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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0010436 carotenoid dioxygenase activity | IEA GO_REF:0000118 | REMOVE | 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. 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). Supporting Evidence: PMID:7763880 Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas |
| GO:0016121 carotene catabolic process | IEA GO_REF:0000118 | REMOVE | 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). Reason: Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter over-propagation of a carotenoid-pathway term. Supporting Evidence: PMID:7763880 Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas |
| GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based (IEA) dioxygenase MF term. Correct general parent of the specific lignostilbene alpha,beta-dioxygenase activity. Reason: Accurate general dioxygenase MF, consistent with the experimental activity. |
| GO:0050054 lignostilbene alpha beta-dioxygenase activity | IEA GO_REF:0000120 | ACCEPT | 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. Reason: Core molecular function - the exact activity of LSD-III - corroborated by the IDA annotation of the same term. |
| GO:0005506 iron ion binding | ISS GO_REF:0000024 | ACCEPT | 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. Reason: Bona fide cofactor binding for this non-heme iron dioxygenase family; a structural/experimental upgrade would strengthen it. |
| GO:0046274 lignin catabolic process | IDA PMID:7763880 Structural and enzymatical comparison of lignostilbene-alpha... | ACCEPT | 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. Reason: Core biological process, experimentally supported; the correct (non-carotenoid) process for this enzyme. Supporting Evidence: PMID:7763880 Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas |
| GO:0050054 lignostilbene alpha beta-dioxygenase activity | IDA PMID:7763880 Structural and enzymatical comparison of lignostilbene-alpha... | ACCEPT | 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. Reason: Core catalytic function, directly demonstrated (EC 1.13.11.43). This is the specific term the TreeGrafter carotenoid annotations should never have overridden. Supporting Evidence: PMID:7763880 Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas |
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Download this section (compressed HTML)Q: 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?
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