Structure of a PLS-class Pentatricopeptide Repeat Protein Provides Insights into Mechanism of RNA Recognition
Structure of a PLS-class Pentatricopeptide Repeat Protein Provides Insights into Mechanism of RNA Recognition
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PLS 级五肽重复蛋白的结构揭示了 RNA 识别机制
DOI：
10.1074/jbc.m113.496828
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发表时间：
2013-11-01
影响因子：
4.8
通讯作者：
Xu, H. Eric
中科院分区：
文献类型：
--
作者：
Ban, Ting;Ke, Jiyuan;Xu, H. Eric
五肽重复序列（PPR）蛋白是序列特异性RNA结合蛋白，其形成在酵母、植物和人类中保守的蛋白质的普遍家族。植物PPR蛋白主要分为P和PLS类。在这里，我们报告的晶体结构的PLS类PPR蛋白从拟南芥THA 8L（THA 8样）在2.0埃。THA 8L类似于THA 8（类囊体组装体8），THA 8是参与叶绿体类囊体膜生物发生的基因的特定II组内含子的剪接所需的蛋白质。THA 8L结构包含三个P型PPR基序，两侧是一个L型基序和一个S型基序。我们确定了几个假定的THA 8L结合位点，富含嘌呤序列，在第二组内含子。重要的是，THA 8L对单链RNA的结合偏好强于单链DNA或双链RNA。结构分析表明，THA 8L含有两个广泛的补丁带正电荷的残基旁边的残基，建议包括RNA结合代码。这两个带正电的斑块中的突变大大降低了THA 8L RNA结合活性。在此基础上，我们构建了THA 8L-RNA结合的模型，该模型依赖于两种力：一种是核苷酸碱基与PPR基序中特定氨基酸（密码子）之间的相互作用，另一种是带负电荷的RNA骨架与带正电荷的PPR基序残基之间的相互作用。总之，这些结果进一步加深了我们对PPR蛋白-RNA相互作用机制的理解。
Pentatricopeptide repeat (PPR) proteins are sequence-specific RNA-binding proteins that form a pervasive family of proteins conserved in yeast, plants, and humans. The plant PPR proteins are grouped mainly into the P and PLS classes. Here, we report the crystal structure of a PLS-class PPR protein from Arabidopsis thaliana called THA8L (THA8-like) at 2.0 angstrom. THA8L resembles THA8 (thylakoid assembly 8), a protein that is required for the splicing of specific group II introns of genes involved in biogenesis of chloroplast thylakoid membranes. The THA8L structure contains three P-type PPR motifs flanked by one L-type motif and one S-type motif. We identified several putative THA8L-binding sites, enriched with purine sequences, in the group II introns. Importantly, THA8L has strong binding preference for single-stranded RNA over single-stranded DNA or double-stranded RNA. Structural analysis revealed that THA8L contains two extensive patches of positively charged residues next to the residues that are proposed to comprise the RNA-binding codes. Mutations in these two positively charged patches greatly reduced THA8L RNA-binding activity. On the basis of these data, we constructed a model of THA8L-RNA binding that is dependent on two forces: one is the interaction between nucleotide bases and specific amino acids in the PPR motifs (codes), and the other is the interaction between the negatively charged RNA backbone and positively charged residues of PPR motifs. Together, these results further our understanding of the mechanism of PPR protein-RNA interactions.