During protein synthesis on ribosome, tRNA recognizes its cognate codon of mRNA through base-pairing with the anticodon. The 5′-end nucleotide of the anticodon is capable of wobble base-pairing, offering a molecular basis for codon degeneracy. The wobble nucleotide is often targeted for post-transcriptional modification, which affects the specificity and fidelity of the decoding process. Flipping-out of a wobble nucleotide in the anticodon loop has been proposed to be necessary for modifying enzymes to access the target nucleotide, which has been captured in selective structures of protein-bound complexes. Meanwhile, all other structures of free or ribosome-bound tRNA display anticodon bases arranged in stacked conformation. We report the X-ray crystal structure of unbound tRNA^Val1 to a 2.04 Å resolution showing two different conformational states of wobble uridine in the anticodon loop, one stacked on the neighboring base and the other swiveled out toward solvent. In addition, the structure reveals a rare magnesium ion coordination to the nitrogen atom of a nucleobase, which has been sampled very rarely among known structures of nucleic acids.

中文翻译：

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未结合的 tRNAVal 晶体结构中具有翻转的摆动核苷酸的独特反密码子环构象

在核糖体上的蛋白质合成过程中，tRNA 通过与反密码子的碱基配对识别其 mRNA 的同源密码子。反密码子的 5'-末端核苷酸能够摆动碱基配对，为密码子简并提供分子基础。摆动核苷酸通常作为转录后修饰的目标，这会影响解码过程的特异性和保真度。已经提出在反密码子环中翻转摆动核苷酸对于修饰酶以接近目标核苷酸是必要的，该目标核苷酸已被捕获在蛋白质结合复合物的选择性结构中。同时，游离或核糖体结合的 tRNA 的所有其他结构都显示以堆叠构象排列的反密码子碱基。^{我们报告了未结合的 tRNA Val1}的 X 射线晶体结构分辨率为 2.04 Å，显示反密码子环中摆动尿苷的两种不同构象状态，一种堆叠在相邻的碱基上，另一种向溶剂旋转。此外，该结构揭示了一种罕见的镁离子与核碱基的氮原子配位，这在已知的核酸结构中很少被采样。