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ScoMcrA system

traitmech:000512 · CLASS · PROPOSED

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.

Trait evidence (7)

  • DOI:10.1371/journal.pgen.1001253
    A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites.

    Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA.

  • DOI:10.1371/journal.pgen.1001253
    Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links.

    Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages.

  • DOI:10.1371/journal.pgen.1001253
    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.

    Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity.

  • DOI:10.1038/s41467-018-07093-1
    Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA.

    Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain.

  • DOI:10.1038/s41467-018-07093-1
    We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo.

    Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity.

  • DOI:10.1093/nar/gkt747
    The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III.

    Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | ScoMcrA | 10\.1038/s41467-018-07093-1 | Structural basis for the recognition of sulfur in phosphorothioated DNA |

    The pinned DefenseFinder article registry maps the ScoMcrA source key to the Liu et al. sulfur-recognition paper.

ScoMcrA restricts phosphorothioated DNA

Conservative system-level sketch linking a ScoMcrA-family locus to phosphorothioated-DNA restriction and to the Type IV restriction parent trait.

NONMECHANISTIC · 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.

ScoMcrA restricts phosphorothioated DNA Interactive directed graph showing evidence-backed causal relationships for ScoMcrA system.

Edge evidence

  • ScoMcrA-family locus enables ScoMcrA phosphorothioated-DNA restriction RO:0002327

    ScoMcrA-family loci encode PT-DNA readers that restrict phosphorothioated DNA.

    • DOI:10.1371/journal.pgen.1001253 A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA.
    • DOI:10.1038/s41467-018-07093-1 Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. Liu et al. support ScoMcrA as a phosphorothioated-DNA-dependent restriction endonuclease with a sulfur-binding domain.
    • DOI:10.1038/s41467-018-07093-1 We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity.
  • ScoMcrA phosphorothioated-DNA restriction mitigates ScoMcrA-targeted phosphorothioated DNA METPO:2007407

    ScoMcrA-family restriction targets phosphorothioated DNA.

    • DOI:10.1371/journal.pgen.1001253 A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Liu et al. support ScoA3McrA cleavage of phosphorothioated DNA and Dcm-methylated DNA.
    • DOI:10.1371/journal.pgen.1001253 Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. Liu et al. support double-strand ScoA3McrA cleavage near DNA phosphorothioate linkages.
    • DOI:10.1038/s41467-018-07093-1 We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. Liu et al. support SBD homologs as phosphorothioated-DNA readers with in vivo PT-DNA restriction activity.
  • ScoMcrA phosphorothioated-DNA restriction confers ScoMcrA system METPO:2007700

    ScoMcrA-family phosphorothioated-DNA restriction realizes the organism-level ScoMcrA system possession trait.

  • ScoMcrA system is a type IV modification-dependent restriction system rdfs:subClassOf

    ScoMcrA system possession is a Type IV modification-dependent restriction system trait.

    • DOI:10.1371/journal.pgen.1001253 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. Liu et al. frame ScoA3McrA as a McrA homolog with phosphorothioated-DNA-specific cleavage activity.
    • DOI:10.1093/nar/gkt747 The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/s41467-018-07093-1

Parent traits (1)

Synonyms (1)

  • ScoMcrA RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

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.

KNOWLEDGE GAP OPEN scomcra-defensefinder-model-gap · raised by codex · 2026-10-01

Attached to causal_graphs#scomcra_restricts_phosphorothioated_dna

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

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    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.