CRYSTALLOGRAPHIC REFINEMENT OF YEAST ASPARTIC-ACID TRANSFER-RNA
CRYSTALLOGRAPHIC REFINEMENT OF YEAST ASPARTIC-ACID TRANSFER-RNA
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DOI：
10.1016/0022-2836(85)90048-8
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发表时间：
1985-01-01
影响因子：
5.6
通讯作者：
MORAS, D
中科院分区：
文献类型：
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作者：
WESTHOF, E;DUMAS, P;MORAS, D
酵母tRNA天冬氨酸tRNAAsp的结构被精炼为1晶体形式至3.ANG。使用 Hendrickson 和 Konnert 的约束最小二乘法进行分辨率计算，并使用 Jones 的 FRODO 程序进行实空间拟合。对于 4585 次反射，最终晶体学差异指数 R 为 23.5%，其幅度为 10 至 3 ANG 之间标准偏差的两倍。由于 D 环、磷酸 U1 和碱基 U33 的某些残基的占用率较低，R 因子为 22.3%。描述了核酸约束最小二乘程序的适应和细化的进展。根据立体化学和主链折叠来分析构象。将二级结构的接触和氢键与酵母 tRNAPhe 的接触和氢键进行了比较。可变环中仅存在 4 个碱基，而不是酵母 tRNAPhe 中的 5 个碱基，导致残基 48 的旋转和残基 46 的横向移动。这 2 个重排导致 [U8...A14]...A21 以及 A9 和 G45 的不同环境。另外，在酵母 tRNAPhe 中观察到的所有三级接触都存在于酵母 tRNAAsp 中，除了 D 环的 G18 和 T 环的 (C56) 之间不存在氢键。反密码子三联体配对的存在导致温度因子的分布与在酵母 tRNAPhe 中观察到的温度因子分布不同，其中 AC 茎环稳定，而 T 环和 D 环不稳定。 T 环和 D 环之间的相互作用是对称相关分子的反密码子三联体通过氢键相互作用的结果，这模拟了 mRNA 上反密码子与其同源密码子之间的相互作用。
The structure of yeast tRNA aspartic acid tRNAAsp was refined in 1 crystal form to 3 .ANG. resolution using the restrained least-squares method of Hendrickson and Konnert and real-space fitting using the FRODO program of Jones. The final crystallographic discrepancy index R is 23.5% for 4585 reflections with magnitudes twice their standard deviations between 10 and 3 .ANG.. With lower occupancies for some residues of the D-loop, the phosphate U1, and the base U33, the R-factor is 22.3%. The adaptation of the restrained least-squares program for nucleic acids and the progress of the refinement are described. The conformations are analyzed with respect to stereochemistry and folding of the backbone. The contacts and hydrogen bonds of the secondary structure are compared with those of yeast tRNAPhe. The presence of only 4 bases in the variable loop, instead of 5 as in yeast tRNAPhe, leads to a rotation of residue 48 and a lateral movement of residue 46. These 2 rearrangements induce different environments for [U8...A14]...A21 and for A9 and G45. Otherwise, all tertiary contacts observed in yeast tRNAPhe are present in yeast tRNAAsp, except for the absence of hydrogen-bonding between G18 of the D-loop and (C56 of the T-loop. The presence of anticodon triplet pairing leads to a distribution of temperature factors different from that observed in yeast tRNAPhe with a stabilization of the AC stem-and-loop and a destabilization of the T and D-loops. It is suggested that the labilization of the interactions between the T and D-loops is a consequence of the interaction of the anticodon triplets of symmetry-related molecules through hydrogen bonding, which mimics the interaction between the anticodon and its cognate codon on the mRNA.