Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38
Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38
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人类 RNase P 蛋白 Rpp38 的古菌同源物识别扭结转向基序的结构基础
DOI：
10.1016/j.bbrc.2016.04.118
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
and M. Yao
中科院分区：
文献类型：
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作者：
179.K. Oshima;Y. Kakiuchi;Y. Tanaka;T. Ueda;T. Nakashima;M. Kimura;and M. Yao
Horikoshii是人类核糖核酸酶P(RNaseP)蛋白Rpp38的同源物，它属于核糖体蛋白L7Ae家族，能特异性识别转折(K-Turn)基序。先前的生化研究表明，PhoRpp38特异性地结合到两个茎环SL12和SL16上，分别含有螺旋P12.1/12.2和P15/16，InP.HorikoshiiRNase P RNA(PhopRNA)。为了深入了解PhoRpp38与PhopRNA的结合模式，我们在3.4 GHz的分辨率下测定了PhoRpp38与SL12突变体(SL12M)的络合物的晶体结构。结构表明，PhoRpp38的β链(β1)上的Lys35和α螺旋(α2)上的Asn38、Glu39和Lys42与SL12M的特征G·A和A·G对相互作用，而位于PhoRpp38的α4和β4之间的环上的Ile93、Glu94和Val95与SL12M的3-核苷酸凸起(G-G-U)相互作用。该结构证明了先前提出的SL12的二级结构，包括螺旋P12.2。基于结构的突变分析表明，参与与SL12结合的氨基酸残基也是与SL16结合的原因。这一结果表明，每个PhoRpp38都与PhopRNA中SL12和SL16的K转弯结合。下拉分析进一步表明，SL12中存在第二个K转弯。在本研究结果的基础上，结合现有数据，我们讨论了PhopRpp38识别PhopRNA中K-转角基序的结构基础。
PhoRpp38 in the hyperthermophilic archaeonPyrococcus horikoshii, a homologue of human ribonuclease P (RNase P) protein Rpp38, belongs to the ribosomal protein L7Ae family that specifically recognizes a kink-turn (K-turn) motif. A previous biochemical study showed thatPhoRpp38 specifically binds to two stem-loops, SL12 and SL16, containing helices P12.1/12.2 and P15/16 respectively, inP. horikoshiiRNase P RNA (PhopRNA). In order to gain insight into thePhoRpp38 binding mode toPhopRNA, we determined the crystal structure ofPhoRpp38 in complex with the SL12 mutant (SL12M) at a resolution of 3.4 Å. The structure revealed that Lys35 on the β-strand (β1) and Asn38, Glu39, and Lys42 on the α-helix (α2) inPhoRpp38 interact with characteristic G•A and A•G pairs in SL12M, where Ile93, Glu94, and Val95, on a loop between α4 and β4 inPhoRpp38, interact with the 3-nucleotide bulge (G-G-U) in the SL12M. The structure demonstrates the previously proposed secondary structure of SL12, including helix P12.2. Structure-based mutational analysis indicated that amino acid residues involved in the binding to SL12 are also responsible for the binding to SL16. This result suggested that eachPhoRpp38 binds to the K-turns in SL12 and SL16 inPhopRNA. A pull-down assay further suggested the presence of a second K-turn in SL12. Based on the present results, together with available data, we discuss a structural basis for recognition of K-turn motifs inPhopRNA byPhoRpp38.