identifier: traitmech:000514 label: VcaM4I system definition: A type IV modification-dependent restriction system in which an organism possesses a VcaM4I-family locus encoding an EVE-HNH restriction endonuclease that recognizes 5-methylcytosine- or 5-hydroxymethylcytosine-modified DNA. definition_source: DOI:10.1093/nar/gkaa1218 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000496 synonyms: - synonym_text: VcaM4I synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1093/nar/gkaa1218 snippet: EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains. notes: Mierzejewska et al. support the EVE-HNH architecture of VcaM4I-family modification-dependent restriction endonucleases. - reference: DOI:10.1093/nar/gkaa1218 snippet: 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. notes: Mierzejewska et al. biochemically characterized VcaM4I and solved structures of apo and modified-DNA-bound enzyme. - reference: DOI:10.1093/nar/gkaa1218 snippet: The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments. notes: Mierzejewska et al. support VcaM4I EVE-domain recognition of 5mC/5hmC-containing DNA. - reference: DOI:10.1093/nar/gkaa1218 snippet: Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease. notes: Mierzejewska et al. support VcaM4I as a nuclease whose domain organization modulates toxic DNA cleavage. - reference: DOI:10.1093/nar/gkaa1218 snippet: 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. notes: Mierzejewska et al. support the VcaM4I EVE base-binding pocket and HNH catalytic residues by digestion and restriction assays. - reference: DOI:10.1093/nar/gkt747 snippet: The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. notes: Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VcaM4I | 10\.1093/nar/gkaa1218 | Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA | ' notes: The pinned DefenseFinder article registry maps the VcaM4I source key to the Mierzejewska et al. structural paper. causal_graphs: - graph_id: vcam4i_restricts_modified_cytosine_dna title: VcaM4I restricts modified-cytosine DNA description: Conservative system-level sketch linking a VcaM4I-family locus to EVE-HNH 5mC/5hmC-dependent DNA restriction and to the Type IV restriction parent trait. scope_status: NONMECHANISTIC scope_notes: The graph captures VcaM4I as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact modified-DNA sequence-context specificity across EVE-HNH homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved. nodes: - node_id: vcam4i_family_locus label: VcaM4I-family locus node_type: GENETIC_ELEMENT description: A locus encoding a VcaM4I-family EVE-HNH modification-dependent restriction endonuclease. - node_id: vcam4i_modified_cytosine_dna label: VcaM4I-targeted modified-cytosine DNA node_type: ENVIRONMENTAL_FACTOR description: DNA containing 5-methylcytosine or 5-hydroxymethylcytosine in a VcaM4I-family recognition context. - node_id: vcam4i_eve_hnh_restriction label: VcaM4I EVE-HNH DNA restriction node_type: BIOLOGICAL_PROCESS description: Modification-dependent restriction of 5mC/5hmC-modified DNA by a VcaM4I-family EVE-HNH endonuclease. - node_id: vcam4i_system_trait label: VcaM4I system node_type: TRAIT grounding: traitmech:000514 description: Possession of a genome-encoded VcaM4I-family modification-dependent restriction system. - node_id: type_iv_modification_dependent_restriction label: type IV modification-dependent restriction system node_type: TRAIT grounding: traitmech:000496 description: Possession of a genome-encoded Type IV modification-dependent restriction system. edges: - subject: vcam4i_family_locus predicate: enables predicate_id: RO:0002327 object: vcam4i_eve_hnh_restriction description: VcaM4I-family loci encode EVE-HNH endonucleases that restrict 5mC/5hmC-modified DNA. evidence: - reference: DOI:10.1093/nar/gkaa1218 snippet: EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains. notes: Mierzejewska et al. support the EVE-HNH architecture of VcaM4I-family modification-dependent restriction endonucleases. - reference: DOI:10.1093/nar/gkaa1218 snippet: 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. notes: Mierzejewska et al. biochemically characterized VcaM4I and solved structures of apo and modified-DNA-bound enzyme. - subject: vcam4i_eve_hnh_restriction predicate: mitigates predicate_id: METPO:2007407 object: vcam4i_modified_cytosine_dna description: VcaM4I-family EVE-HNH restriction targets 5mC- or 5hmC-modified DNA. evidence: - reference: