Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme
Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme
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DOI：
10.1016/j.str.2004.03.003
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发表时间：
2004-04-01
期刊：
影响因子：
5.7
通讯作者：
Yokoyama, S
中科院分区：
文献类型：
--
作者：
Nureki, O;Watanabe, K;Yokoyama, S
tRNA（Gm 18）甲基转移酶（TrmH）催化tRNA的鸟苷18（Gua 18）的2 '-O甲基化。我们解决了Thermus thermophilus TrmH与S-腺苷-L-蛋氨酸复合物的晶体结构在1.85埃分辨率。催化结构域包含一个深三叶结，突变分析显示，催化位点和辅因子结合口袋的形成是至关重要的。tRNA二氢尿苷（D）臂可以对接到二聚体TrmH上，使得tRNA D-茎被来自一个亚基的N-和C-末端螺旋夹持，而Gua 18被另一个亚基修饰。来自另一个亚基的Arg 41进入催化位点，与结合的硫酸根离子（RNA主链磷酸盐类似物）形成氢键，从而激活其亲核状态。基于Gua 18对活性位点的建模，我们提出，一旦Gua 18结合，磷酸基团激活Arg 41，Arg 41然后使2 '-OH基团去质子化以进行甲基化。
The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophi-lus TrmH complexed with S-adenosyl-L-methionine at 1.85 Angstrom 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.