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

Abstract

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.

RNF 4 interacts with both SUMO and nucleosomes to promote the DNA damage response

“…Together, the foregoing data show that the hRNF4 RING domain contains a non-specific DNA binding element related to that in the RING1b RING domain [28]. However, we note that DNA binding per se may not be the key function of the hRNF4 basic cluster, as it is structurally related to motifs in the RNF168 and RING1b RING domains that support nucleosome-targeting [4,28].…”

“…However, we note that DNA binding per se may not be the key function of the hRNF4 basic cluster, as it is structurally related to motifs in the RNF168 and RING1b RING domains that support nucleosome-targeting [4,28]. This structural homology has interesting implications for hRNF4 function in the DDR.…”

“…Like hRNF4, RNF168 and RING1b also contain this three residue basic cluster adjacent to their zinc-binding site (Fig 1A), while other RING-type E3 ubiquitin ligases do not ( Supplementary Fig S1). Interestingly, this basic cluster supports nucleosome-specific ubiquitination of H2A by both RNF168 and RING1b, and additionally, DNA binding by RING1b [4,28].…”

“…As both RNF168 and RING1b utilize their basic clusters to selectively modify histones within the nucleosomal context [4,28], we tested for similar functionality of hRNF4. Assayed against free histone, both wild-type and K179D hRNF4 strongly promoted H3 ubiquitination (Fig 2D and E).…”

RNF2/Ring1b negatively regulates p53 expression in selective cancer cell types to promote tumor development

“…For example, PRC1 poly-ubiquitinates Geminin, a DNA replication inhibitor, to sustain adult hematopoietic stem cell activity (23). Protein structure analysis revealed that within the PRC1 complex, Bmi1 and RNF2 heterodimerize via their N-terminal RING domains to form an active E3 ubiquitin ligase (24)(25)(26). The overexpression of Rnf2 has also been documented in clinical gastrointestinal tumors and lymphomas (27).…”