    2. Benjamin Stieglitz & Rohini R. Rana & Marios G. Koliopoulos & Aylin C. Morris-Davies & Veronique Schaeffer & Evangelos Christodoulou & Steven Howell & Nicholas R. Brown & Ivan Dikic & Katrin Rittinger, 2013. "Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP," Nature, Nature, vol. 503(7476), pages 422-426, November.
    3. Man Pan & Qingyun Zheng & Tian Wang & Lujun Liang & Junxiong Mao & Chong Zuo & Ruichao Ding & Huasong Ai & Yuan Xie & Dong Si & Yuanyuan Yu & Lei Liu & Minglei Zhao, 2021. "Structural insights into Ubr1-mediated N-degron polyubiquitination," Nature, Nature, vol. 600(7888), pages 334-338, December.
    4. Chao Liu & Weixiao Liu & Yihong Ye & Wei Li, 2017. "Ufd2p synthesizes branched ubiquitin chains to promote the degradation of substrates modified with atypical chains," Nature Communications, Nature, vol. 8(1), pages 1-15, April.
    5. Xiangwei Wu & Yunxiang Du & Lu-Jun Liang & Ruichao Ding & Tianyi Zhang & Hongyi Cai & Xiaolin Tian & Man Pan & Lei Liu, 2024. "Structure-guided engineering enables E3 ligase-free and versatile protein ubiquitination via UBE2E1," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Mai Morita & Miyu Takao & Honoka Tokuhisa & Ryotaro Chiba & Shota Tomomatsu & Yoshino Akizuki & Takuya Tomita & Akinori Endo & Yasushi Saeki & Yusuke Sato & Fumiaki Ohtake, 2025. "Combinatorial ubiquitin code degrades deubiquitylation-protected substrates," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    2. Xiangwei Wu & Yunxiang Du & Lu-Jun Liang & Ruichao Ding & Tianyi Zhang & Hongyi Cai & Xiaolin Tian & Man Pan & Lei Liu, 2024. "Structure-guided engineering enables E3 ligase-free and versatile protein ubiquitination via UBE2E1," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Bianca D. M. Tol & Bjorn R. Doodewaerd & Guinevere S. M. Lageveen-Kammeijer & Bas C. Jansen & Cami M. P. Talavera Ormeño & Paul J. M. Hekking & Aysegul Sapmaz & Robbert Q. Kim & Angeliki Moutsiopoulou, 2023. "Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Yesheng Fu & Lei Li & Xin Zhang & Zhikang Deng & Ying Wu & Wenzhe Chen & Yuchen Liu & Shan He & Jian Wang & Yuping Xie & Zhiwei Tu & Yadi Lyu & Yange Wei & Shujie Wang & Chun-Ping Cui & Cui Hua Liu & , 2024. "Systematic HOIP interactome profiling reveals critical roles of linear ubiquitination in tissue homeostasis," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    5. Juraj Ahel & Arda Balci & Victoria Faas & Daniel B. Grabarczyk & Roosa Harmo & Daniel R. Squair & Jiazhen Zhang & Elisabeth Roitinger & Frederic Lamoliatte & Sunil Mathur & Luiza Deszcz & Lillie E. Be, 2025. "ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    6. Sunan Li & Rongrong Li & Iqbal Ahmad & Xiaomeng Liu & Silas F. Johnson & Liangliang Sun & Yong-Hui Zheng, 2022. "Cul3-KLHL20 E3 ubiquitin ligase plays a key role in the arms race between HIV-1 Nef and host SERINC5 restriction," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Yifei Zhou & Hongjun Li & Yi Huang & Jiahui Li & Guiyu Deng & Gong Chen & Zhen Xi & Chuanzheng Zhou, 2023. "Suppression of alpha-carbon racemization in peptide synthesis based on a thiol-labile amino protecting group," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    8. Yu-Hsuan Chen & Han-Hsiun Chen & Won-Jing Wang & Hsin-Yi Chen & Wei-Syun Huang & Chien-Han Kao & Sin-Rong Lee & Nai Yang Yeat & Ruei-Liang Yan & Shu-Jou Chan & Kuen-Phon Wu & Ruey-Hwa Chen, 2023. "TRABID inhibition activates cGAS/STING-mediated anti-tumor immunity through mitosis and autophagy dysregulation," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    9. Diego Esposito & Jane Dudley-Fraser & Acely Garza-Garcia & Katrin Rittinger, 2022. "Divergent self-association properties of paralogous proteins TRIM2 and TRIM3 regulate their E3 ligase activity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    10. Xiangyi S. Wang & Thomas R. Cotton & Sarah J. Trevelyan & Lachlan W. Richardson & Wei Ting Lee & John Silke & Bernhard C. Lechtenberg, 2023. "The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Fredrik Trulsson & Vyacheslav Akimov & Mihaela Robu & Nila Overbeek & David Aureliano Pérez Berrocal & Rashmi G. Shah & Jürgen Cox & Girish M. Shah & Blagoy Blagoev & Alfred C. O. Vertegaal, 2022. "Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    12. Jane Dudley-Fraser & Diego Esposito & Katherine A. McPhie & Coltrane Morley-Williams & Tania Auchynnikava & Katrin Rittinger, 2025. "Identification of RING E3 pseudoligases in the TRIM protein family," Nature Communications, Nature, vol. 16(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59569-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.