ArticleNucleic acids research2016
On the role of steric clashes in methylation control of restriction endonuclease activity.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Article
- Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE.Nature communications · 2022Article
- Molecular basis of the selective processing of short mRNA substrates by the DcpS mRNA decapping enzyme.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.Nucleic acids research · 2020Article
- Substrate recognition by a bifunctional GH30-7 xylanase B from Talaromyces cellulolyticus.FEBS open bio · 2020Article
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Authors and funding
3 authors.
Funding
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Abstract
Restriction-modification systems digest non-methylated invading DNA, while protecting host DNA against the endonuclease activity by methylation. It is widely believed that the methylated DNA would not 'fit' into the binding site of the endonuclease in the productive orientation, and thus steric clashes should account for most of the protection. We test this concept statistically by grafting methyl groups in silico onto non-methylated DNA in co-crystal structures with restriction endonucleases. Clash scores are significantly higher for protective than non-protective methylation (P < 0.05% according to the Wilcoxon rank sum test). Structural data alone are sufficient to distinguish between protective and non-protective DNA methylation with 90% confidence and decision thresholds of 1.1 Å and 48 Å(3) for the most severe distance-based and cumulative volume-based clash with the protein, respectively (0.1 Å was deducted from each interatomic distance to allow for coordinate errors). The most severe clashes are more pronounced for protective methyl groups attached to the nitrogen atoms (N6-methyladenines and N4-methylcytosines) than for C5-methyl groups on cytosines. Cumulative clashes are comparable for all three types of protective methylation.
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