id: Q88QV4
gene_symbol: pqqA
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida KT2440
status: COMPLETE
locus_tag: PP_0380
description: >-
  NCBI PGAP names WP_003243383.1 "pyrroloquinoline quinone precursor peptide
  PqqA" from the TIGR02107 equivalog HMM and passes on two GO terms; no EC
  number is predicted. The name and the process term, pyrroloquinoline quinone
  biosynthetic process, are correct and match the main review. The function
  term, catalytic activity (GO:0003824), is wrong: PqqA is a 23-residue
  ribosomally made peptide whose conserved glutamate and tyrosine are
  cross-linked by the radical SAM enzyme PqqE and then excised to become PQQ.
  It is the pathway's substrate, not one of its enzymes. The model's own product
  name calls the protein a precursor peptide, so the error lies in the GO
  mapping of TIGR02107 itself and reaches every genome whose PqqA it names; the
  domain model NF019654 for the same family carries only the process term.
references:
- id: PMID:33270901
  title: 'RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.'
- id: PMID:26961875
  title: Demonstration That the Radical S-Adenosylmethionine (SAM) Enzyme PqqE Catalyzes de Novo Carbon-Carbon
    Cross-linking within a Peptide Substrate PqqA in the Presence of the Peptide Chaperone PqqD.
- id: PMID:30811189
  title: Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone
    Biosynthetic Pathway.
- id: file:PSEPK/pqqA/pqqA-uniprot.txt
  title: UniProtKB entry for pqqA (Q88QV4)
- id: file:PSEPK/pqqA/pqqA-pgap-prediction-evidence/WP_003243383.1.gp
  title: RefSeq GenPept record WP_003243383.1
- id: file:PSEPK/pqqA/pqqA-pgap-prediction-evidence/pgap_models.yaml
  title: PGAP naming model and matched NCBI HMMs for pqqA
source_documents:
- genes/PSEPK/pqqA/pqqA-pgap-prediction-evidence/WP_003243383.1.gp
- genes/PSEPK/pqqA/pqqA-pgap-prediction-evidence/pgap_models.yaml
predictions:
- source_method: NCBI PGAP
  source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0003824
    label: catalytic activity
  predicted_term_type: GO_MF
  review:
    assessment: NPI
    confidence_score: 0
    error_type: CURATION_MISTAKE
    summary: >-
      Wrong. PqqA is the precursor peptide of PQQ: PqqE (with the chaperone
      PqqD) cross-links its conserved Glu and Tyr side chains, and PqqF/G,
      PqqB and PqqC process the excised product. PqqA is acted upon and
      catalyses nothing, and the main review describes it as a pathway
      substrate rather than an enzyme. The root-level term carries no
      information and is false here. It comes from the TIGR02107 model's GO
      list, which contradicts the model's own product name ("precursor
      peptide"), so the mistake is on the HMM and propagates to every genome.
    supported_by:
    - reference_id: PMID:26961875
      supporting_text: "The radical S -adenosylmethionine (SAM) protein PqqE is predicted to function in the pyrroloquinoline quinone (PQQ) biosynthetic pathway via catalysis of carbon-carbon bond formation between a glutamate and tyrosine side chain within the small peptide substrate PqqA."
    - reference_id: PMID:30811189
      supporting_text: "The first step is a C-C crosslinking reaction between the conserved Glu and Tyr residues within the peptide substrate PqqA"
    - reference_id: file:PSEPK/pqqA/pqqA-pgap-prediction-evidence/pgap_models.yaml
      supporting_text: "product_name: pyrroloquinoline quinone precursor peptide PqqA"
- source_method: NCBI PGAP
  source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0018189
    label: pyrroloquinoline quinone biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: CNN
    confidence_score: 2
    summary: >-
      Correct and already in GOA (UniRule IEA), accepted by the main review as
      PqqA's core role. PqqA supplies the Glu and Tyr atoms that become PQQ,
      the scaffold case in which a substrate does part of the work of the
      process.
    supported_by:
    - reference_id: PMID:26961875
      supporting_text: "The PQQ molecule derives from the evolutionarily conserved glutamate and tyrosine side chains within a ribosomally produced peptide substrate PqqA"
    - reference_id: file:PSEPK/pqqA/pqqA-uniprot.txt
      supporting_text: "FUNCTION: Required for coenzyme pyrroloquinoline quinone (PQQ)"