PP_3197 encodes a predicted VOC-superfamily dioxygenase in the KT2440 flavonoid-degradation locus. Orthology and conserved locus organization identify it as an FdeC-like enzyme predicted to cleave the A-ring of the trihydroxyflavanone produced during naringenin catabolism. The target protein has not been characterized directly, so its exact substrate, product, and catalytic metal remain unverified in P. putida.
Definition: Catalysis of the incorporation of both atoms of molecular oxygen during extradiol cleavage of the A-ring of 5,7,8-trihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one.
Justification: KEGG reaction R13075 and the FdeC mutant study define this substrate-specific cleavage, whereas GO:0016702 captures only the general two-oxygen-atom incorporation mechanism.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | ISS file:PSEPK/PP_3197/PP_3197-deep-research-openscientist.md | NEW | Summary: PP_3197 is predicted to be an FdeC-like flavonoid ring-cleavage dioxygenase. Reason: KEGG assigns PP_3197 to FdeC orthology group K26181, and the report finds strong whole-protein similarity to the experimentally characterized Herbaspirillum FdeC. GO lacks a term for the exact naringenin-intermediate A-ring cleavage, so the most specific supported extradiol-dioxygenase parent is used. Supporting Evidence: file:PSEPK/PP_3197/PP_3197-deep-research-openscientist.md KEGG orthology places PP_3197 in ortholog group **K26181 (fdeC)** and assigns it reaction **R13075** within pathway **ppu00946 / map00946 ("Degradation of flavonoids")**. PMID:27059806 that is subsequently dioxygenated and cleaved at the A-ring by the FdeC |
| GO:0046275 flavonoid catabolic process | ISS file:PSEPK/PP_3197/PP_3197-deep-research-openscientist.md | NEW | Summary: PP_3197 is predicted to perform an A-ring cleavage step in naringenin degradation. Reason: K26181/R13075 pathway placement and orthology to experimentally tested Hsero_1005 support flavonoid catabolism. GO:0046275 flavonoid catabolic process is used; GO has no naringenin-specific catabolic child. Supporting Evidence: file:PSEPK/PP_3197/PP_3197-deep-research-openscientist.md KEGG orthology places PP_3197 in ortholog group **K26181 (fdeC)** and assigns it reaction **R13075** within pathway **ppu00946 / map00946 ("Degradation of flavonoids")**. PMID:27059806 that is subsequently dioxygenated and cleaved at the A-ring by the FdeC |
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Download this section (compressed HTML)Q: Does PP_3197 catalyze KEGG reaction R13075 on the FdeE-generated trihydroxyflavanone in KT2440, and which divalent metal supports turnover?
Experiment: Purify PP_3197 and assay the FdeE-generated trihydroxyflavanone with oxygen and a divalent-metal panel, identifying the ring-cleavage product by LC-MS/MS.
Type: biochemical reconstitution and product analysis
Experiment: Compare wild type, a PP_3197 deletion, and a complemented strain during growth on naringenin, measuring substrate use and accumulation of the trihydroxyflavanone intermediate.
Type: genetics and targeted metabolomics
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: PP_3197's exact physiological substrate, ring-cleavage product, and catalytic metal have not been measured in KT2440.
OPEN BIOLOGYCURATION
What is known: Orthology, locus context, and sequence conservation support an FdeC-like extradiol dioxygenase, but all substrate-specific chemistry is transferred from Hsero_1005 and KEGG R13075.
Significance: Direct evidence is required before assigning a future substrate-specific GO molecular-function term to PP_3197 experimentally.
What would resolve it: Reconstitute PP_3197 with its proposed substrate and identify product and metal dependence, then test a native deletion for intermediate accumulation.
Provenance (the field's own admissions):
Gap: The electron-transfer relationship between PP_3198/FdeD and the upstream monooxygenase candidate PP_3199/FdeE remains untested in KT2440.
OPEN BIOLOGY
What is known: The paired FdeD/FdeE assignment belongs to the preceding hydroxylation reaction and must not be treated as evidence that PP_3198 is a redox partner for PP_3197.
What would resolve it: Reconstitute PP_3198 and PP_3199 together and test naringenin hydroxylation independently of the downstream PP_3197 reaction.
Provenance (the field's own admissions):
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