Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding.
The SET- and MYND-domain containing (Smyd) proteins constitute a special subfamily of the SET-containing lysine methyltransferases. Here we present the structure of full-length human Smyd3 in complex with S-adenosyl-L-homocysteine at 2.8 Å resolution. Smyd3 affords the first example that other region(s) besides the SET domain and its flanking regions participate in the formation of the active site. Structural analysis shows that the previously uncharacterized C-terminal domain of Smyd3 contains a tetratrico-peptide repeat (TPR) domain which together with the SET and post-SET domains forms a deep, narrow substrate binding pocket. Our data demonstrate the important roles of both TPR and post-SET domains in the histone lysine methyltransferase (HKMT) activity of Smyd3, and show that the hydroxyl group of Tyr239 is critical for the enzymatic activity. The characteristic MYND domain is located nearby to the substrate binding pocket and exhibits a largely positively charged surface. Further biochemical assays show that DNA binding of Smyd3 can stimulate its HKMT activity and the process may be mediated via the MYND domain through direct DNA binding.
State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.
Shutong
S
Xu
Jian
J
Wu
Bingfa
B
Sun
Chen
C
Zhong
Jianping
J
Ding
D001665:Binding Sites; D055162:Biocatalysis; D004247:DNA / Q000378:metabolism*; D011495:Histone-Lysine N-Methyltransferase / Q000737:chemistry* / Q000378:metabolism; D006657:Histones / Q000737:chemistry; D006801:Humans; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D020449:Repetitive Sequences, Amino Acid; D012435:S-Adenosylhomocysteine / Q000737:chemistry
D006657:Histones; D004247:DNA; D012435:S-Adenosylhomocysteine; D011495:Histone-Lysine N-Methyltransferase; C506278:SMYD3 protein, human; D008239:Lysine
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