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

Xiangwei Wu, Yunxiang Du, Lu-Jun Liang (), Ruichao Ding, Tianyi Zhang, Hongyi Cai, Xiaolin Tian, Man Pan () and Lei Liu ()
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Xiangwei Wu: Tsinghua 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

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-45635-y

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