Saro_2809

id: Q2G4H8
gene_symbol: Saro_2809
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:279238
  label: Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034
    / CIP 105152 / NBRC 16084 / F199)
description: >-
  Saro_2809 encodes NOV2, the second stilbene cleavage oxygenase (SCO) of Novosphingobium
  aromaticivorans and a paralog of NOV1 (Saro_0802). It is a non-heme Fe(II) enzyme of the carotenoid
  cleavage oxygenase (CCO/RPE65) superfamily that oxidatively cleaves the interphenyl Calpha-Cbeta
  double bond of stilbenoids; NOV2 was characterized biochemically and spectroscopically alongside
  Neurospora CAO-1, using resveratrol and piceatannol as substrates. Like the other SCOs, and despite
  automated annotations to the contrary, NOV2 is a stilbenoid cleaver, not a carotenoid enzyme.
existing_annotations:
- term:
    id: GO:0010436
    label: carotenoid dioxygenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: enables
  review:
    summary: >-
      Automated (IEA / TreeGrafter) carotenoid dioxygenase activity. NOV2 is a stilbene cleavage
      oxygenase assayed with resveratrol and piceatannol (PMID:28493664), not a carotenoid enzyme; the
      carotenoid term is a TreeGrafter over-propagation from the mixed CCO family.
    action: REMOVE
    reason: >-
      Rule/tree-based over-annotation of the wrong substrate class. Correct specific term is GO:7770086
      (resveratrol dioxygenase activity; go-ontology PR #32332, merged 2026-07-17, live in QuickGO); the
      general activity is covered by GO:0016702. Same error as NOV1 and cao-1.
    supported_by:
      - reference_id: PMID:28493664
        supporting_text: >-
          resveratrol and piceatannol for NOV2 and CAO1
- term:
    id: GO:0016121
    label: carotene catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: involved_in
  review:
    summary: >-
      Automated (IEA / TreeGrafter) carotene catabolic process. Wrong substrate class; NOV2 acts in
      stilbene/lignin-derived compound catabolism.
    action: MODIFY
    reason: >-
      Replace with GO:0046272 (stilbene catabolic process). Same TreeGrafter over-propagation as the
      carotenoid MF term.
    proposed_replacement_terms:
      - id: GO:0046272
        label: stilbene catabolic process
    supported_by:
      - reference_id: PMID:28493664
        supporting_text: >-
          resveratrol and piceatannol for NOV2 and CAO1
- term:
    id: GO:0016702
    label: oxidoreductase activity, acting on single donors with incorporation of
      molecular oxygen, incorporation of two atoms of oxygen
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro-based (IEA) dioxygenase MF term; correct general parent for the stilbenoid-cleavage
      activity of NOV2.
    action: ACCEPT
    reason: >-
      Accurate general dioxygenase MF; consistent with the demonstrated stilbenoid cleavage.
core_functions:
- description: >-
    Non-heme Fe(II) stilbene cleavage dioxygenase (SCO) that cleaves the interphenyl Calpha-Cbeta double
    bond of stilbenoids (resveratrol, piceatannol) into aromatic aldehydes. GO:0016702 is the validated
    MF term available in the ontology snapshot this repo validates against; the specific term is
    GO:7770086 (resveratrol dioxygenase activity, RHEA:73735; go-ontology PR #32332, merged
    2026-07-17).
  molecular_function:
    id: GO:0016702
    label: oxidoreductase activity, acting on single donors with incorporation of
      molecular oxygen, incorporation of two atoms of oxygen
  directly_involved_in:
    - id: GO:0046272
      label: stilbene catabolic process
  supported_by:
    - reference_id: PMID:28493664
      supporting_text: >-
        resveratrol and piceatannol for NOV2 and CAO1
suggested_questions:
- question: >-
    NOV2's carotenoid annotations come from TreeGrafter (GO_REF:0000118); should the rule be corrected
    so it does not assign carotenoid terms to the stilbene-cleaving (SCO) branch of the CCO family?
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: []
  reference_review:
    relevance: LOW
    correctness: MISCITED
    review_notes: >-
      TreeGrafter propagated carotenoid dioxygenase activity and carotene catabolic process to NOV2, a
      stilbene cleavage oxygenase - the same substrate-class over-annotation seen on NOV1, LSD-III, and
      cao-1.
- id: PMID:28493664
  title: Structure and Spectroscopy of Alkene-Cleaving Dioxygenases Containing an
    Atypically Coordinated Non-Heme Iron Center.
  findings:
  - statement: >-
      NOV2 is a stilbenoid cleavage oxygenase characterized (with CAO-1) using resveratrol and
      piceatannol as substrates; it shares the four-His non-heme iron center of the CCO family.
    supporting_text: >-
      resveratrol and piceatannol for NOV2 and CAO1
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Biochemical/spectroscopic study characterizing NOV2 (alongside CAO-1) as a stilbenoid cleavage
      oxygenase using resveratrol/piceatannol substrates. PMC full text verified.