A three-dimensional model of RNase P of the hyperthermophilic archaeon Pyrococcus horikoshii OT3
A three-dimensional model of RNase P of the hyperthermophilic archaeon Pyrococcus horikoshii OT3
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超嗜热古菌堀越火球菌 OT3 的 RNase P 三维模型
DOI：
10.1016/j.bbrc.2017.09.085
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
and M. Kimura
中科院分区：
文献类型：
--
作者：
X. Gao;K. Oshima;T. Ueda;T. Nakashima;and M. Kimura
核糖核酸酶P（RNase P）是一种核糖核酸内切酶，参与tRNA 5′-末端的成熟。我们以前发现，超嗜热古菌Pyrococcus horikoshiiOT 3中的RNase P由催化RNase P RNA（PhopRNA）和五种蛋白质辅因子PhoPop 5、PhoRpp 21、PhoRpp 29、PhoRpp 30和PhoRpp 38组成。这五种蛋白质的晶体结构已经确定，一个三维（3-D）模型ofPhopRNA已经构建，和生化数据，包括蛋白质-RNA相互作用的网站，已经成为可用的。在这里，结合这些信息来确定蛋白质的晶体结构相对于PhopRNA模型中RNA结合位点的方向。对PhopRNA模型进行了一些修改以提高拟合。在所得结构中，由PhoPop 5和PhoRpp 30组成的异源四聚体桥接PhopRNA C结构域中的螺旋P3和P16，从而可能稳定双链RNA结构PhoRpp 21和PhoRpp 29的异二聚体位于特异性结构域中连接螺旋P11和P12的单链环上（S-结构域）在PhopRNA，可能形成前体tRNA（前tRNA）结合位点的适当构象。第五种蛋白质PhoRpp 38结合PhopRNA中螺旋P12.1、P12.2和P16中的每个扭结-转角（K-turn）基序。与细菌RNase P的三维模型的结构的比较表明，从细菌RNase P的RNA-RNA相互作用的古细菌RNase P的蛋白质-RNA相互作用的过渡。提出的3-D模型ofP. horikoshiiRNase P将作为一个框架，为进一步的结构和功能的研究古细菌，以及真核生物，RNase Ps。
Ribonuclease P (RNase P) is an endoribonuclease involved in maturation of the 5′-end of tRNA. We found previously that RNase P in the hyperthermophilic archaeonPyrococcus horikoshiiOT3 consists of a catalytic RNase P RNA (PhopRNA) and five protein cofactors designatedPhoPop5,PhoRpp21,PhoRpp29,PhoRpp30, andPhoRpp38. The crystal structures of the five proteins have been determined, a three-dimensional (3-D) model ofPhopRNA has been constructed, and biochemical data, including protein-RNA interaction sites, have become available. Here, this information was combined to orient the crystallographic structures of the proteins relative to their RNA binding sites in thePhopRNA model. Some alterations were made to thePhopRNA model to improve the fit. In the resulting structure, a heterotetramer composed ofPhoPop5 andPhoRpp30 bridges helices P3 and P16 in thePhopRNA C-domain, thereby probably stabilizing a double-stranded RNA structure (helix P4) containing catalytic Mg2+ions, while a heterodimer ofPhoRpp21 andPhoRpp29 locates on a single-stranded loop connecting helices P11 and P12 in the specificity domain (S-domain) inPhopRNA, probably forming an appropriate conformation of the precursor tRNA (pre-tRNA) binding site. The fifth proteinPhoRpp38 binds each kink-turn (K-turn) motif in helices P12.1, P12.2, and P16 inPhopRNA. Comparison of the structure of the resulting 3-D model with that of bacterial RNase P suggests transition from RNA-RNA interactions in bacterial RNase P to protein-RNA interactions in archaeal RNase P. The proposed 3-D model ofP. horikoshiiRNase P will serve as a framework for further structural and functional studies on archaeal, as well as eukaryotic, RNase Ps.