Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase

• Published in: Nature (London) 2023-04, Vol.616 (7955), p.176-182
• Main Authors: Ge, Weiran, Yu, Cong, Li, Jingjing, Yu, Zhenyu, Li, Xiaorong, Zhang, Yan, Liu, Chao-Pei, Li, Yingfeng, Tian, Changlin, Zhang, Xinzheng, Li, Guohong, Zhu, Bing, Xu, Rui-Ming
• Format: Article
• Language: English
• Subjects: 101/1; 101/28; 13; 38; 38/91; 631/337/176; 631/535/1258; 82; 82/16; 82/80; 82/83; Binding; Catalytic Domain; Cryoelectron Microscopy; Deubiquitinating Enzymes - classification; Deubiquitinating Enzymes - metabolism; Deubiquitinating Enzymes - ultrastructure; DNA methylation; Electron microscopy; Embryogenesis; Embryonic growth stage; Gene expression; Gene silencing; Genes; Histone H2A; Histones; Histones - chemistry; Histones - metabolism; Humanities and Social Sciences; Humans; Insects; Microscopy; multidisciplinary; Mutation; Nucleosomes - chemistry; Nucleosomes - genetics; Nucleosomes - metabolism; Peptides; Polycomb group proteins; Polycomb Repressive Complex 1 - chemistry; Polycomb Repressive Complex 1 - metabolism; Polycomb Repressive Complex 1 - ultrastructure; Polycomb-Group Proteins - chemistry; Polycomb-Group Proteins - metabolism; Polycomb-Group Proteins - ultrastructure; Proteins; Repressor Proteins - chemistry; Repressor Proteins - metabolism; Repressor Proteins - ultrastructure; Science; Science (multidisciplinary); Substrate Specificity; Substrates; Ubiquitin; Ubiquitin - metabolism; Ubiquitin Thiolesterase - chemistry; Ubiquitin Thiolesterase - metabolism; Ubiquitin Thiolesterase - ultrastructure; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - chemistry; Ubiquitin-Protein Ligases - metabolism; Ubiquitin-Protein Ligases - ultrastructure; Ubiquitination
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-023-05841-y

Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification 1 – 3 . The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome 4 , counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1) 5 to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. 6 – 9 ). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3–H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A–H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1. The cryo-electron microscopy structure of the Polycomb repressive deubiquitinase (PR-DUB) in complex with the H2AK119ub1 nucleosome provides insight into how the substrate specificity of PR-DUB is achieved.