Structural insights into SETD3-mediated histidine methylation on β-actin

Qiong Guo,Jinrong Min,Chao Xu,Xiaoming Tu,Weronika Tomaka,Gao Wu,Sebastian Kwiatkowski,Jakub Drozak,Shanhui Liao,Huijuan Yu

doi:10.7554/elife.43676

Abstract

SETD3 is a member of the SET (Su(var)3-9, Enhancer of zeste, and Trithorax) domain protein superfamily and plays important roles in hypoxic pulmonary hypertension, muscle differentiation, and carcinogenesis. Previously, we identified SETD3 as the actin-specific methyltransferase that methylates the N3 of His73 on β-actin (Kwiatkowski et al., 2018). Here, we present two structures of S-adenosyl-L-homocysteine-bound SETD3 in complex with either an unmodified β-actin peptide or its His-methylated variant. Structural analyses, supported by biochemical experiments and enzyme activity assays, indicate that the recognition and methylation of β-actin by SETD3 are highly sequence specific, and that both SETD3 and β-actin adopt pronounced conformational changes upon binding to each other. In conclusion, this study is the first to show a catalytic mechanism of SETD3-mediated histidine methylation on β-actin, which not only throws light on the protein histidine methylation phenomenon but also facilitates the design of small molecule inhibitors of SETD3.

Highlights

Microfilaments are the building blocks of the cytoskeleton and are made up of actin proteins
We and others had previously shown that SETD3 acts as an actin-specific histidine N-methyltransferase, but the molecular basis for the selective histidine methylation catalyzed by SETD3 remained unknown (Kwiatkowski et al, 2018; Wilkinson et al, 2019)
We measured the binding affinity of the SETD3 core region to a His73-containing fragment of b-actin by isothermal calorimetry titration (ITC) and found that SETD3 binds to the b-actin peptide with a Kd of 0.17 mM (Figure 1A–B and Table 1)

Summary

Introduction

Microfilaments are the building blocks of the cytoskeleton and are made up of actin proteins (dos Remedios et al, 2003; Theriot and Mitchison, 1991). There are six actin isoforms in mammalian cells that are characterized on the basis of their different expression profiles and cellular functions, including askeletal-, acardiac-, asmooth-, bcyto-, gcyto-, and gsmooth-actins (Gunning et al, 1983; Herman, 1993; Perrin and Ervasti, 2010). B-actin is ubiquitously expressed and plays critical roles in a wide variety of cellular functions, such as cytoskeleton formation, cell motility and maintenance of cell stability (Leterrier et al, 2017; Nudel et al, 1983). Many different types of post-translational modifications (PTMs) have been found in actin proteins, including acetylation, methylation, SUMOylation and ubiquitination (Terman and Kashina, 2013). We and others identified SETD3 as the actin-specific histidine Nmethyltransferase that methylates actin at His (Kwiatkowski et al, 2018; Wilkinson et al, 2019)

Results

Discussion

Conclusion