A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.,Journal of Molecular Biology

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A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.
Journal of Molecular Biology ( IF 4.7 ) Pub Date : 2020-01-14 , DOI: 10.1016/j.jmb.2019.12.016
Sweta Vangaveti ₁ , William A Cantara ₂ , Jessica L Spears ₂ , Hasan DeMirci ₃ , Frank V Murphy ₄ , Sri V Ranganathan ₁ , Kathryn L Sarachan ₅ , Paul F Agris ₅

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Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNAArg isoacceptors. The anticodon stem and loop (ASL) domains of tRNAArg1 and tRNAArg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I34) and 37 (m2A37). tRNAArg1 is also modified from cytidine to 2-thiocytidine at position 32 (s2C32). The s2C32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s2C32 for C32 in the Saccharomyces cerevisiae tRNAIleIAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s2C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASLArg1ICG and ASLArg2ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C32-A38 cross-loop interaction but failed to fully explain the means by which s2C32 restricts I34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C32-A38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.

中文翻译：

在包含摆动位置肌苷的tRNA中2-硫胞苷介导的限制性密码子识别的结构基础。

六个精氨酸密码子中的三个（CGU，CGC和CGA）由两个大肠杆菌tRNAArg同工受体解码。tRNAArg1和tRNAArg2的反密码子茎和环（ASL）域都在位置34（I34）和37（m2A37）处含有肌苷和2-甲基腺苷修饰。tRNAArg1在位置32（s2C32）也从胞苷修饰为2-硫代胞苷。已知s2C32修改可通过未知机制消除稀有CGA密码子的摆动密码子识别，同时仍允许CGU和CGC的解码。用酿酒酵母tRNAIleIAU反密码子茎和环域（ASL）中的C32取代s2C32可以避免对其同义的A末端密码子进行摆动解码，这表明s2C在32位的这种功能是可推广的特性。结合到核糖体上同源密码子和摆动密码子的各种修饰的ASLArg1ICG和ASLArg2ICG构建体的X射线晶体结构揭示了C32-A38交叉环相互作用的破坏，但未能完全解释s2C32限制I34摆动的方式。计算研究表明，在密码子的摆动位置采用空间上宽泛的肌苷-腺苷碱基对不能与规范的ASL掉头模体同时使用。C32-A38交叉环相互作用是核糖体A位点反密码子/密码子相互作用的稳定性所必需的。计算研究表明，在密码子的摆动位置采用空间上宽泛的肌苷-腺苷碱基对不能与规范的ASL掉头模体同时使用。C32-A38交叉环相互作用是核糖体A位点反密码子/密码子相互作用的稳定性所必需的。计算研究表明，在密码子的摆动位置采用空间上宽泛的肌苷-腺苷碱基对不能与规范的ASL掉头模体同时使用。C32-A38交叉环相互作用是核糖体A位点反密码子/密码子相互作用的稳定性所必需的。

更新日期：2020-01-14

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