Fu Weiqi, Liu Nan, Qiao Qi, Wang Mingzhu, Min Jinrong, Zhu Bing, Xu Rui-Ming, Yang Na
From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, the University of Chinese Academy of Sciences, Beijing 100049, China, and.
From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
J Biol Chem. 2016 Apr 22;291(17):9173-80. doi: 10.1074/jbc.M115.709832. Epub 2016 Feb 29.
SMYD3 is a SET domain-containing N-lysine methyltransferase associated with multiple cancers. Its reported substrates include histones (H3K4 and H4K5), vascular endothelial growth factor receptor 1 (VEGFR1 Lys(831)) and MAP3 kinase kinase (MAP3K2 Lys(260)). To reveal the structural basis for substrate preference and the catalytic mechanism of SMYD3, we have solved its co-crystal structures with VEGFR1 and MAP3K2 peptides. Our structural and biochemical analyses show that MAP3K2 serves as a robust substrate of SMYD3 because of the presence of a phenylalanine residue at the -2 position. A shallow hydrophobic pocket on SMYD3 accommodates the binding of the phenylalanine and promotes efficient catalytic activities of SMYD3. By contrast, SMYD3 displayed a weak activity toward a VEGFR1 peptide, and the location of the acceptor lysine in the folded kinase domain of VEGFR1 requires drastic conformational rearrangements for juxtaposition of the acceptor lysine with the enzymatic active site. Our results clearly revealed structural determinants for the substrate preference of SMYD3 and provided mechanistic insights into lysine methylation of MAP3K2. The knowledge should be useful for the development of SMYD3 inhibitors in the fight against MAP3K2 and Ras-driven cancer.
SMYD3是一种与多种癌症相关的含SET结构域的N - 赖氨酸甲基转移酶。其已报道的底物包括组蛋白（H3K4和H4K5）、血管内皮生长因子受体1（VEGFR1 Lys(831)）和丝裂原活化蛋白激酶激酶激酶（MAP3K2 Lys(260)）。为了揭示SMYD3底物偏好的结构基础及其催化机制，我们解析了它与VEGFR1和MAP3K2肽段的共晶体结构。我们的结构和生化分析表明，由于在 -2 位存在苯丙氨酸残基，MAP3K2是SMYD3的有效底物。SMYD3上一个浅的疏水口袋容纳苯丙氨酸的结合并促进SMYD3的高效催化活性。相比之下，SMYD3对VEGFR1肽段的活性较弱，并且VEGFR1折叠激酶结构域中受体赖氨酸的位置需要剧烈的构象重排才能使受体赖氨酸与酶活性位点并列。我们的结果清楚地揭示了SMYD3底物偏好的结构决定因素，并为MAP3K2的赖氨酸甲基化提供了机制性见解。这些知识对于开发对抗MAP3K2和Ras驱动癌症的SMYD3抑制剂应该是有用的。
