Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator
Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator
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DOI：
10.1021/acs.biochem.7b00123
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发表时间：
2017-05-30
期刊：
影响因子：
2.9
通讯作者：
Nikonowicz, Edward P.
中科院分区：
文献类型：
--
作者：
Chang, Andrew T.;Tran, Michelle;Nikonowicz, Edward P.
提出了含有噬菌体GA外壳蛋白的RNA操纵子结合位点的RNA发夹的三维结构。噬菌体GA操纵子含有不对称（A-A）-U序列基序，并由四腺嘌呤（四-A）环加帽。（A-A）-U基序的尿苷优先与5 '-近端交叉链腺嘌呤配对，3'-近端腺嘌呤堆叠成螺旋。四-A环是有序的，腺嘌呤残基2-4形成3'堆叠。这种环构象与相关噬菌体MS 2操纵子的5 ′-AUUA环的结构形成对比，在该结构中残基1和2形成5 ′堆叠。使用来自蛋白质数据库的76个独特出现的结构来检查（A-A）-U序列基序构象的上下文依赖性。基序几乎总是有一个腺嘌呤凸出，另一个腺嘌呤采用A-U碱基对。在（A-A）-U基序侧接仅一个沃森-克里克碱基对的情况下，邻近侧翼碱基对的腺嘌呤倾向于凸出; 80%的具有3'侧翼对的基序具有3'凸出腺嘌呤，84%的具有5'侧翼对的基序具有5'凸出腺嘌呤。当（A-A）-U基序两侧都有碱基对时，3 '-和5'-近端腺嘌呤凸出的频率分别为33%和67%。尽管3'侧翼胞苷与5'-近端腺嘌呤的凸出相关（88%），但对于5'侧没有鉴定出对侧翼核苷酸同一性的严格依赖性。
The three-dimensional structure of a RNA hairpin containing the RNA operator binding site for bacteriophage GA coat protein is presented. The phage GA operator contains the asymmetric (A-A)-U sequence motif and is capped by a four-adenine (tetra-A) loop. The uridine of the (A-A)-U motif preferentially pairs with the 5'-proximal cross-strand adenine, and the 3'-proximal adenine stacks into the helix. The tetra-A loop is well-ordered with adenine residues 2-4 forming a 3' stack. This loop conformation stands in contrast to the structure of the 5'-AUUA loop of the related phage MS2 operator in which residues 1 and 2 form a 5' stack. The context dependence of the (A-A)-U sequence motif conformation was examined using structures of 76 unique occurrences from the Protein Data Bank. The motif almost always has one adenine bulged and the other adenine adopting an A-U base pair. In the case in which the (A-A)-U motif is flanked by only one Watson-Crick base pair, the adenine adjacent to the flanking base pair tends to bulge; 80% of motifs with a 3' flanking pair have a 3' bulged adenine, and 84% of motifs with a 5' flanking pair have a 5' bulged adenine. The frequencies of 3'- and 5'-proximal adenines bulging are 33 and 67%, respectively, when the (A-A)-U motif is flanked by base pairs on both sides. Although a 3' flanking cytidine correlates (88%) with bulging of the 5'-proximal adenine, no strict dependence on flanking nucleotide identity was identified for the 5' side.