identifier: traitmech:000512 label: ScoMcrA system definition: A type IV modification-dependent restriction system in which an organism possesses a ScoMcrA-family locus encoding a sulfur-binding-domain phosphorothioated-DNA restriction endonuclease. definition_source: DOI:10.1038/s41467-018-07093-1 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000496 synonyms: - synonym_text: ScoMcrA synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1371/journal.pgen.1001253 snippet: A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. notes: Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA. - reference: DOI:10.1371/journal.pgen.1001253 snippet: Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. notes: Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages. - reference: DOI:10.1371/journal.pgen.1001253 snippet: This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA. notes: Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity. - reference: DOI:10.1038/s41467-018-07093-1 snippet: Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. notes: Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain. - reference: DOI:10.1038/s41467-018-07093-1 snippet: We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. notes: Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity. - 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: '| ScoMcrA | 10\.1038/s41467-018-07093-1 | Structural basis for the recognition of sulfur in phosphorothioated DNA | ' notes: The pinned DefenseFinder article registry maps the ScoMcrA source key to the Liu et al. sulfur-recognition paper. causal_graphs: - graph_id: scomcra_restricts_phosphorothioated_dna title: ScoMcrA restricts phosphorothioated DNA description: Conservative system-level sketch linking a ScoMcrA-family locus to phosphorothioated-DNA restriction and to the Type IV restriction parent trait. scope_status: NONMECHANISTIC scope_notes: The graph captures ScoMcrA as a named Type IV modification-dependent restriction family while leaving natural host breadth, exact PT-DNA sequence-context specificity across characterized homologs, Dcm-methylated DNA target breadth, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved. nodes: - node_id: scomcra_family_locus label: ScoMcrA-family locus node_type: GENETIC_ELEMENT description: A locus encoding a ScoMcrA-family phosphorothioated-DNA restriction endonuclease. - node_id: scomcra_phosphorothioated_dna label: ScoMcrA-targeted phosphorothioated DNA node_type: ENVIRONMENTAL_FACTOR description: DNA containing phosphorothioate linkages in a ScoMcrA-family recognition context. - node_id: scomcra_phosphorothioated_dna_restriction label: ScoMcrA phosphorothioated-DNA restriction node_type: BIOLOGICAL_PROCESS description: Modification-dependent restriction of phosphorothioated DNA by a ScoMcrA-family endonuclease. - node_id: scomcra_system_trait label: ScoMcrA system node_type: TRAIT grounding: traitmech:000512 description: Possession of a genome-encoded ScoMcrA-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: scomcra_family_locus predicate: enables predicate_id: RO:0002327 object: scomcra_phosphorothioated_dna_restriction description: ScoMcrA-family loci encode PT-DNA readers that restrict phosphorothioated DNA. evidence: - reference: DOI:10.1371/journal.pgen.1001253 snippet: A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. notes: Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA. - reference: DOI:10.1038/s41467-018-07093-1 snippet: Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. notes: Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain. - reference: DOI:10.1038/s41467-018-07093-1 snippet: We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. notes: Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity. - subject: scomcra_phosphorothioated_dna_restriction predicate: mitigates predicate_id: METPO:2007407 object: scomcra_phosphorothioated_dna description: ScoMcrA-family restriction targets phosphorothioated DNA. evidence: - reference: DOI:10.1371/journal.pgen.1001253 snippet: A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. notes: Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA. - reference: DOI:10.1371/journal.pgen.1001253 snippet: Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. notes: Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages. - reference: DOI:10.1038/s41467-018-07093-1 snippet: We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. notes: Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity. - subject: scomcra_phosphorothioated_dna_restriction predicate: confers predicate_id: METPO:2007700 object: scomcra_system_trait description: ScoMcrA-family phosphorothioated-DNA restriction realizes the organism-level ScoMcrA system possession trait. evidence: - reference: DOI:10.1371/journal.pgen.1001253 snippet: This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA. notes: Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| ScoMcrA | 10\.1038/s41467-018-07093-1 | Structural basis for the recognition of sulfur in phosphorothioated DNA | ' notes: The pinned DefenseFinder article registry maps the ScoMcrA source key to the Liu et al. sulfur-recognition paper. - subject: scomcra_system_trait predicate: is a predicate_id: rdfs:subClassOf object: type_iv_modification_dependent_restriction description: ScoMcrA system possession is a Type IV modification-dependent restriction system trait. evidence: - reference: DOI:10.1371/journal.pgen.1001253 snippet: This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA. notes: Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity. - 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: scomcra-defensefinder-model-gap prompt: Resolve ScoMcrA-family breadth, phosphorothioated-DNA sequence-context specificity across natural hosts, methylated-DNA target breadth, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower ScoMcrA mechanism or component traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Liu et al. support ScoA3McrA as a Type IV McrA homolog that cleaves S-modified DNA in vitro and support ScoMcrA as a PT-dependent endonuclease with a sulfur-binding domain. The pinned DefenseFinder article registry maps ScoMcrA to the sulfur-recognition paper, but the pinned HMM inventory and rules table have no exact ScoMcrA rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of ScoMcrA-like systems across natural hosts, the complete set of natural phosphorothioated-DNA contexts, or the breadth of methylated-DNA target contexts. evidence: - reference: DOI:10.1371/journal.pgen.1001253 snippet: A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. notes: Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA. - reference: DOI:10.1371/journal.pgen.1001253 snippet: Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. notes: Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages. - reference: DOI:10.1371/journal.pgen.1001253 snippet: This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA. notes: Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity. - reference: DOI:10.1038/s41467-018-07093-1 snippet: Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. notes: Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain. - reference: DOI:10.1038/s41467-018-07093-1 snippet: We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. notes: Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| ScoMcrA | 10\.1038/s41467-018-07093-1 | Structural basis for the recognition of sulfur in phosphorothioated DNA | ' notes: The pinned DefenseFinder article registry maps the ScoMcrA source key to the Liu et al. sulfur-recognition 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 ScoMcrA 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 ScoMcrA system row. attaches_to: - causal_graphs#scomcra_restricts_phosphorothioated_dna posed_by: codex posed_date: '2026-10-01' curation_history: - timestamp: '2026-10-01T10:14:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted ScoMcrA 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_v389. llm_assisted: true - timestamp: '2026-10-01T10:14:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed ScoMcrA system during initial curation and left canonical_examples empty because Liu et al. support ScoA3McrA and sulfur-binding-domain homologs, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level ScoMcrA system trait. No paid research was used. llm_assisted: true