Structure of the PRC2 complex and application to drug discovery

Abstract

The polycomb repressive complexes 2 (PRC2) complex catalyzes tri-methylation of histone H3 lysine 27 (H3K27), a repressive chromatin marker associated with gene silencing. Overexpression and mutations of PRC2 are found in a wide variety of cancers, making the catalytic activity of PRC2 an important target of cancer therapy. This review highlights recent structural breakthroughs of the human PRC2 complex bound to the H3K27 peptide and a small molecule inhibitor, which provide critically needed insight into PRC2-targeted drug discovery.

The Polycomb repressive complex PRC2. (A) Domain organization of each subunit in the human PRC2 complex. aa, amino acid; SBD, SANT1-binding domain; EBD, the EED-binding domain; BAM, β-addition motif; SAL, SET activation loop; SRM, stimulation-responsive motif; MCSS, motif connecting SANT1 and SANT2; SANT, SWI3, ADA2, N-CoR and TFIIIB DNA-binding domain; CXC, cysteine-rich domain; SET, Su(var) 3–9, enhancer of zeste, trithorax domain; WD, WD-40 domain; WDB, WD-40 binding domain; Zn, Zn-finger region; VEFS, conserved among VRN2-EMF2-FIS2-SU(Z)12; JmjN, Jumonji N; ARID, AT-rich interaction domain; JmjC, Jumonji C; PHD, plant homeodomain. (B) Model of the human PRC2 complex. EZH2, EED, SUZ12, and RbA48 are core subunits, while JARID2, PCLs, AEBP2 are auxiliary subunits. PRC2 complex catalyzes tri-methylation of H3K27, leading to compaction of nucleosome and transcription silencing.

Figure 2

The structure of human PRC2 and fungal PRC2. The structure of human PRC2 (PDB ID: 5HYN) and fungal (C thermophilum) PRC2 (PDB ID: 5CH1). (A) The structure of human PRC2. Green: EZH2, cyan: EED, magenta: SUZ12 (VEFS), yellow: H3K27M peptide, orange: SAH, tint: JARID2K116me3 peptide, red: Zn²⁺. (B) The structure of fungal PRC2. Green: EZH2, cyan: EED, magenta: SUZ12 (VEFS), yellow: H3K27M peptide, orange: SAH, tint: H3K27me3 peptide, red: Zn²⁺. (C) Alignment of human and fungal PRC2 structure. Structural overlay of human PRC2 (PDB ID: 5HYN) and fungal PRC2 (PDB ID: 5CH1) Green: human EZH2, cyan: human EED, magenta: human SUZ12(VEFS), orange: fungal EZH2, gray: fungal EED, wheat: fungal SUZ12 (VEFS).

Figure 3

Interaction of PRC2 and substrate. (A) Interaction of human PRC2 with H3K27M peptide. (B) Interaction of human PRC2 with JARID2K116me3 peptide. (C) Interaction of human PRC2 with SAH. (D) Interaction of fungal PRC2 with H3K27me3 peptide. The specific interactions between PRC2 and peptide or SAH are indicated by blue lines. The interactions were analyzed by LigPlus and graphed using PyMol.

Figure 4

Allosteric regulation of PRC2 activity. The flexible stimulation-responsive motif (SRM) of EZH2 is absent in the electron density map of the PRC2 ternary complex in the basal state. The H3K27me3 peptide interaction with the SRM induces SRM structure and allows it to bind the catalytic SET-I domain of EZH2. These coupled interactions are associated with a rotation of SET-I and opening of the substrate-binding cleft, resulting in stimulation of PRC2 activity.

Figure 5

Overlay of the active and inhibitory states of human PRC2. The structure of active (PDB ID: 5HYN) and inhibited PRC2 (PDB ID: 5IJ7). Green: active PRC2, magenta: inhibitory PRC2, red: JARID2K116me2 peptide, cyan: H3K27M peptide, orange: SAH, wheat: Inhibitor 1 from structure 5IJ7.

Figure 6

Interaction of PRC2-inhibitor. The program Autodock was used to dock the PRC2 inhibitors EPZ6438, GSK126, and UNC1999 into the crystal structure of the PRC2/Inhibitor 1 complex (PDB code 5ij7). (A) PRC2-inhibitor 1 interactions. (B) PRC2-EPZ6438 interactions. (C) PRC2-GSK126 interactions. (D) PRC2-UNC1999 interactions.