Chemical mechanisms of nucleosomal histone ubiquitination by RING-type E3 enzymes

Various E3 enzymes present in cells selectively ubiquitinate different lysine sites on the nucleosomes, recruiting downstream effector proteins to participate in the regulation of a variety of cellular processes, such as transcription activation, gene silencing, and DNA damage repair. Recently, the continuous development of chemical synthesis of complex post-translationally modified proteins and their complexes, as well as the advances in biophysical techniques such as cryo-electron microscopy, nuclear magnetic resonance and cross-linked mass spectrometry have promoted the elucidation of the chemical mechanism of nucleosome ubiquitination by E3 enzymes. This paper reviews the recent chemical, biochemical, and structural biological studies of four E3 enzymes for specific ubiquitination of nucleosome substrates, including PRC1, BRCA1/BARD1, RNF168, and Bre1. These E3 enzymes bind to acidic patch of nucleosome through the classical “arginine anchor” for localization. By multivalent interactions between E3 enzyme with other core histones and E2 enzyme with DNA, the active cysteine of E2 enzyme is oriented towards specific ubiquitinated sites of substrates, inducing the site-specific transfer of ubiquitin from E2 enzyme to the substrate lysine. These studies reveal the chemical basis of selective ubiquitination of nucleosomes by E3 enzymes, clarify the mechanism of site-specific ubiquitination on nucleosomes, and provide structural basis for the design of small drug molecules to intervene in the ubiquitination level of nucleosomes in cells to treat related diseases.