id: A0A223HCL9
gene_symbol: mcr-3
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:651
  label: Aeromonas media
description: mcr-3 encodes a membrane-associated phosphoethanolamine transferase in Aeromonas media. UniProt/CARD identify this entry as an MCR-family polymyxin resistance determinant. The expected core activity is transfer of phosphoethanolamine from phosphatidylethanolamine to lipid A, which lowers polymyxin/colistin binding and confers antibiotic resistance. UniProt names the protein 'Phosphoethanolamine--lipid A transferase MCR-3.7' (accession A0A223HCL9).
existing_annotations:
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: The cellular location is compatible with the encoded AMR enzyme and is retained.
    action: ACCEPT
    reason: The location is consistent with the protein type and existing UniProt/GOA evidence.
- term:
    id: GO:0009244
    label: lipopolysaccharide core region biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: involved_in
  review:
    summary: This over-propagates lipid A phosphoethanolamine transfer into LPS core-region biosynthesis.
    action: MARK_AS_OVER_ANNOTATED
    reason: MCR proteins modify lipid A to confer polymyxin resistance; they are not core LPS oligosaccharide biosynthetic enzymes.
    supported_by:
    - reference_id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
      supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: located_in
  review:
    summary: Correct but broad membrane location; the more informative location for this determinant is plasma membrane.
    action: MODIFY
    reason: Use plasma membrane rather than the generic membrane term where possible.
    proposed_replacement_terms:
    - id: GO:0005886
      label: plasma membrane
    supported_by:
    - reference_id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
      supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
- term:
    id: GO:0016772
    label: transferase activity, transferring phosphorus-containing groups
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: The existing MF term is directionally correct but less informative than the family-specific AMR activity phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity.
    action: MODIFY
    reason: Replace the broad or over-specific electronic term 'transferase activity, transferring phosphorus-containing groups' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.
    proposed_replacement_terms:
    - id: GO:0043838
      label: phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity
    supported_by:
    - reference_id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
      supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
- term:
    id: GO:0016776
    label: phosphotransferase activity, phosphate group as acceptor
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: enables
  review:
    summary: The existing MF term is directionally correct but less informative than the family-specific AMR activity phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity.
    action: MODIFY
    reason: Replace the broad or over-specific electronic term 'phosphotransferase activity, phosphate group as acceptor' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.
    proposed_replacement_terms:
    - id: GO:0043838
      label: phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity
    supported_by:
    - reference_id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
      supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
- term:
    id: GO:0043838
    label: phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity
  evidence_type: RCA
  original_reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  qualifier: enables
  review:
    summary: 'NEW candidate annotation from the curated ARO->GO mapping: phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity.'
    action: NEW
    reason: The UniProt record cross-references a CARD/ARO AMR determinant, and the curated ARO->GO mapping projects the family-specific molecular function phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity. This focused draft accepts the candidate as a curator lead for this AMR determinant.
    additional_reference_ids:
    - file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv
    - file:genes/AERME/mcr-3/mcr-3-uniprot.txt
    supported_by:
    - reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv
      supporting_text: "A0A223HCL9\tARO:3004510\tARO:3004112\tnarrower\tRO:0002327\tGO:0043838\tphosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity"
    - reference_id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
      supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
- term:
    id: GO:0046677
    label: response to antibiotic
  evidence_type: RCA
  original_reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  qualifier: involved_in
  review:
    summary: 'NEW process annotation: mcr-3 is an AMR determinant involved in antibiotic response/resistance.'
    action: NEW
    reason: CARD/ARO identity places this gene in an antimicrobial-resistance determinant family; response to antibiotic is the appropriate high-level GO biological process for the resistance role.
    additional_reference_ids:
    - file:genes/AERME/mcr-3/mcr-3-uniprot.txt
    supported_by:
    - reference_id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
      supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
  title: UniProt flat file for mcr-3 (A0A223HCL9)
  findings:
  - statement: UniProt/CARD identity and protein naming for mcr-3.
    supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
- id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  title: Curated ARO to GO mapping set for AMR gene families
  findings:
  - statement: Manual ARO-to-GO mappings used to identify focused AMR annotation gains.
    supporting_text: 'mapping_set_title: ARO to GO mapping (AMR gene families and resistance mechanisms)'
- id: file:projects/ANTIMICROBIAL_RESISTANCE/data/candidate_new_annotations.tsv
  title: Annotation-gain candidates from ARO to GO mappings
  findings:
  - statement: Candidate GO annotations projected from the ARO-to-GO mapping set.
    supporting_text: Candidate GO annotations that UniProtKB entries with a CARD cross-reference would gain from the
core_functions:
- description: mcr-3 modifies lipid A with phosphoethanolamine in the bacterial membrane, a target-modification mechanism that reduces polymyxin/colistin susceptibility.
  molecular_function:
    id: GO:0043838
    label: phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity
  directly_involved_in:
  - id: GO:0046677
    label: response to antibiotic
  supported_by:
  - reference_id: file:genes/AERME/mcr-3/mcr-3-uniprot.txt
    supporting_text: DR   CARD; ARO:3004510; MCR-3.7; ARO:0001001; antibiotic target alteration.
  locations:
  - id: GO:0005886
    label: plasma membrane
suggested_questions:
- question: Is the ARO-derived phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity annotation sufficiently specific for mcr-3, or is a narrower substrate/site-specific GO term warranted?
  experts: []
suggested_experiments:
- description: Biochemically assay purified mcr-3 against representative antibiotic substrates for the inferred AMR family and measure loss of drug activity or target modification.
  experiment_type: in vitro enzyme assay