id: A0A8C2TBA7
gene_symbol: PAM
taxon:
  id: NCBITaxon:93934
  label: Coturnix japonica
status: COMPLETE
description: >-
  The bifunctional PAM architecture supports PAL catalysis and ascorbate interaction through the PHM module.
  PAL activity is already annotated; ascorbate binding is an additional supported molecular function.
source_documents:
  - genes/COTJA/A0A8C2TBA7/A0A8C2TBA7-uniprot.txt
  - genes/COTJA/A0A8C2TBA7/A0A8C2TBA7-goa.tsv
  - publications/PMID_19604476.md
  - publications/PMID_35380039.md
predictions:
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0004598
      label: peptidylamidoglycolate lyase activity
    predicted_term_type: GO_MF
    review:
      assessment: CNN
      confidence_score: 2
      summary: >-
        The target is assigned to the peptidylglycine alpha-amidating monooxygenase family and contains
        the PHM/PAL architecture. Structural and substrate-complex experiments on rat PAL establish cleavage
        of peptidyl-alpha-hydroxyglycine to an amidated peptide and glyoxylate (PMID:19604476), supporting
        transfer of this conserved reaction to avian PAM. The exact peptidylamidoglycolate lyase activity
        is already present in cached UniProt and GOA. Domain and reaction evidence support correctness
        independently of the existing electronic annotation.
      supported_by:
        - reference_id: file:COTJA/A0A8C2TBA7/A0A8C2TBA7-uniprot.txt
          supporting_text: >-
            ID   A0A8C2TBA7_COTJA        Unreviewed;       846 AA. ... DR   GO; GO:0004598; F:peptidylamidoglycolate
            lyase activity; IEA:UniProtKB-EC. ... DR   InterPro; IPR000323; Cu2_ascorb_mOase_N. ... DR   InterPro;
            IPR024548; Cu2_monoox_C. ... DR   InterPro; IPR000720; PHM/PAL. ... FT   SIGNAL          1..21
            ... FT   TRANSMEM        734..758 ... FT   DOMAIN          61..172 ... FT                   /note="Copper
            type II ascorbate-dependent monooxygenase N- ... FT   DOMAIN          197..342 ... FT                   /note="Copper
            type II ascorbate-dependent monooxygenase C-
        - reference_id: PMID:19604476
          supporting_text: >-
            The structures show that PAL folds as a six-bladed beta-propeller
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0031418
      label: L-ascorbic acid binding
    predicted_term_type: GO_MF
    review:
      assessment: COR
      confidence_score: 2
      summary: >-
        The target contains the conserved PHM copper-monooxygenase module of bifunctional PAM. Pre-steady-state
        experiments on PHM support ascorbate interaction during reduction and conformational activation
        (PMID:35380039), providing a biochemical basis for transfer of ascorbate binding to this avian
        homolog. This concerns the PHM module rather than PAL catalysis and does not specify an unverified
        binding-site geometry. Ascorbate binding itself is absent from the cached annotations.
      supported_by:
        - reference_id: file:COTJA/A0A8C2TBA7/A0A8C2TBA7-uniprot.txt
          supporting_text: >-
            ID   A0A8C2TBA7_COTJA        Unreviewed;       846 AA. ... DR   InterPro; IPR000323; Cu2_ascorb_mOase_N.
            ... DR   InterPro; IPR024548; Cu2_monoox_C. ... DR   InterPro; IPR000720; PHM/PAL. ... FT   SIGNAL          1..21
            ... FT   TRANSMEM        734..758 ... FT   DOMAIN          61..172 ... FT                   /note="Copper
            type II ascorbate-dependent monooxygenase N- ... FT   DOMAIN          197..342 ... FT                   /note="Copper
            type II ascorbate-dependent monooxygenase C-
        - reference_id: PMID:35380039
          supporting_text: >-
            ascorbate binds to the enzyme to accomplish reduction
references:
  - id: file:COTJA/A0A8C2TBA7/A0A8C2TBA7-uniprot.txt
    title: A0A8C2TBA7-uniprot.txt
  - id: PMID:19604476
    title: 'Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme.'
  - id: PMID:35380039
    title: Pre-Steady-State Reactivity of Peptidylglycine Monooxygenase Implicates Ascorbate in
      Substrate Triggering of the Active Conformer.