Structure, mechanism, and regulation of polycomb-repressive complex 2

Abstract

Polycomb repressive complex 2 (PRC2) methylates lysine 27 in histone H3, a modification associated with epigenetic gene silencing. This complex plays a fundamental role in regulating cellular differentiation and development, and PRC2 overexpression and mutations have been implicated in numerous cancers. In this Minireview, we examine recent studies elucidating the first crystal structures of the PRC2 core complex, yielding seminal insights into its catalytic mechanism, substrate specificity, allosteric regulation, and inhibition by a class of small molecules that are currently undergoing cancer clinical trials. We conclude by exploring unresolved questions and future directions for inquiry regarding PRC2 structure and function.

Keywords: Enhancer of Zeste 2 (EZH2); Polycomb repressive complex 2 (PRC2); SET domain; cancer; chromatin; crystal structure; epigenetics; gene silencing; histone methylation; lysine methyltransferase.

Figure 1.

Crystal structures of PRC2 core subunits. A, ribbon rendering of the β-propeller domain of mouse EED bound to the EBD motif of EZH2 (PDB accession code 2QXV). For clarity, proteins, domains, and motifs are uniformly color-coded throughout the figures (color key provided in Fig. 2A). B, human EED β-propeller domain bound to an H3K27me3 peptide (PDB code 3IIW). The H3K27me3 peptide and the side chains of interacting residues in EED are depicted in stick form, with the EED residues that compose the aromatic cage highlighted in orange. Hydrogen bonds are indicated by orange dashes. EED is rotated ∼180° relative to its orientation in A. C, ribbon diagram of the isolated catalytic domain of human EZH2 (PDB code 4MI0). Zinc ions are illustrated as gray spheres.

Figure 2.

Structure and allosteric activation of the CtPRC2 core complex. A, ribbon representation of the stimulated state of CtPRC2 bound to an H3K27me3 peptide and AdoHcy (PDB code 5KJH). Ligands are shown in stick form, and zinc ions are rendered as spheres. The inset key denotes the color code used to distinguish the different proteins, domains, and motifs composing the complex. B, close-up view of the interface between the regulatory and catalytic lobes. The side chains of key residues in the SAL domain are illustrated. C, superimposition of the basal and stimulated states of PRC2 with the basal state denoted in gray (PDB codes 5KJI and 5KJH). D, zoomed-in view of the stimulated state of CtPRC2 (PDB code 5KJH). The surface of EED is depicted, and the EZH2 domains and motifs are rendered in ribbon representation. The H3K27me3 peptide, AdoHcy, and the side chains of relevant residues in the SRM and iSET motifs and the SET domain are shown in stick form. Hydrogen bonds are denoted by orange dashes.

Figure 3.

Structure and regulation of the HsPRC2 core complex. A, ribbon diagram of the stimulated state of HsPRC2 in complex with JARID2K116me3 and H3K27M peptides and AdoHcy (PDB code 5HYN). Proteins, domains, and motifs are colored as in Fig. 2. Peptides and AdoHcy are rendered as sticks, and zinc ions are depicted as spheres. B, superimposition of the stimulated CtPRC2 complex (gray) and the stimulated human PRC2 complex (PDB codes 5KJH and 5HYN). C, structural alignment of the isolated SET domain of EZH2 (gray) and the SAL, SRM, iSET, cSET, and SET domains of EZH2 in the HsPRC2-stimulated complex (PDB codes 4MI0 and 5HYN). D, close-up view of the H3K27M peptide and AdoHcy bound to HsPRC2 (PDB code 5HYN). The H3K27M peptide, AdoHcy, and the side chains of interacting residues are illustrated as sticks. Hydrogen bonds are indicated by orange dashes.

Figure 4.

Structural basis for small molecule inhibition of PRC2. A, structure of inhibitor-1, a pyridone-based EZH2 inhibitor. B, structure of the human/anole chimeric PRC2 core complex bound to inhibitor-1 that is depicted in sphere mode (PDB code 5IJ7). C, close-up view of the pyridone inhibitor-binding cleft, highlighting residues that make key interactions with inhibitor-1. The inhibitor and interacting residues in PRC2 are represented as sticks. Hydrogen bonds are denoted by orange dashes. D, superimposition of the active sites of the PRC2–inhibitor-1 complex and the HsPRC2–AdoHcy–JARID1K116me3–H3K27M peptide complex (PDB codes 5IJ7 and 5HYN).