Nureki Osamu, Watanabe Kazunori, Fukai Shuya, Ishii Ryohei, Endo Yaeta, Hori Hiroyuki, Yokoyama Shigeyuki
Department of Biotechnology, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan.
Structure. 2004 Apr;12(4):593-602. doi: 10.1016/j.str.2004.03.003.
The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.
tRNA（Gm18）甲基转移酶（TrmH）催化tRNA中鸟苷18（Gua18）的2'-O甲基化。我们解析了嗜热栖热菌TrmH与S-腺苷-L-甲硫氨酸复合物的晶体结构，分辨率为1.85埃。催化结构域包含一个深三叶结，突变分析表明其对催化位点和辅因子结合口袋的形成至关重要。tRNA二氢尿嘧啶（D）臂可以对接在二聚体TrmH上，使得tRNA D茎被一个亚基的N端和C端螺旋夹住，而Gua18由另一个亚基修饰。来自另一个亚基的Arg41进入催化位点并与结合的硫酸根离子（一种RNA主链磷酸类似物）形成氢键，从而激活其亲核状态。基于将Gua18模拟到活性位点上，我们提出一旦Gua18结合，磷酸基团会激活Arg41，然后Arg41使2'-OH基团去质子化以进行甲基化。
