id: Q2GA76
gene_symbol: Saro_0802
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_0802 encodes NOV1, a bacterial resveratrol-cleaving dioxygenase (stilbene cleavage oxygenase,
  SCO) of Novosphingobium aromaticivorans. It is a non-heme Fe(II) enzyme of the carotenoid cleavage
  oxygenase (CCO/RPE65) superfamily that oxidatively cleaves the central interphenyl Calpha-Cbeta
  double bond of stilbenes into two aromatic aldehydes; it has been structurally characterized in
  complex with the substrate resveratrol and the product vanillin. NOV1 is a seven-bladed beta-propeller
  with an iron cofactor coordinated by four histidines, and its mechanism proceeds via a side-on
  ferric-superoxide that reacts with substrate activated by deprotonation of the 4-hydroxyl (4'-OH),
  making the 4'-OH catalytically essential; NOV1 cleaves a wide range of 4'-hydroxy stilbene-like
  compounds. It also converts the lignin-derived phenylpropene isoeugenol to vanillin and is of interest
  for lignin valorization. Despite automated annotations to the contrary, NOV1 is not a carotenoid
  cleavage 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) annotation of carotenoid dioxygenase activity. This is the wrong
      substrate class: NOV1 is a stilbene cleavage oxygenase that cleaves resveratrol (and other 4'-OH
      stilbenes) and isoeugenol, demonstrated structurally with resveratrol bound (PMID:27911781). The
      carotenoid term is a TreeGrafter over-propagation from the mixed-specificity CCO family.
    action: REMOVE
    reason: >-
      Rule/tree-based over-annotation contradicted by the enzyme's structural and functional
      characterization as a resveratrol/stilbene dioxygenase. The correct specific term is GO:7770086
      (resveratrol dioxygenase activity, RHEA:73735; added go-ontology master Jul 2026); the real
      activity is already covered generally by GO:0016702. Same substrate-class error as cao-1, here via
      TreeGrafter (GO_REF:0000118) rather than manual IBA.
    supported_by:
      - reference_id: PMID:27911781
        supporting_text: >-
          Stilbene cleavage oxygenases (SCOs) cleave the central double
      - reference_id: PMID:27911781
        supporting_text: >-
          NOV1 cleaves a wide range of other stilbene-like compounds with a 4'-OH group
- 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) annotation of carotene catabolic process. Wrong substrate class:
      NOV1 acts in stilbene / lignin-derived compound catabolism, not carotene catabolism.
    action: MODIFY
    reason: >-
      Replace with GO:0046272 (stilbene catabolic process), matching the demonstrated stilbene-cleavage
      activity. Same TreeGrafter over-propagation as the carotenoid MF term.
    proposed_replacement_terms:
      - id: GO:0046272
        label: stilbene catabolic process
    supported_by:
      - reference_id: PMID:27911781
        supporting_text: >-
          Stilbene cleavage oxygenases (SCOs) cleave the central double
- 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 (incorporation of two oxygen atoms). Correct and
      consistent with the demonstrated stilbene dioxygenase activity of NOV1.
    action: ACCEPT
    reason: >-
      Accurate general dioxygenase MF; the specific activity (resveratrol/stilbene cleavage) sits under
      this term.
    supported_by:
      - reference_id: PMID:27911781
        supporting_text: >-
          an iron cofactor coordinated by four histidines
core_functions:
- description: >-
    Non-heme Fe(II) stilbene cleavage dioxygenase that oxidatively cleaves the interphenyl Calpha-Cbeta
    double bond of resveratrol and other 4'-hydroxy stilbenes (and isoeugenol) into aromatic aldehydes.
    The 4'-OH is catalytically essential (its deprotonation activates the substrate for the side-on
    ferric-superoxide). GO:0016702 is used here because it is the most specific MF term present 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, live in QuickGO).
  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:27911781
      supporting_text: >-
        activated by deprotonation of a phenol group at position 4 of the substrate
suggested_questions:
- question: >-
    The carotenoid dioxygenase activity/process annotations on NOV1 come from the TreeGrafter rule
    (GO_REF:0000118); should this rule be corrected so it does not assign carotenoid terms to the
    stilbene-cleaving (SCO) branch of the CCO family?
suggested_experiments:
- description: >-
    Comparative substrate-panel + structural analysis of NOV1 versus CAO-1 to test whether the wider
    4'-hydroxy-stilbene tolerance of NOV1 reflects a more open binding cleft than CAO-1's two-anchor
    (4'-OH -> Tyr/Lys; 3/5-OH -> Glu) pocket.
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 onto NOV1,
      a stilbene cleavage oxygenase - a substrate-class over-annotation from the mixed CCO family. The
      InterPro2GO dioxygenase term is fine; the two carotenoid terms are the error.
- id: PMID:27911781
  title: Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase.
  findings:
  - statement: >-
      NOV1 is a resveratrol-cleaving stilbene cleavage oxygenase with a seven-bladed beta-propeller and
      a four-His non-heme iron center; solved with resveratrol (substrate) and vanillin (product).
    supporting_text: >-
      an iron cofactor coordinated by four histidines
  - statement: >-
      Catalysis requires deprotonation of the substrate 4-hydroxyl to activate it for the ferric-
      superoxide, so NOV1 cleaves a wide range of 4'-OH stilbene-like compounds.
    supporting_text: >-
      NOV1 cleaves a wide range of other stilbene-like compounds with a 4'-OH group
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary structural + mechanistic paper establishing NOV1 as a resveratrol/stilbene cleavage
      dioxygenase (not carotenoid) and defining the 4'-OH-deprotonation mechanism. PMC full text verified.
- id: PMID:35687874
  title: Rationally Guided Improvement of NOV1 Dioxygenase for the Conversion of Lignin-Derived
    Isoeugenol to Vanillin.
  findings:
  - statement: >-
      NOV1 also cleaves the lignin-derived phenylpropene isoeugenol to vanillin and has been engineered
      for improved conversion - a lignin-valorization application.
    supporting_text: >-
      Isoeugenol to Vanillin
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Establishes a second (biotechnologically relevant) substrate for NOV1; supports the broader
      substrate range and the non-carotenoid function. PMC full text available.