The crystal structure of the Pyrococcus abyssi mono-functional methyltransferase PaTrm5b
The crystal structure of the Pyrococcus abyssi mono-functional methyltransferase PaTrm5b
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深渊火球菌单功能甲基转移酶 PaTrm5b 的晶体结构
DOI：
10.1016/j.bbrc.2017.09.038
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发表时间：
2017
影响因子：
3.1
通讯作者：
Xie Wei
中科院分区：
文献类型：
--
作者：
Wu Jialiang;Jia Qian;Wu Saibin;Zeng Hui;Sun Yujie;Wang Caiyan;Ge Ruiguang;Xie Wei
真核生物和古生物中tRNAPhein的G37区所特有的wyosine高度修饰是一个非常复杂的过程，涉及多个步骤和酶，其衍生物在翻译过程中对维持阅读框架是必不可少的。在考古热球菌属中，Trm5家族的两个关键酶，分别命名为PaTrm5a和PaTrm5b，通过形成N1甲基化鸟苷(M1G37)开始这一过程。此外，PaTrm5a还催化C7在4-去甲基肌苷(IMG-14)上进一步甲基化，在相同的位置产生异鸟苷(ImG2)。Trm5酶在催化过程中表现出的不同甲基化能力和可能的构象变化的结构基础尚未得到很好的研究。这里我们报道了单功能的PaTrm5b的3.3°晶体结构，它与PaTrm5a有32%的序列同源性。有趣的是，结构叠加表明PaTrm5b蛋白显示出与简氏甲烷球菌(MjTrm5b)tRNA结合的Trm5b相似的延伸构象，但与先前报道的apo-PaTrm5a或折叠良好的apo-MjTrm5b的开放构象有很大不同。N-末端D1域的截断导致tRNA结合减少以及PaTrm5b的甲基转移活性降低。对已报道的三种Trm5结构中D1结构域的差异定位进行了合理的解释，这可能是由于不同的结构域间相互作用和晶体堆积模式所致。这项研究扩大了我们对Trm5酶的甲基化机制和Wyosine超修饰的理解。
The wyosine hypermodification found exclusively at G37 of tRNAPhein eukaryotes and archaea is a very complicated process involving multiple steps and enzymes, and the derivatives are essential for the maintenance of the reading frame during translation. In the archaeaPyrococcus abyssi, two key enzymes from the Trm5 family, named PaTrm5a and PaTrm5b respectively, start the process by forming N1-methylated guanosine (m1G37). In addition, PaTrm5a catalyzes the further methylation of C7 on 4-demethylwyosine (imG-14) to produce isowyosine (imG2) at the same position. The structural basis of the distinct methylation capacities and possible conformational changes during catalysis displayed by the Trm5 enzymes are poorly studied. Here we report the 3.3 Å crystal structure of the mono-functional PaTrm5b, which shares 32% sequence identity with PaTrm5a. Interestingly, structural superposition reveals that the PaTrm5b protein exhibits an extended conformation similar to that of tRNA-bound Trm5b fromMethanococcus jannaschii(MjTrm5b), but quite different from the open conformation of apo-PaTrm5a or well folded apo-MjTrm5b reported previously. Truncation of the N-terminal D1 domain leads to reduced tRNA binding as well as the methyltransfer activity of PaTrm5b. The differential positioning of the D1 domains from three reported Trm5 structures were rationalized, which could be attributable to the dissimilar inter-domain interactions and crystal packing patterns. This study expands our understanding on the methylation mechanism of the Trm5 enzymes and wyosine hypermodification.