Mechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168

Huasong Ai; Zebin Tong; Zhiheng Deng; Qiang Shi; Shixian Tao; Gaoge Sun; Jiawei Liang; Maoshen Sun; Xiangwei Wu; Qingyun Zheng; Lujun Liang; Hang Yin; Jia-Bin Li; Shuai Gao; Changlin Tian; Lei Liu; Man Pan

doi:10.1038/s41589-024-01750-x

Mechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168

Nat Chem Biol. 2024 Oct 11. doi: 10.1038/s41589-024-01750-x. Online ahead of print.

Authors

Huasong Ai^#^{1

2

3}, Zebin Tong^#², Zhiheng Deng^#², Qiang Shi², Shixian Tao², Gaoge Sun⁴, Jiawei Liang², Maoshen Sun^{2

5}, Xiangwei Wu², Qingyun Zheng^{1

3}, Lujun Liang⁶, Hang Yin⁴, Jia-Bin Li⁷, Shuai Gao⁸, Changlin Tian⁹, Lei Liu¹⁰, Man Pan^{11

12}

Affiliations

¹ Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
² New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China.
³ School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
⁴ School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
⁵ Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
⁶ Center for Bioanalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, China.
⁷ College of Pharmaceutical Sciences, Soochow University, Suzhou, China.
⁸ Department of Urology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
⁹ School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China. [email protected].
¹⁰ New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China. [email protected].
¹¹ Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China. [email protected].
¹² School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China. [email protected].

^# Contributed equally.

PMID: 39394267
DOI: 10.1038/s41589-024-01750-x

Abstract

The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent K13 and K15 (K13/15) sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to site-specifically ubiquitinate H2A K13/15 has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c~Ub (ubiquitin) in complex with nucleosomes. Here we developed chemical strategies and determined the cryo-electron microscopy structures of the RNF168-UbcH5c~Ub-nucleosome complex captured in transient H2A K13/15 monoubiquitination and adjacent dual monoubiquitination reactions, providing a 'helix-anchoring' mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the 'compass-binding' mode of dimeric E3 ligases. Our work not only provides structural snapshots of H2A K13/15 site-specific monoubiquitination and adjacent dual monoubiquitination but also offers a near-atomic-resolution structural framework for understanding pathogenic amino acid substitutions and physiological modifications of RNF168.