文献类型：期刊文献

英文题名：DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses

作者：Yu, Hao[1];Li, Jiayi[1];Liu, Guang[2];Zhao, Gong[1];Wang, Yuli[1];Hu, Wenyue[1];Deng, Zixin[1];Wu, Geng[1];Gan, Jianhua[3];Zhao, Yi-Lei[1];He, Xinyi[1]

机构：[1]Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, State Key Lab Microbial Metab, Joint Int Res Lab Metab & Dev Sci, 800 Dongchuan Rd, Shanghai 200240, Peoples R China;[2]East China Univ Sci & Technol, State Key Lab Bioreactor Engn, Shanghai 200237, Peoples R China;[3]Fudan Univ, Shanghai Publ Hlth Clin Ctr, Collaborat Innovat Ctr Genet & Dev, State Key Lab Genet Engn,Sch Life Sci,Dept Physio, Shanghai 200433, Peoples R China

年份：2020

卷号：48

期号：15

起止页码：8755

外文期刊名：NUCLEIC ACIDS RESEARCH

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000574315100043)】；

基金：National Natural Science Foundation of China [31770070, 31970041, 31670106, 31872627]; Chinese Postdoctoral Science Foundation [2019M661493]; National Key Research and Development Program of China [2018YFA0901900]. Funding for open access charge: National Natural Science Foundation of China [31770070]; Chinese Postdoctoral Science Foundation [2019M661493].

语种：英文

摘要：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 G(PS)GCC, G(PS)ATC and G(PS)AAC 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-G(PS)GCC, 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 negativelycharged 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.