Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases
Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases
复制标题
DOI：
10.1261/rna.029983.111
复制
发表时间：
2012-02-01
期刊：
影响因子：
4.5
通讯作者：
Hou, Ya-Ming
中科院分区：
文献类型：
--
作者：
Liu, Cuiping;Sanders, Jeffrey M.;Hou, Ya-Ming
I类氨酰-tRNA合成酶（aaRSs）使用Rossmann折叠结构域来催化解码遗传信息所需的氨酰-tRNA的合成。虽然罗斯曼折叠结构域在进化中是保守的，但氨酰化位点附近的受体茎在tRNA底物中不同，这就提出了保守的蛋白折叠如何适应RNA序列变异的问题。感兴趣的是在1-72位存在细菌起始tRNA（fMet）特有的未配对的C-A错配，而在延伸tRNA中不存在。在这里，我们表明，第一类甲硫氨酰-tRNA合成酶（MetRS）的大肠杆菌和其密切的结构同系物半胱氨酰-tRNA合成酶（CysRS）显示不同的模式识别的1-72碱基对。虽然罗斯曼折叠结构域中的两种酶的结构同源性表现在氨酰化动力学的共同爆发特征中，但CysRS区分未配对的1-72，而MetRS缺乏这种区分。Rossmann折叠的基于结构的比对鉴定了α-螺旋基序的插入，所述α-螺旋基序特异于CysRS但不存在于MetRS，其停靠在1-72上并且可以区分错配。事实上，CysRS螺旋基序的取代消除了对未配对1-72的歧视。额外的结构比对显示，除了MetRS之外，I类tRNA合成酶含有停靠在1-72上的结构基序。这项工作表明，通过灵活插入一个结构基序停靠在1-72，I类tRNA合成酶的催化结构域可以获得结构可塑性，以适应tRNA受体茎末端的变化。
Class I aminoacyl-tRNA synthetases (aaRSs) use a Rossmann-fold domain to catalyze the synthesis of aminoacyl-tRNAs required for decoding genetic information. While the Rossmann-fold domain is conserved in evolution, the acceptor stem near the aminoacylation site varies among tRNA substrates, raising the question of how the conserved protein fold adapts to RNA sequence variations. Of interest is the existence of an unpaired C-A mismatch at the 1-72 position unique to bacterial initiator tRNA(fMet) and absent from elongator tRNAs. Here we show that the class I methionyl-tRNA synthetase (MetRS) of Escherichia coli and its close structural homolog cysteinyl-tRNA synthetase (CysRS) display distinct patterns of recognition of the 1-72 base pair. While the structural homology of the two enzymes in the Rossmann-fold domain is manifested in a common burst feature of aminoacylation kinetics, CysRS discriminates against unpaired 1-72, whereas MetRS lacks such discrimination. A structure-based alignment of the Rossmann fold identifies the insertion of an a-helical motif, specific to CysRS but absent from MetRS, which docks on 1-72 and may discriminate against mismatches. Indeed, substitutions of the CysRS helical motif abolish the discrimination against unpaired 1-72. Additional structural alignments reveal that with the exception of MetRS, class I tRNA synthetases contain a structural motif that docks on 1-72. This work demonstrates that by flexible insertion of a structural motif to dock on 1-72, the catalytic domain of class I tRNA synthetases can acquire structural plasticity to adapt to changes at the end of the tRNA acceptor stem.