Structure of the Catalytic Domain of EZH2 Reveals Conformational Plasticity in Cofactor and Substrate Binding Sites and Explains Oncogenic Mutations

Alma Seitova,Masoud Vedadi,Matthieu Schapira,Hong Zeng,Guillermo Senisterra,Shili Duan,Fengling Li,Peter J Brown,Aiping Dong,Cheryl H Arrowsmith,Hao He,Hong Wu,Sonia Rocha

doi:10.1371/journal.pone.0083737

Abstract

Polycomb repressive complex 2 (PRC2) is an important regulator of cellular differentiation and cell type identity. Overexpression or activating mutations of EZH2, the catalytic component of the PRC2 complex, are linked to hyper-trimethylation of lysine 27 of histone H3 (H3K27me3) in many cancers. Potent EZH2 inhibitors that reduce levels of H3K27me3 kill mutant lymphoma cells and are efficacious in a mouse xenograft model of malignant rhabdoid tumors. Unlike most SET domain methyltransferases, EZH2 requires PRC2 components, SUZ12 and EED, for activity, but the mechanism by which catalysis is promoted in the PRC2 complex is unknown. We solved the 2.0 Å crystal structure of the EZH2 methyltransferase domain revealing that most of the canonical structural features of SET domain methyltransferase structures are conserved. The site of methyl transfer is in a catalytically competent state, and the structure clarifies the structural mechanism underlying oncogenic hyper-trimethylation of H3K27 in tumors harboring mutations at Y641 or A677. On the other hand, the I-SET and post-SET domains occupy atypical positions relative to the core SET domain resulting in incomplete formation of the cofactor binding site and occlusion of the substrate binding groove. A novel CXC domain N-terminal to the SET domain may contribute to the apparent inactive conformation. We propose that protein interactions within the PRC2 complex modulate the trajectory of the post-SET and I-SET domains of EZH2 in favor of a catalytically competent conformation.

Highlights

Enhancer of zeste homolog 2 (EZH2) is the catalytic component of polycomb repressive complex 2 (PRC2), an epigenetic regulator of stem cell pluripotency, and expression of tissue-specific genes involved in cellular differentiation and developmental programs [1,2,3,4,5]
The crystal structure presented here reveals that EZH2 adopts a canonical SET domain methyltransferase fold in the absence of binding partners, and that the catalytic site is well formed (Figure 1D)
We find that the structure of the cofactor site is compatible with the formation of four of six hydrogen bonds with the cofactor that are conserved across all SET domain complex structures (Figure S9) [56]

Summary

Introduction

Enhancer of zeste homolog 2 (EZH2) is the catalytic component of polycomb repressive complex 2 (PRC2), an epigenetic regulator of stem cell pluripotency, and expression of tissue-specific genes involved in cellular differentiation and developmental programs [1,2,3,4,5]. EZH2 carries out a key function of the PRC2 complex, namely the sequential mono-, di- and trimethylation of Lysine 27 of histone H3 (H3K27) within chromatin. EZH2 contains a C-terminal SETdomain, a conserved feature of histone lysine methyltransferases [6,7,8]. The catalytic activity of EZH2 requires the presence of at least two other members of the PRC2 complex, namely embryonic ectoderm development (EED) and suppressor of zeste 12 (SUZ12) [9,10,11]. The histone-binding protein RBBP4 and the Zinc finger protein AEBP2 together further stimulate EZH2 enzymatic activity [12]

Methods

Results

Conclusion