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Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

机译：T-box核糖开关茎I结构域与其同源tRNA的共晶体结构

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摘要

In Gram-positive bacteria, T-box riboswitches regulate the expression of aminoacyl-tRNA synthetases and other proteins in response to fluctuating transfer RNA aminoacylation levels under various nutritional states~1. T-boxes reside in the 5'-untranslated regions of the messenger RNAs they regulate, and consist of two conserved domains. Stem I contains the specifier trinucleotide that base pairs with the anticodon of cognate tRNA. 3' to stem I is the antiterminator domain, which base pairs with the tRNA acceptor end and evaluates its aminoacylation state~2. Despite high phylo-genetic conservation and widespread occurrence in pathogens, the structural basis of tRNA recognition~(3'4) by this riboswitch remains ill defined. Here we demonstrate that the ~100-nucleotide T-box stem I is necessary and sufficient for specific, high-affinity (dissociation constant (Kd) ~150 nM) tRNA binding, and report the structure of Oceanobacillus iheyensis glyQ stem I in complex with its cognate tRNA at 3.2 A resolution. Stem I recognizes the overall architecture of tRNA in addition to its anticodon, something accomplished by large ribonucleoproteins such as the ribosome, or proteins such as aminoacyl-tRNA synthetases~5, but is unprecedented for a compact mRN A domain. The C-shaped stem I cradles the L-shaped tRNA, forming an extended (1,604 A~2) intermolecu-lar interface. In addition to the specifier-anticodon interaction, two interdigitated T- loops near the apex of stem I stack on the tRNA elbow in a manner analogous to those of the J11/12-J12/11 motif~6 of RNase P and the LI stalk~7 of the ribosomal E-site. Because these ribonucleoproteins and T-boxes are unrelated, this strategy to recognize a universal tRNA feature probably evolved convergently. Mutually induced fit of stem I and the tRNA exploiting the intrinsic flexibility of tRNA and its conserved post-transcriptional modifications results in high shape complementarity, which in addition to providing specificity and affinity, globally organizes the T-box to orchestrate tRNA-dependent transcription regulation.
机译：在革兰氏阳性细菌中，T-box核糖开关响应各种营养状态〜1下波动的转移RNA氨酰化水平，调节氨酰基-tRNA合成酶和其他蛋白质的表达。 T-box位于它们调节的信使RNA的5'-非翻译区，由两个保守结构域组成。词干I包含与同源tRNA的反密码子碱基配对的指定三核苷酸。茎I的3'是抗终止子结构域，它与tRNA受体末端碱基配对，并评估其氨酰化状态〜2。尽管有很高的系统遗传学保守性，并在病原体中广泛存在，但该核糖开关对tRNA识别〜（3'4）的结构基础仍然不清楚。在这里，我们证明了〜100个核苷酸的T-box茎I对于特异性，高亲和力（解离常数（Kd）〜150 nM）tRNA结合是必要的，并且报告了大肠埃希氏菌glyQ茎I的结构与其同源的tRNA的分辨率为3.2A。茎I识别tRNA的整体结构，除了其反密码子外，它还可以通过核糖体等大型核糖核蛋白或氨酰基-tRNA合成酶〜5等蛋白质来实现，但对于紧凑的mRN A结构域而言却是空前的。 C形茎I支撑L形tRNA，形成一个扩展的（1604 A〜2）分子间界面。除了指定者与反齿动物的相互作用外，tRNA肘上茎I的茎尖附近的两个相互交叉的T环以类似于RNase P和LI茎的J11 / 12-J12 / 11基序〜6的方式堆叠〜7个核糖体E位点。由于这些核糖核蛋白和T-box无关，因此这种识别通用tRNA功能的策略可能会逐渐发展。利用tRNA的内在灵活性及其保守的转录后修饰，茎I和tRNA相互诱导适应，从而形成高度的形状互补性，除了提供特异性和亲和力外，还可以全局组织T-box来协调tRNA依赖性转录调控。

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  • 来源
    《Nature》 |2013年第7462期|363-366|共4页
  • 作者

    Jinwei Zhang; Adrian R. Ferre-DAmare;

  • 作者单位

    National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, Maryland 20892-8012, USA;

    National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, Maryland 20892-8012, USA;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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