IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-45635-y.html
   My bibliography  Save this article

Structure-guided engineering enables E3 ligase-free and versatile protein ubiquitination via UBE2E1

Author

Listed:
  • Xiangwei Wu

    (Tsinghua University
    Shanghai Jiao Tong University)

  • Yunxiang Du

    (Tsinghua University)

  • Lu-Jun Liang

    (University of Science and Technology of China)

  • Ruichao Ding

    (Tsinghua University)

  • Tianyi Zhang

    (Tsinghua University)

  • Hongyi Cai

    (Tsinghua University)

  • Xiaolin Tian

    (Tsinghua University)

  • Man Pan

    (Shanghai Jiao Tong University)

  • Lei Liu

    (Tsinghua University)

Abstract

Ubiquitination, catalyzed usually by a three-enzyme cascade (E1, E2, E3), regulates various eukaryotic cellular processes. E3 ligases are the most critical components of this catalytic cascade, determining both substrate specificity and polyubiquitination linkage specificity. Here, we reveal the mechanism of a naturally occurring E3-independent ubiquitination reaction of a unique human E2 enzyme UBE2E1 by solving the structure of UBE2E1 in complex with substrate SETDB1-derived peptide. Guided by this peptide sequence-dependent ubiquitination mechanism, we developed an E3-free enzymatic strategy SUE1 (sequence-dependent ubiquitination using UBE2E1) to efficiently generate ubiquitinated proteins with customized ubiquitinated sites, ubiquitin chain linkages and lengths. Notably, this strategy can also be used to generate site-specific branched ubiquitin chains or even NEDD8-modified proteins. Our work not only deepens the understanding of how an E3-free substrate ubiquitination reaction occurs in human cells, but also provides a practical approach for obtaining ubiquitinated proteins to dissect the biochemical functions of ubiquitination.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45635-y
    DOI: 10.1038/s41467-024-45635-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-45635-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-45635-y?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. Daniel Horn-Ghetko & David T. Krist & J. Rajan Prabu & Kheewoong Baek & Monique P. C. Mulder & Maren Klügel & Daniel C. Scott & Huib Ovaa & Gary Kleiger & Brenda A. Schulman, 2021. "Ubiquitin ligation to F-box protein targets by SCF–RBR E3–E3 super-assembly," Nature, Nature, vol. 590(7847), pages 671-676, February.
    2. 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.
    3. Indrajit Sahu & Sachitanand M. Mali & Prasad Sulkshane & Cong Xu & Andrey Rozenberg & Roni Morag & Manisha Priyadarsini Sahoo & Sumeet K. Singh & Zhanyu Ding & Yifan Wang & Sharleen Day & Yao Cong & O, 2021. "The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag," Nature Communications, Nature, vol. 12(1), pages 1-21, December.
    4. Kheewoong Baek & David T. Krist & J. Rajan Prabu & Spencer Hill & Maren Klügel & Lisa-Marie Neumaier & Susanne Gronau & Gary Kleiger & Brenda A. Schulman, 2020. "NEDD8 nucleates a multivalent cullin–RING–UBE2D ubiquitin ligation assembly," Nature, Nature, vol. 578(7795), pages 461-466, February.
    5. Byung-Hoon Lee & Ying Lu & Miguel A. Prado & Yuan Shi & Geng Tian & Shuangwu Sun & Suzanne Elsasser & Steven P. Gygi & Randall W. King & Daniel Finley, 2016. "USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites," Nature, Nature, vol. 532(7599), pages 398-401, April.
    6. 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.
    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. Ka Ying Sharon Hung & Sven Klumpe & Markus R. Eisele & Suzanne Elsasser & Geng Tian & Shuangwu Sun & Jamie A. Moroco & Tat Cheung Cheng & Tapan Joshi & Timo Seibel & Duco Dalen & Xin-Hua Feng & Ying L, 2022. "Allosteric control of Ubp6 and the proteasome via a bidirectional switch," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. 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.
    3. 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.
    4. Anthony J. Asmar & Shaun R. Abrams & Jenny Hsin & Jason C. Collins & Rita M. Yazejian & Youmei Wu & Jean Cho & Andrew D. Doyle & Samhitha Cinthala & Marleen Simon & Richard H. Jaarsveld & David B. Bec, 2023. "A ubiquitin-based effector-to-inhibitor switch coordinates early brain, craniofacial, and skin development," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Tom Dixon & Derek MacPherson & Barmak Mostofian & Taras Dauzhenka & Samuel Lotz & Dwight McGee & Sharon Shechter & Utsab R. Shrestha & Rafal Wiewiora & Zachary A. McDargh & Fen Pei & Rajat Pal & João , 2022. "Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry," Nature Communications, Nature, vol. 13(1), pages 1-24, December.
    6. Wai Tuck Soh & Hanna P. Roetschke & John A. Cormican & Bei Fang Teo & Nyet Cheng Chiam & Monika Raabe & Ralf Pflanz & Fabian Henneberg & Stefan Becker & Ashwin Chari & Haiyan Liu & Henning Urlaub & Ju, 2024. "Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
    7. Tian-Chen Xiong & Ming-Cong Wei & Fang-Xu Li & Miao Shi & Hu Gan & Zhen Tang & Hong-Peng Dong & Tianzi Liuyu & Pu Gao & Bo Zhong & Zhi-Dong Zhang & Dandan Lin, 2022. "The E3 ubiquitin ligase ARIH1 promotes antiviral immunity and autoimmunity by inducing mono-ISGylation and oligomerization of cGAS," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    8. Dongni Shi & Xianqiu Wu & Yunting Jian & Junye Wang & Chengmei Huang & Shuang Mo & Yue Li & Fengtian Li & Chao Zhang & Dongsheng Zhang & Huizhong Zhang & Huilin Huang & Xin Chen & Y. Alan Wang & Chuyo, 2022. "USP14 promotes tryptophan metabolism and immune suppression by stabilizing IDO1 in colorectal cancer," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    9. Fenglei Li & Qiaoyu Hu & Xianglei Zhang & Renhong Sun & Zhuanghua Liu & Sanan Wu & Siyuan Tian & Xinyue Ma & Zhizhuo Dai & Xiaobao Yang & Shenghua Gao & Fang Bai, 2022. "DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    10. Julia Reichelt & Wiebke Sachs & Sarah Frömbling & Julia Fehlert & Maja Studencka-Turski & Anna Betz & Desiree Loreth & Lukas Blume & Susanne Witt & Sandra Pohl & Johannes Brand & Maire Czesla & Jan Kn, 2023. "Non-functional ubiquitin C-terminal hydrolase L1 drives podocyte injury through impairing proteasomes in autoimmune glomerulonephritis," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    11. Fanindra Kumar Deshmukh & Gili Ben-Nissan & Maya A. Olshina & Maria G. Füzesi-Levi & Caley Polkinghorn & Galina Arkind & Yegor Leushkin & Irit Fainer & Sarel J. Fleishman & Dan Tawfik & Michal Sharon, 2023. "Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
    12. 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.

    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:15:y:2024:i:1:d:10.1038_s41467-024-45635-y. 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.