id: Q52008
gene_symbol: lsdB
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:13689
  label: Sphingomonas paucimobilis
description: >-
  lsdB encodes lignostilbene-alpha,beta-dioxygenase isozyme III (LSD-III) of Sphingomonas
  paucimobilis (Pseudomonas paucimobilis TMY1009), one of the founding members of the stilbene
  cleavage oxygenase (SCO) / carotenoid cleavage oxygenase (CCO) superfamily. 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. LSD was the first
  enzyme shown to cleave the central stilbene double bond; three isozymes (I, II, III) were purified
  and compared from the same organism. Despite automated annotations to the contrary, LSD-III 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 the specific lignostilbene
      alpha,beta-dioxygenase activity (GO:0050054, IDA, PMID:7763880). A TreeGrafter over-propagation
      from the mixed-specificity CCO family.
    action: REMOVE
    reason: >-
      LSD-III 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 cao-1 (IBA) and NOV1 (IEA/TreeGrafter).
    supported_by:
      - reference_id: PMID:7763880
        supporting_text: >-
          Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
- 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-III's real
      process is lignin/stilbene catabolism, already captured experimentally by lignin catabolic process
      (GO:0046274, IDA).
    action: REMOVE
    reason: >-
      Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter
      over-propagation of a carotenoid-pathway term.
    supported_by:
      - reference_id: PMID:7763880
        supporting_text: >-
          Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
- 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
      alpha,beta-dioxygenase activity.
    action: ACCEPT
    reason: >-
      Accurate general dioxygenase MF, consistent with the experimental activity.
- 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
      (EC 1.13.11.43; reaction lignostilbene + O2 = 2 vanillin). This is the correct, specific MF term,
      also supported by IDA.
    action: ACCEPT
    reason: >-
      Core molecular function - the exact activity of LSD-III - corroborated by the IDA annotation of
      the same term.
- term:
    id: GO:0005506
    label: iron ion binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      Sequence-based (ISS) iron ion binding. LSD/SCO enzymes use a non-heme mononuclear iron center
      (four-His coordination in the family), so iron binding is expected and consistent.
    action: ACCEPT
    reason: >-
      Bona fide cofactor binding for this non-heme iron dioxygenase family; a structural/experimental
      upgrade would strengthen it.
- 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
      stilbenes (lignostilbene) to vanillin, a step in the microbial catabolism of lignin degradation
      products.
    action: ACCEPT
    reason: >-
      Core biological process, experimentally supported; the correct (non-carotenoid) process for this
      enzyme.
    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 and enzymatic characterization of the three LSD isozymes. The core, correct molecular
      function of LSD-III.
    action: ACCEPT
    reason: >-
      Core catalytic function, directly demonstrated (EC 1.13.11.43). This is 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
core_functions:
- description: >-
    Non-heme iron lignostilbene-alpha,beta-dioxygenase (EC 1.13.11.43): cleaves the interphenyl
    Calpha-Cbeta double bond of lignostilbene (1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene) with O2 to
    yield two molecules of vanillin, in the catabolism of lignin-derived stilbenes. 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: >-
    LSD-III already carries the correct specific IDA annotations (lignostilbene alpha,beta-dioxygenase
    activity; lignin catabolic process); should the contradictory TreeGrafter carotenoid terms
    (GO_REF:0000118) 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:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to
    orthologs using Ensembl Compara
  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-III,
      a genuine lignostilbene dioxygenase - directly contradicting the gene's own experimental (IDA)
      annotations. A clean example of automated carotenoid over-annotation of the stilbene-cleaving clade.
- 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 enzymatically
      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: >-
      Primary purification/characterization of the LSD isozymes; source of the IDA lignostilbene
      dioxygenase activity and lignin catabolic process annotations. Abstract-only cache.
- id: PMID:8534977
  title: Cloning of a lignostilbene-alpha,beta-dioxygenase isozyme gene from Pseudomonas
    paucimobilis TMY1009.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Cloning/identification of the LSD-III (lsdB) gene; establishes EC 1.13.11.43 and the
      lignostilbene + O2 = 2 vanillin reaction.