Structural basis for the recognition of sulfur in phosphorothioated DNA

Guang Liu, Wencheng Fu, Zhenyi Zhang, Yao He, Hao Yu, Yuli Wang, Xiaolei Wang, Yi Lei Zhao, Zixin Deng, Geng Wu*, Xinyi He

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

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 S 187 RGRR 191 loop inserts into the DNA major groove to make contacts with the bases of the G PS GCC 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.

Original languageEnglish (US)
Article number4689
JournalNature Communications
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2018

Bibliographical note

Funding Information:
Dr. Neil Price (NCAUR-USDA, Peoria, IL) undertook an initial review prior to publication. We thank Jianhua He, Wenming Qin, Lijie Wu, and other staff at the beamline BL17U1 at Shanghai Synchrotron Radiation Facility (SSRF) and the beamline BL19U1 at National Center for Protein Science Shanghai (NCPSS). This work was supported by grants from the National Natural Science Foundation of China (grant numbers 31670034, 31470223, 31670106, 31130068, 31770070, and 21661140002), and the Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning.

Publisher Copyright:
© 2018, The Author(s).

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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