title: On the role of steric clashes in methylation control of restriction endonuclease activity.
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.
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Karolina
authors.initials: K
authors.lastname: Mierzejewska
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland honorata@iimcb.gov.pl.
authors.forename: Matthias
authors.initials: M
authors.lastname: Bochtler
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland honorata@iimcb.gov.pl.
authors.forename: Honorata
authors.initials: H
authors.lastname: Czapinska
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000737:chemistry* / Q000378:metabolism; D066264:Datasets as Topic; D004789:Enzyme Activation; D008968:Molecular Conformation; D013379:Substrate Specificity
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes