DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses
DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses
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DNA 主链相互作用影响 DNA 硫结合域的序列特异性：结构分析的启示
DOI：
10.1093/nar/gkaa574
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发表时间：
2020
影响因子：
14.9
通讯作者：
He Xinyi
中科院分区：
文献类型：
--
作者：
Yu Hao;Li Jiayi;Liu Guang;Zhao Gong;Wang Yuli;Hu Wenyue;Deng Zixin;Wu Geng;Gan Jianhua;Zhao Yi-Lei;He Xinyi
摘要硫代磷酸脱氧核糖核酸(PT-DNA)的硫原子被IV型限制性内切酶保守的硫结合结构域(SBD)表面空穴配位。然而，一些SBD在某些序列环境中不能识别硫原子。为了说明序列特异性的结构决定因素，我们从内切酶SprMcrA与GPSGCC、GPSATC和GPSAAC的DNA形成的复合体中解析了SBDSpr的结构。结构和计算分析解释了为什么它以递减的顺序与上述PT-DNA结合。SBDSpr-GPSGCC和SBDS co-GPSGCC的结构分析表明，SBDSpr-GPSGCC和SBDS co-GPSGCC只识别GPSGCC的DNA，硫配位空穴上方的正电荷环与邻近的DNA磷酸键发生静电相互作用。结构分析表明，DNA-蛋白质的氢键模式和弱的非键相互作用对SBD蛋白的序列特异性起着重要作用。环中带正电荷的氨基酸残基与带负电荷的残基的交换将使SBDSco能够扩大对更多PT-DNA序列的识别，这意味着可以设计IV型核酸内切酶来识别新的靶序列中的PT-DNA。
Abstract The sulfur atom of phosphorothioated DNA (PT-DNA) is coordinated by a surface cavity in the conserved sulfur-binding domain (SBD) of type IV restriction enzymes. However, some SBDs cannot recognize the sulfur atom in some sequence contexts. To illustrate the structural determinants for sequence specificity, we resolved the structure of SBDSpr, from endonuclease SprMcrA, in complex with DNA of GPSGCC, GPSATC and GPSAAC contexts. Structural and computational analyses explained why it binds the above PT-DNAs with an affinity in a decreasing order. The structural analysis of SBDSpr–GPSGCC and SBDSco–GPSGCC, the latter only recognizes DNA of GPSGCC, revealed that a positively charged loop above the sulfur-coordination cavity electrostatically interacts with the neighboring DNA phosphate linkage. The structural analysis indicated that the DNA–protein hydrogen bonding pattern and weak non-bonded interaction played important roles in sequence specificity of SBD protein. Exchanges of the positively-charged amino acid residues with the negatively-charged residues in the loop would enable SBDSco to extend recognization for more PT-DNA sequences, implying that type IV endonucleases can be engineered to recognize PT-DNA in novel target sequences.