id: P06107
gene_symbol: lnuA
product_type: PROTEIN
aliases:
- linA
status: DRAFT
taxon:
  id: NCBITaxon:1283
  label: Staphylococcus haemolyticus
description: >-
  lnuA, historically named linA in Staphylococcus haemolyticus, encodes a
  lincosamide resistance enzyme. The enzyme family inactivates lincomycin and
  clindamycin by O-nucleotidylation/adenylation, producing lincosamide
  5'-adenylate derivatives. The fetched GOA file is empty for this accession,
  and GO lacks a lincosamide O-nucleotidyltransferase molecular-function term.
existing_annotations:
- term:
    id: GO:0046677
    label: response to antibiotic
  evidence_type: RCA
  original_reference_id: file:genes/STAHA/lnuA/lnuA-uniprot.txt
  qualifier: involved_in
  review:
    summary: NEW high-level process annotation for a lincosamide-resistance determinant.
    action: NEW
    reason: >-
      The GOA TSV is empty, but the UniProt flat file carries response to
      antibiotic and CARD identifies the entry as lnuA, an antibiotic
      inactivation determinant.
    additional_reference_ids:
    - PMID:3091456
    - PMID:2846528
    supported_by:
    - reference_id: file:genes/STAHA/lnuA/lnuA-uniprot.txt
      supporting_text: "DR   CARD; ARO:3002835; lnuA; ARO:0001004; antibiotic inactivation."
    - reference_id: PMID:3091456
      supporting_text: "confers resistance to lincomycin by inactivating it in Staphylococcus haemolyticus."
- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: RCA
  original_reference_id: PMID:2846528
  qualifier: enables
  review:
    summary: NEW broad molecular-function annotation for lincosamide O-nucleotidyltransferase activity.
    action: NEW
    reason: >-
      GO lacks a lincosamide O-nucleotidyltransferase term. The broad transferase
      parent is a defensible interim MF, but the proposed new term below is the
      biologically useful target.
    additional_reference_ids:
    - file:genes/STAHA/lnuA/lnuA-uniprot.txt
    - file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
    supported_by:
    - reference_id: PMID:2846528
      supporting_text: "Identification of lincosaminide O-nucleotidyltransferases"
    - reference_id: PMID:2846528
      supporting_text: "linA encoding the 3-lincomycin, 4-clindamycin O-nucleotidyltransferase"
references:
- id: file:genes/STAHA/lnuA/lnuA-uniprot.txt
  title: UniProt flat file for lnuA/linA (P06107)
  findings:
  - statement: UniProt/CARD identifies this entry as lnuA/linA, a lincosamide antibiotic-inactivation determinant.
    supporting_text: "DR   CARD; ARO:3002835; lnuA; ARO:0001004; antibiotic inactivation."
- id: PMID:3091456
  title: Nucleotide sequence of gene linA encoding resistance to lincosamides in Staphylococcus haemolyticus.
  findings:
  - statement: The original linA sequence paper supports the lincosamide resistance and inactivation phenotype.
    supporting_text: "which confers resistance to lincomycin by inactivating it in Staphylococcus haemolyticus."
- id: PMID:2846528
  title: Inactivation of lincosaminide antibiotics in Staphylococcus. Identification of lincosaminide O-nucleotidyltransferases and comparison of the corresponding resistance genes.
  findings:
  - statement: The biochemical follow-up identifies LinA-family lincosamide O-nucleotidyltransferase products.
    supporting_text: "inactivation of lincomycin gave rise to lincomycin 3-(5'-adenylate)"
- id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
  title: Curated ARO to GO mapping set for AMR gene families
  findings:
  - statement: The AMR mapping records Lnu/lincosamide nucleotidyltransferase as a GO molecular-function gap.
    supporting_text: "GO has no lincosamide (O-)nucleotidyltransferase MF term"
core_functions:
- description: >-
    Lincosamide O-nucleotidyltransferase activity that inactivates lincomycin
    and clindamycin by producing adenylated lincosamide derivatives.
  molecular_function:
    id: GO:0016740
    label: transferase activity
  directly_involved_in:
  - id: GO:0046677
    label: response to antibiotic
  supported_by:
  - reference_id: PMID:2846528
    supporting_text: "clindamycin was inactivated through its conversion to clindamycin 4-(5'-adenylate)."
  - reference_id: file:genes/STAHA/lnuA/lnuA-uniprot.txt
    supporting_text: "DE   RecName: Full=Lincosamide resistance protein;"
proposed_new_terms:
- proposed_name: lincosamide O-nucleotidyltransferase activity
  proposed_definition: >-
    Catalysis of the transfer of a nucleotidyl group from a nucleoside
    5'-triphosphate donor to a lincosamide antibiotic such as lincomycin or
    clindamycin, producing an O-nucleotidylated lincosamide with reduced
    antibiotic activity.
  justification: >-
    The Lnu/LinA mechanism is a direct antibiotic-inactivation activity, but GO
    currently lacks a lincosamide O-nucleotidyltransferase term. The AMR mapping
    records this as an explicit NoTermFound gap.
  proposed_parent:
    id: GO:0016740
    label: transferase activity
  proposed_mappings:
  - predicate: skos:exactMatch
    target_term:
      id: ARO:3000221
      label: lincosamide nucleotidyltransferase (LNU)
  supported_by:
  - reference_id: PMID:2846528
    supporting_text: "Identification of lincosaminide O-nucleotidyltransferases"
  - reference_id: file:projects/ANTIMICROBIAL_RESISTANCE/aro2go.sssom.yaml
    supporting_text: "GO has no lincosamide (O-)nucleotidyltransferase MF term"
suggested_questions:
- question: Should GO name this term lincosamide O-nucleotidyltransferase activity or lincosamide adenylyltransferase activity?
  experts: []
suggested_experiments:
- description: >-
    Reconstitute purified LnuA/LinA with lincomycin and clindamycin plus ATP,
    GTP, CTP, or UTP donors and quantify nucleotidylated products by NMR or LC-MS.
  experiment_type: in vitro enzyme assay