ArticleNucleic acids research2021
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 14 citations in OpenAlex.
- END nucleases are antiphage defence systems targeting multiple phages with modified genomes.Nature microbiology · 2026Article
- A bacterial defense system targeting modified cytosine of phage genomic DNA.Nature communications · 2026Article
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Argonaute-HNH filaments triggered by invader DNA confer bacterial immunity.Nature communications · 2025Article
- Unveiling the multifaceted domain polymorphism of the Menshen antiphage system.Nucleic acids research · 2025Article
- Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains.Molecular cell · 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
- Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains.bioRxiv : the preprint server for biology · 2023Article
- A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease.Nucleic acids research · 2022Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many modification-dependent restriction endonucleases (MDREs) are fusions of a PUA superfamily modification sensor domain and a nuclease catalytic domain. EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains. Here, we present a biochemical characterization of the EVE-HNH endonuclease VcaM4I and crystal structures of the protein alone, with EVE domain bound to either 5mC modified dsDNA or to 5mC/5hmC containing ssDNA. The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments. It flips the modified nucleotide, to accommodate it in a hydrophobic pocket of the enzyme, primarily formed by P24, W82 and Y130 residues. In the crystallized conformation, the EVE domain and linker helix between the two domains block DNA binding to the catalytic domain. Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease. The role of the key residues in the EVE and HNH domains of VcaM4I is confirmed by digestion and restriction assays with the enzyme variants that differ from the wild-type by changes to the base binding pocket or to the catalytic residues.
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