PP_3206 encodes an epimerase/dehydratase-fold protein in the KT2440 flavonoid-degradation locus. KEGG assigns it to FdeJ orthology group K26183 and reaction R13076, a predicted hydrolytic carbon-carbon cleavage that releases oxaloacetate from a ring-opened flavonoid intermediate. Neither the target nor its Herbaspirillum counterpart has been assayed directly for this reaction, so the substrate and chemistry remain pathway-level predictions.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0046275 flavonoid catabolic process | ISS file:PSEPK/PP_3206/PP_3206-deep-research-openscientist.md | REMOVE | Summary: Withdraw the inherited FdeJ process proposal; an individual flavonoid-catabolic step has not been established. Reason: The conserved locus and orthology identify a candidate FdeJ protein, but the epimerase/dehydratase fold and similarity to unassayed Hsero_1012 do not establish the proposed oxaloacetate-releasing R13076 reaction. The available whole-operon phenotype, including the probably polar fdeA insertion, does not show which step this individual protein performs. There is no independently assayed donor for this particular role; the corresponding BRADU comparator bll6421 likewise carries no process assertion. Retain the original source payload and row position while withdrawing the active proposal. The retired flag records this curator decision, not disappearance of an upstream GOA row or proof of biological absence. Native participation remains an open question. REMOVE records withdrawal of this earlier curator-authored NEW proposal, not removal of a current GOA assertion. It does not claim that the protein is biologically incapable of participating in flavonoid catabolism. Supporting Evidence: file:PSEPK/PP_3206/PP_3206-deep-research-openscientist.md KEGG assigns `ppu:PP_3206` to orthology **K26183 (fdeJ, "naringenin degradation protein FdeJ"; COG0451)** within pathway **ppu00946 "Degradation of flavonoids."** PMID:8071218 Pseudomonas putida degraded quercetin via an initial fission in its A-ring |
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Download this section (compressed HTML)Q: Does PP_3206 directly catalyze R13076, and is its epimerase/dehydratase-fold dinucleotide required catalytically or only structurally?
Q: If the candidate reaction is experimentally established, would "naringenin-degradation oxaloacetate-releasing hydrolase activity" be an appropriate GO term? The provisional definition was: Catalysis of the hydrolytic carbon-carbon cleavage of the ring-opened naringenin A-ring intermediate represented by KEGG reaction R13076, yielding a hydroxyphenyl oxovalero-lactone and oxaloacetate. This is a future terminology question, not a current request or asserted activity.
Experiment: Purify PP_3206, synthesize or generate the R13076 substrate enzymatically, and identify oxaloacetate and the co-product by LC-MS/MS while testing NAD(H) and NADP(H) dependence.
Type: biochemical reconstitution and product analysis
Experiment: Compare wild type, a PP_3206 deletion, and a complemented strain during naringenin utilization using targeted metabolomics for the R13076 substrate and products.
Type: genetics and targeted metabolomics
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: No FdeJ-family protein has been shown biochemically to catalyze R13076, and PP_3206 has not been tested genetically in KT2440.
OPEN BIOLOGYCURATION
What is known: FdeJ membership and pathway placement nominate a candidate; they do not establish which native flavonoid-catabolic step the target performs. The inherited process proposal is retired pending participation evidence.
Significance: A reaction-level molecular-function annotation should not be assigned until a member of the family is characterized.
What would resolve it: Reconstitute PP_3206 with the chemically defined R13076 substrate and identify products and any dinucleotide requirement; pair this with a native knockout metabolomics experiment.
Provenance (the field's own admissions):
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