lsdB / LSD-III (Q52008, Sphingomonas paucimobilis) — review notes

Lignostilbene-α,β-dioxygenase isozyme III (LSD-III), EC 1.13.11.43, of Sphingomonas
(Pseudomonas) paucimobilis TMY1009 — one of the founding members of the stilbene cleavage
oxygenase (SCO) / CCO superfamily. Non-heme iron dioxygenase.

• Reaction: lignostilbene (1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene) + O2 = 2 vanillin
  (RHEA:21340). Acts in lignin-derived stilbene catabolism.
• Three isozymes (I, II, III) purified and compared PMID:7763880; gene cloned PMID:8534977.

The key point for the SCO project

LSD-III is the experimentally-grounded anchor of the stilbene-cleavage clade: it already carries the
correct specific IDA annotations — lignostilbene α,β-dioxygenase activity (GO:0050054) and lignin
catabolic process (GO:0046274). Yet it also carries the wrong TreeGrafter carotenoid terms
(GO:0010436, GO:0016121; GO_REF:0000118) — the same over-annotation seen on cao-1 (IBA) and NOV1
(IEA/TreeGrafter). Here the contradiction is starkest: the automated carotenoid terms directly conflict
with the gene's own experimental annotations.

GO:0050054 (lignostilbene α,β-dioxygenase activity) is the existing leaf term that the proposed
grouping stilbene α,β-dioxygenase activity would parent, alongside the resveratrol leaf GO:7770086
(go-ontology #32332, merged 2026-07-17).

Decisions

• REMOVE the two TreeGrafter carotenoid terms (contradicted by own IDA).
• ACCEPT GO:0050054 (IEA + IDA), GO:0046274 (IDA), GO:0016702 (IEA), GO:0005506 iron (ISS).
• Core function: lignostilbene α,β-dioxygenase in lignin catabolic process.