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Structural basis for the recognition of sulfur in phosphorothioated DNA

Author

Listed:
  • Guang Liu

    (Shanghai Jiao Tong University
    East China University of Science and Technology)

  • Wencheng Fu

    (Shanghai Jiao Tong University)

  • Zhenyi Zhang

    (Shanghai Jiao Tong University)

  • Yao He

    (King Abdullah University of Science and Technology)

  • Hao Yu

    (Shanghai Jiao Tong University)

  • Yuli Wang

    (Shanghai Jiao Tong University)

  • Xiaolei Wang

    (Shanghai Jiao Tong University)

  • Yi-Lei Zhao

    (Shanghai Jiao Tong University)

  • Zixin Deng

    (Shanghai Jiao Tong University)

  • Geng Wu

    (Shanghai Jiao Tong University)

  • Xinyi He

    (Shanghai Jiao Tong University)

Abstract

There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The S187RGRR191 loop inserts into the DNA major groove to make contacts with the bases of the GPSGCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.

Suggested Citation

  • Guang Liu & Wencheng Fu & Zhenyi Zhang & Yao He & Hao Yu & Yuli Wang & Xiaolei Wang & Yi-Lei Zhao & Zixin Deng & Geng Wu & Xinyi He, 2018. "Structural basis for the recognition of sulfur in phosphorothioated DNA," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07093-1
    DOI: 10.1038/s41467-018-07093-1
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    Cited by:

    1. Haiyan Gao & Xinqi Gong & Jinchuan Zhou & Yubing Zhang & Jinsong Duan & Yue Wei & Liuqing Chen & Zixin Deng & Jiawei Wang & Shi Chen & Geng Wu & Lianrong Wang, 2022. "Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

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