ArticleNucleic acids research2020
DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences.Nature microbiology · 2026Article
- Harnessing sulfur-binding domains to separate Sp and Rp isomers of phosphorothioate oligonucleotides.Applied microbiology and biotechnology · 2024Article
- Characterization of a promiscuous DNA sulfur binding domain and application in site-directed RNA base editing.Nucleic acids research · 2023Article
- A rapid nucleic acid detection platform based on phosphorothioate-DNA and sulfur binding domain.Synthetic and systems biotechnology · 2023Article
- High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution.PLoS genetics · 2022Article
- Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Phosphorothioate-DNA bacterial diet reduces the ROS levels in C. elegans while improving locomotion and longevity.Communications biology · 2021Article
- Characterization of BisI Homologs.Frontiers in microbiology · 2021Article
- Protein Domain Guided Screen for Sequence Specific and Phosphorothioate-Dependent Restriction Endonucleases.Frontiers in microbiology · 2020Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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