The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
Nature. 2009 Dec 10;462(7274):808-12. doi: 10.1038/nature08612.
Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly. One checkpoint is the AlaRS editing centre, and the other is from widely distributed AlaXps-free-standing, genome-encoded editing proteins that clear Ser-tRNA(Ala). The paradox of misincorporating both a smaller (glycine) and a larger (serine) amino acid suggests a deep conflict for nature-designed AlaRS. Here we show the chemical basis for this conflict. Nine crystal structures, together with kinetic and mutational analysis, provided snapshots of adenylate formation for each amino acid. An inherent dilemma is posed by constraints of a structural design that pins down the alpha-amino group of the bound amino acid by using an acidic residue. This design, dating back more than 3 billion years, creates a serendipitous interaction with the serine OH that is difficult to avoid. Apparently because no better architecture for the recognition of alanine could be found, the serine misactivation problem was solved through free-standing AlaXps, which appeared contemporaneously with early AlaRSs. The results reveal unconventional problems and solutions arising from the historical design of the protein synthesis machinery.
丙氨酰-tRNA 合成酶（AlaRS）将丝氨酸错译为丙氨酸会产生深远的功能后果。在整个进化过程中，两个编辑检查点可防止疾病相关的误译将甘氨酸或丝氨酸在 AlaRS 的活性部位错译为丙氨酸。在细菌和小鼠中，丝氨酸比甘氨酸更具挑战性。一个检查点是 AlaRS 编辑中心，另一个是广泛分布的 AlaXps 独立、基因组编码的编辑蛋白，它们可清除 Ser-tRNA（Ala）。将较小的（甘氨酸）和较大的（丝氨酸）氨基酸错误掺入的悖论表明，天然设计的 AlaRS 存在深刻的冲突。在这里，我们展示了这种冲突的化学基础。九个晶体结构，以及动力学和突变分析，为每个氨基酸的腺苷酸形成提供了快照。一个固有的困境是由结构设计的约束造成的，该设计通过使用酸性残基将结合氨基酸的α-氨基基团固定下来。这种设计可以追溯到 30 多亿年前，它与丝氨酸 OH 形成了一种偶然的相互作用，很难避免。显然，由于无法找到更好的用于识别丙氨酸的结构，因此通过独立的 AlaXps 解决了丝氨酸的错误激活问题，而 AlaXps 与早期的 AlaRS 同时出现。研究结果揭示了蛋白质合成机制历史设计所产生的非常规问题和解决方案。
