ArticleNucleic acids research2014
Structural basis of the methylation specificity of R.DpnI.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Development of the Efficient Electroporation Protocol forInternational journal of molecular sciences · 2025Article
- Structural analysis of the BisI family of modification dependent restriction endonucleases.Nucleic acids research · 2024Article
- Characterization of winged helix domain fusion endonucleases as N6-methyladenine-dependent type IV restriction systems.Frontiers in microbiology · 2024Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications.Advances in experimental medicine and biology · 2022Article
- Characterization of BisI Homologs.Frontiers in microbiology · 2021Article
- Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å.Nucleic acids research · 2020Article
- Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.PLoS computational biology · 2020Article
- Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.Nucleic acids research · 2018Article
- UbaLAI is a monomeric Type IIE restriction enzyme.Nucleic acids research · 2017Article
- Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations.Journal of molecular modeling · 2017Article
- Characterization of eukaryotic DNA N(6)-methyladenine by a highly sensitive restriction enzyme-assisted sequencing.Nature communications · 2016Article
- On the role of steric clashes in methylation control of restriction endonuclease activity.Nucleic acids research · 2016Article
- DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications.Advances in experimental medicine and biology · 2016Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support 'crosstalk' between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.
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