Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
RNA. 2012 Feb;18(2):213-21. doi: 10.1261/rna.029983.111. Epub 2011 Dec 19.
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 α-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.
I 类氨酰-tRNA 合成酶（aaRSs）利用 Rossmann 折叠结构域催化合成用于解码遗传信息的氨酰-tRNA。虽然 Rossmann 折叠结构域在进化中是保守的，但接近氨酰化位点的接受茎在 tRNA 底物中存在差异，这就提出了一个问题，即保守的蛋白质折叠如何适应 RNA 序列的变化。有趣的是，细菌起始 tRNA(fMet)中存在独特的 1-72 位未配对的 C-A 错配，而延伸 tRNA 中则没有。在这里，我们展示了大肠杆菌的 I 类甲硫氨酰-tRNA 合成酶（MetRS）及其紧密结构同源物半胱氨酰-tRNA 合成酶（CysRS）对 1-72 碱基对的识别模式存在明显差异。尽管这两种酶在 Rossmann 折叠结构域的结构同源性表现为氨酰化动力学的共同爆发特征，但 CysRS 对未配对的 1-72 具有鉴别能力，而 MetRS 则缺乏这种鉴别能力。基于结构的 Rossmann 折叠比对确定了插入一个螺旋结构基序，该基序特异性存在于 CysRS 中而不存在于 MetRS 中，它与 1-72 对接，并可能对错配进行鉴别。事实上，CysRS 螺旋结构基序的取代会消除对未配对 1-72 的鉴别能力。额外的结构比对表明，除了 MetRS 之外，I 类 tRNA 合成酶还含有一个结构基序，该基序与 1-72 对接。这项工作表明，通过将一个结构基序灵活地插入到 1-72 对接，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 接受茎末端的变化。