DOI:10.1093/nar/gkaa1218 snippet: The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments. notes: Mierzejewska et al. support VcaM4I EVE-domain recognition of 5mC/5hmC-containing DNA. - reference: DOI:10.1093/nar/gkaa1218 snippet: 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. notes: Mierzejewska et al. support the VcaM4I EVE base-binding pocket and HNH catalytic residues by digestion and restriction assays. - subject: vcam4i_eve_hnh_restriction predicate: confers predicate_id: METPO:2007700 object: vcam4i_system_trait description: VcaM4I-family EVE-HNH DNA restriction realizes the organism-level VcaM4I system possession trait. evidence: - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VcaM4I | 10\.1093/nar/gkaa1218 | Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA | ' notes: The pinned DefenseFinder article registry maps the VcaM4I source key to the Mierzejewska et al. structural paper. - subject: vcam4i_system_trait predicate: is a predicate_id: rdfs:subClassOf object: type_iv_modification_dependent_restriction description: VcaM4I system possession is a Type IV modification-dependent restriction system trait. evidence: - reference: DOI:10.1093/nar/gkaa1218 snippet: Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease. notes: Mierzejewska et al. support VcaM4I as a nuclease whose domain organization modulates toxic DNA cleavage. - reference: DOI:10.1093/nar/gkt747 snippet: The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. notes: Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes. discussions: - discussion_id: vcam4i-defensefinder-model-gap prompt: Resolve VcaM4I-family breadth, modified-cytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower VcaM4I mechanism or component traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Mierzejewska et al. support VcaM4I as an EVE-HNH modification-dependent restriction endonuclease that recognizes 5mC/5hmC DNA and validate EVE-domain modified-base binding plus HNH catalytic residues by digestion and restriction assays. The pinned DefenseFinder article registry maps VcaM4I to that paper, but the pinned HMM inventory and rules table have no exact VcaM4I rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of VcaM4I-like systems across natural hosts, or the complete set of natural modified-cytosine sequence contexts. evidence: - reference: DOI:10.1093/nar/gkaa1218 snippet: EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains. notes: Mierzejewska et al. support the EVE-HNH architecture of VcaM4I-family modification-dependent restriction endonucleases. - reference: DOI:10.1093/nar/gkaa1218 snippet: 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. notes: Mierzejewska et al. biochemically characterized VcaM4I and solved structures of apo and modified-DNA-bound enzyme. - reference: DOI:10.1093/nar/gkaa1218 snippet: The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments. notes: Mierzejewska et al. support VcaM4I EVE-domain recognition of 5mC/5hmC-containing DNA. - reference: DOI:10.1093/nar/gkaa1218 snippet: 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. notes: Mierzejewska et al. support the VcaM4I EVE base-binding pocket and HNH catalytic residues by digestion and restriction assays. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| VcaM4I | 10\.1093/nar/gkaa1218 | Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA | ' notes: The pinned DefenseFinder article registry maps the VcaM4I source key to the Mierzejewska et al. structural paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md notes: A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact VcaM4I row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: A structured first-pass search of the pinned DefenseFinder rules table found no exact VcaM4I system row. attaches_to: - causal_graphs#vcam4i_restricts_modified_cytosine_dna posed_by: codex posed_date: '2026-10-01' curation_history: - timestamp: '2026-10-01T11:48:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted VcaM4I system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v391. llm_assisted: true - timestamp: '2026-10-01T11:48:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed VcaM4I system during initial curation and left canonical_examples empty because Mierzejewska et al. support the purified VcaM4I enzyme, structures, and restriction assays, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level VcaM4I system trait. No paid research was used. llm_assisted: true