Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex

• Published in: The EMBO journal Vol. 30; no. 16; pp. 3285 - 3297
• Main Authors: Bentley, Matthew L, Corn, Jacob E, Dong, Ken C, Phung, Qui, Cheung, Tommy K, Cochran, Andrea G
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 17.08.2011; Blackwell Publishing Ltd; Nature Publishing Group
• Subjects: Binding Sites; Bmi1; Computer applications; Crystal structure; Crystallography, X-Ray; Deoxyribonucleic acid; DNA; DNA - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Enzymes; Gene expression; Histones - metabolism; Humans; Models, Molecular; Molecular biology; Mutagenesis, Site-Directed; Nuclear Proteins - chemistry; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; nucleosome; Nucleosomes - metabolism; Polycomb repression; Polycomb Repressive Complex 1; Protein Binding; Protein Conformation; Proto-Oncogene Proteins - chemistry; Proto-Oncogene Proteins - genetics; Proto-Oncogene Proteins - metabolism; Recombinant Fusion Proteins - chemistry; Recombinant Fusion Proteins - metabolism; Repressor Proteins - chemistry; Repressor Proteins - genetics; Repressor Proteins - metabolism; Ring1b; Sodium Chloride - pharmacology; UbcH5c; Ubiquitin-Conjugating Enzymes - chemistry; Ubiquitin-Conjugating Enzymes - genetics; Ubiquitin-Conjugating Enzymes - metabolism; Ubiquitin-Protein Ligases - chemistry; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism; Ubiquitination
• ISSN: 0261-4189; 1460-2075
• DOI: 10.1038/emboj.2011.243

The Polycomb repressive complex 1 (PRC1) mediates gene silencing, in part by monoubiquitination of histone H2A on lysine 119 (uH2A). Bmi1 and Ring1b are critical components of PRC1 that heterodimerize via their N‐terminal RING domains to form an active E3 ubiquitin ligase. We have determined the crystal structure of a complex between the Bmi1/Ring1b RING–RING heterodimer and the E2 enzyme UbcH5c and find that UbcH5c interacts with Ring1b only, in a manner fairly typical of E2–E3 interactions. However, we further show that the Bmi1/Ring1b RING domains bind directly to duplex DNA through a basic surface patch unique to the Bmi1/Ring1b RING–RING dimer. Mutation of residues on this interaction surface leads to a loss of H2A ubiquitination activity. Computational modelling of the interface between Bmi1/Ring1b–UbcH5c and the nucleosome suggests that Bmi1/Ring1b interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve specific monoubiquitination of H2A. Our results point to a novel mechanism of substrate recognition, and control of product formation, by Bmi1/Ring1b. How specific substrate lysines can be selected for ubiquitination is little understood. New structural data on a histone‐modifying ubiquitin ligase reveal how the nucleosomal context may restrict its activity towards specific target residues as well as towards monoubiquitination.