PP_3195 is a FrsA-like alpha/beta-fold hydrolase candidate in a conserved aromatic-compound catabolic locus. It is related to FdeB proteins proposed to act in the lower naringenin-degradation pathway. Its physiological substrate and ester-versus-carbon-carbon bond specificity remain unresolved, and no peptidase activity has been demonstrated.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006508 proteolysis | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: The S9-like catalytic domain does not establish physiological peptide-bond hydrolysis. Reason: The IPR001375 catalytic-domain match is shared with non-peptidase hydrolases. FrsA-like family membership, alpha/beta-hydrolase architecture and close FdeB homologs favor a small-molecule hydrolase candidate, but do not constitute a negative peptide assay or a demonstrated loss of peptidase activity. The physiological peptide/proteolysis specificity is therefore over-annotation. The FdeB candidates share this uncertainty; differences in locus phenotype do not resolve their untested bond specificity. Supporting Evidence: file:PSEPK/PP_3195/PP_3195-uniprot.txt InterPro; IPR050261; FrsA_esterase. file:PSEPK/PP_3195/PP_3195-hypotheses/function-hypothesis-go-0008236/openscientist.md far too small** to contain the ~250β300-aa seven-bladed Ξ²-propeller that is a defining, substrate-gating feature of bona fide S9-family peptidases |
| GO:0008236 serine-type peptidase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: The S9-like catalytic domain does not establish physiological peptide-bond hydrolysis. Reason: The IPR001375 catalytic-domain match is shared with non-peptidase hydrolases. FrsA-like family membership, alpha/beta-hydrolase architecture and close FdeB homologs favor a small-molecule hydrolase candidate, but do not constitute a negative peptide assay or a demonstrated loss of peptidase activity. The physiological peptide/proteolysis specificity is therefore over-annotation. The FdeB candidates share this uncertainty; differences in locus phenotype do not resolve their untested bond specificity. Supporting Evidence: file:PSEPK/PP_3195/PP_3195-hypotheses/function-hypothesis-go-0008236/openscientist.md far too small** to contain the ~250β300-aa seven-bladed Ξ²-propeller that is a defining, substrate-gating feature of bona fide S9-family peptidases file:PSEPK/PP_3195/PP_3195-deep-research-openscientist.md KEGG independently classifies the FdeB reaction (R13077) as a hydrolase acting on a **lactone**, not a peptide bond. |
| GO:0052689 carboxylic ester hydrolase activity | IEA GO_REF:0000117 | UNDECIDED | Summary: Ester versus carbon-carbon hydrolysis remains unresolved for the FdeB candidates. Reason: IPR050261 includes ester and experimentally characterized C-C hydrolases, so the family name and catalytic motif do not choose the bond class. K26184/R13077 is a proposed lactone reaction, and no FdeB member in this panel has a substrate-resolved assay. The close sequence comparison is to another unassayed FdeB candidate and cannot provide an independent biochemical donor. All three FdeB candidates share this uncertainty; lack of an assay does not refute a plausible ester reaction. Supporting Evidence: file:PSEPK/PP_3195/PP_3195-deep-research-openscientist.md KEGG links FdeB (K26184) to **reaction R13077**, classified as a **hydrolase** file:PSEPK/PP_3195/PP_3195-bioinformatics/RESULTS.md Target nucleophile-motif candidate `GVSLG`: present at Q88I07 residues 266-270 and D8J0W6 residues 231-235 PMID:16321959 The enzyme catalyzing the hydrolytic cleavage of 2,6-dihydroxypseudooxynicotine to 2,6-dihydroxypyridine and gamma-N-methylaminobutyrate |
| GO:0046275 flavonoid catabolic process | ISS file:PSEPK/PP_3195/PP_3195-deep-research-openscientist.md | REMOVE | Summary: Withdraw the inherited process proposal pending evidence that this candidate executes a flavonoid-catabolic step. Reason: The conserved locus and K26184 assignment identify a plausible FdeB candidate, but the inherited proposal relies on the untested R13077 assignment and similarity to another unassayed candidate. The broad hydrolase fold does not establish which native step the protein performs. Whole-operon phenotypes do not settle this individual role. Retain the original proposal row for provenance while withdrawing its assertion, consistently with the same-role BRADU bll6428 comparator; possible participation remains a knowledge gap rather than an asserted core process. The retired flag records deliberate withdrawal of this curator-authored proposal from the active set; it does not report disappearance of an upstream GOA annotation. 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_3195/PP_3195-deep-research-openscientist.md KEGG assigns PP_3195 to ortholog **K26184** (SYMBOL *fdeB*, "naringenin degradation protein FdeB"), places it in pathway **ppu00946 "Degradation of flavonoids,"** and classifies it in **COG1506**. file:PSEPK/PP_3195/PP_3195-bioinformatics/RESULTS.md Pairwise identity over aligned residue pairs: 81.6% |
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Download this section (compressed HTML)Q: Does PP_3195 hydrolyze the R13077 delta-lactone in KT2440, and are the predicted serine-hydrolase residues required for turnover?
Q: Do PP_3195 D195 and H394 contribute to hydrolysis, and does comparison with the provider-proposed H405 distinguish the alternative active-site assignments?
Q: If the candidate reaction is experimentally established, would "flavonoid-derived delta-lactone hydrolase activity" be an appropriate GO term? The provisional definition was: Catalysis of hydrolytic ring opening of 5-(4-hydroxyphenyl)-3-oxovalero-delta-lactone to 5-hydroxy-5-(4-hydroxyphenyl)-3-oxopentanoate in bacterial flavonoid degradation. This is a future terminology question, not a current request or asserted activity.
Experiment: Purify PP_3195 and assay the proposed R13077 lactone, identifying the ring-opened product and testing a catalytic-serine substitution.
Type: biochemical reconstitution and site-directed mutagenesis
Experiment: Compare wild type, a PP_3195 deletion, and a complemented strain during naringenin utilization using targeted metabolomics for the R13077 substrate and product.
Type: genetics and targeted metabolomics
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: No FdeB-family protein has been assayed directly with the R13077 lactone, and PP_3195 has not been tested genetically in KT2440.
OPEN BIOLOGYCURATION MF_DARK
What is known: Orthology, fold and conserved candidate catalytic residues support a broad hydrolase inference, but do not resolve ester versus carbon-carbon bond specificity or the physiological substrate/product. R13077 remains a candidate reaction, not an established target activity. The molecular mechanism remains unmeasured: substrate, cleaved bond and target active-site roles are unresolved. MF_DARK records this mechanistic gap despite broad hydrolase inference; it does not assert that native pathway participation is established.
Significance: Direct evidence is needed before assigning a substrate-specific lactonase term experimentally or treating R13077 as established chemistry.
What would resolve it: Purify PP_3195, generate the proposed delta-lactone substrate enzymatically, and identify the ring-opened product; test a native deletion for substrate accumulation during naringenin utilization.
Provenance (the field's own admissions):
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