Q53353

id: Q53353
gene_symbol: Q53353
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:13689
  label: Sphingomonas paucimobilis
description: >-
  Q53353 (LSD-I) is lignostilbene-alpha,beta-dioxygenase isozyme I of Sphingomonas (Pseudomonas)
  paucimobilis TMY1009, one of the founding members of the stilbene cleavage oxygenase (SCO) /
  carotenoid cleavage oxygenase (CCO) superfamily and a companion isozyme to LSD-III (lsdB). It is a
  non-heme iron dioxygenase that cleaves the interphenyl (Calpha-Cbeta) double bond of lignostilbene
  (1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene) with molecular oxygen to yield two molecules of vanillin
  (EC 1.13.11.43), acting in the catabolism of lignin-derived stilbenes. Despite automated annotations
  to the contrary, LSD-I 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) carotenoid dioxygenase activity - wrong substrate class and directly
      contradicted by this gene's own experimental annotation to lignostilbene alpha,beta-dioxygenase
      activity (GO:0050054, IDA). A TreeGrafter over-propagation from the mixed CCO family.
    action: REMOVE
    reason: >-
      LSD-I is an experimentally characterized lignostilbene dioxygenase (EC 1.13.11.43), not a
      carotenoid enzyme; the correct specific MF (GO:0050054) is already present by IDA. Same
      substrate-class error as LSD-III, NOV1/NOV2, Rco1, and cao-1.
- 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; LSD-I's real
      process is lignin/stilbene catabolism, already captured experimentally (GO:0046274, IDA).
    action: REMOVE
    reason: >-
      Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter
      over-propagation.
- 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 of the specific lignostilbene
      activity.
    action: ACCEPT
    reason: >-
      Accurate general dioxygenase MF.
- term:
    id: GO:0050054
    label: lignostilbene alpha beta-dioxygenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Automated (IEA) annotation of the specific lignostilbene alpha,beta-dioxygenase activity, also
      supported by IDA. The correct, specific MF term for LSD-I.
    action: ACCEPT
    reason: >-
      Core molecular function, corroborated by IDA.
- term:
    id: GO:0046274
    label: lignin catabolic process
  evidence_type: IDA
  original_reference_id: PMID:7763880
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental (IDA) annotation of lignin catabolic process; LSD cleaves lignin-derived
      stilbene (lignostilbene) to vanillin.
    action: ACCEPT
    reason: >-
      Core biological process, experimentally supported; the correct (non-carotenoid) process.
    supported_by:
      - reference_id: PMID:7763880
        supporting_text: >-
          Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
- term:
    id: GO:0050054
    label: lignostilbene alpha beta-dioxygenase activity
  evidence_type: IDA
  original_reference_id: PMID:7763880
  qualifier: enables
  review:
    summary: >-
      Direct experimental (IDA) annotation of lignostilbene alpha,beta-dioxygenase activity from the
      purification/characterization of the LSD isozymes. Core, correct molecular function of LSD-I.
    action: ACCEPT
    reason: >-
      Core catalytic function (EC 1.13.11.43), directly demonstrated. The specific term the TreeGrafter
      carotenoid annotations should never have overridden.
    supported_by:
      - reference_id: PMID:7763880
        supporting_text: >-
          Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
- term:
    id: GO:0005506
    label: iron ion binding
  evidence_type: IDA
  original_reference_id: DOI:10.1271/bbb1961.53.2757
  qualifier: enables
  review:
    summary: >-
      Direct experimental (IDA) annotation of iron binding from the original LSD-I purification. LSD/SCO
      enzymes use a non-heme mononuclear iron center.
    action: ACCEPT
    reason: >-
      Bona fide cofactor of this non-heme iron dioxygenase, experimentally supported.
- term:
    id: GO:0046274
    label: lignin catabolic process
  evidence_type: IDA
  original_reference_id: DOI:10.1271/bbb1961.53.2757
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental (IDA) annotation of lignin catabolic process from the original LSD-I
      characterization.
    action: ACCEPT
    reason: >-
      Core biological process, experimentally supported (duplicate term from a distinct reference).
- term:
    id: GO:0050054
    label: lignostilbene alpha beta-dioxygenase activity
  evidence_type: IDA
  original_reference_id: DOI:10.1271/bbb1961.53.2757
  qualifier: enables
  review:
    summary: >-
      Direct experimental (IDA) annotation of lignostilbene alpha,beta-dioxygenase activity from the
      original LSD-I purification and characterization.
    action: ACCEPT
    reason: >-
      Core catalytic function, experimentally supported (the founding LSD-I characterization).
core_functions:
- description: >-
    Non-heme iron lignostilbene-alpha,beta-dioxygenase (EC 1.13.11.43): cleaves the interphenyl
    Calpha-Cbeta double bond of lignostilbene with O2 to two molecules of vanillin, in lignin-derived
    stilbene catabolism. GO:0050054 is the exact, experimentally-supported MF term (a sibling of the
    resveratrol leaf GO:7770086, added by go-ontology PR #32332 merged 2026-07-17, and a child of the
    proposed stilbene alpha,beta-dioxygenase grouping).
  molecular_function:
    id: GO:0050054
    label: lignostilbene alpha beta-dioxygenase activity
  directly_involved_in:
    - id: GO:0046274
      label: lignin catabolic process
  supported_by:
    - reference_id: PMID:7763880
      supporting_text: >-
        Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
suggested_questions:
- question: >-
    Like LSD-III, LSD-I carries the correct specific IDA annotations yet also the contradictory
    TreeGrafter carotenoid terms; should these be removed and the TreeGrafter rule corrected for the 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 onto LSD-I,
      a genuine lignostilbene dioxygenase - directly contradicting the gene's own experimental (IDA)
      annotations.
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:7763880
  title: Structural and enzymatical comparison of lignostilbene-alpha,beta-dioxygenase
    isozymes, I, II, and III, from Pseudomonas paucimobilis TMY1009.
  findings:
  - statement: >-
      Three lignostilbene alpha,beta-dioxygenase isozymes (I, II, III) were purified and characterized
      from Pseudomonas (Sphingomonas) paucimobilis TMY1009.
    supporting_text: >-
      Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Comparison of the LSD isozymes; supports the IDA lignostilbene dioxygenase activity and lignin
      catabolic process annotations for LSD-I. Abstract-only cache.
- id: DOI:10.1271/bbb1961.53.2757
  title: Purification and some properties of lignostilbene-.ALPHA.,.BETA.-dioxygenase responsible
    for the C.ALPHA.-C.BETA. cleavage of a diarylpropane type lignin model compound from Pseudomonas
    sp. TMY1009.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Original LSD-I purification/characterization; source of the IDA lignostilbene dioxygenase
      activity, lignin catabolic process, and iron-binding annotations. Not cached (DOI, pre-PMC era).