Beta-ketoadipyl-CoA thiolase of the shared lower beta-ketoadipate pathway. PcaF-I catalyzes thiolytic cleavage of 3-oxoadipyl-CoA to succinyl-CoA and acetyl-CoA, completing assimilation of aromatic carbon entering through catechol- or protocatechuate-derived branches into central metabolism. Available evidence supports a degradative thiolase specialized for aromatic compound catabolism rather than a general lipid-metabolism enzyme.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003988 acetyl-CoA C-acyltransferase activity | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Correct as a broad parent activity for a thiolase, but it is less informative than the specific 3-oxoadipyl-CoA thiolase term already present. Reason: PcaF-I is a C-acyltransferase/thiolase, but the curated core function should use GO:0033812 to capture substrate specificity. Supporting Evidence: file:PSEPK/pcaF/pcaF-uniprot.txt RecName: Full=Beta-ketoadipyl-CoA thiolase |
| GO:0016746 acyltransferase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Too general to be useful for this gene and likely inherited from family-level domain mappings rather than pathway-specific evidence. Reason: The specific thiolase activity is already represented by GO:0033812, so this broad umbrella term adds little biological information. Supporting Evidence: file:PSEPK/pcaF/pcaF-uniprot.txt RecName: Full=Beta-ketoadipyl-CoA thiolase |
| GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Mechanistically true at a very high level, but still a redundant broad family term relative to the specific 3-oxoadipyl-CoA thiolase annotation. Reason: Pathway-specific curation should prefer the substrate-resolved thiolase term. Supporting Evidence: file:PSEPK/pcaF/pcaF-uniprot.txt Catalyzes thiolytic cleavage of beta-ketoadipyl-CoA to |
| GO:0033812 3-oxoadipyl-CoA thiolase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Best current molecular function term for PcaF-I and consistent with UniProt pathway assignment, classical pcaF genetics, KT2440 proteomics, and the KT2440 structural degradative-thiolase paper. Reason: This term captures the specific beta-ketoadipyl-CoA/3-oxoadipyl-CoA thiolase activity that defines the enzyme. Supporting Evidence: file:PSEPK/pcaF/pcaF-uniprot.txt Catalyzes thiolytic cleavage of beta-ketoadipyl-CoA to PMID:7961399 pcaF encodes beta-ketoadipyl-coenzyme A thiolase, the last enzyme in the pathway. PMID:32647822 Ξ²-Ketoadipyl CoA is the natural substrate of PcaF file:PSEPK/pcaF/pcaF-deep-research-falcon.md The UniProt accession Q88N39 corresponds to *Pseudomonas putida* KT2440 locus PP_1377 annotated as PcaF (PcaF-I), a Ξ²-ketoadipyl-CoA thiolase (syn. 3βoxoadipylβCoA thiolase; EC 2.3.1.174). |
| GO:0006629 lipid metabolic process | IEA GO_REF:0000117 | REMOVE | Summary: Not supported as a core role for this gene. The enzyme functions in aromatic compound degradation through the beta-ketoadipate pathway, not in canonical lipid metabolism. Reason: This appears to be a family-level ARBA over-projection from thiolase chemistry. The target record places PcaF-I in aromatic beta-ketoadipate catabolism. The structural paper does show broad acyl-chain accommodation, but its long-chain ligands were trapped in active-site mutants under crystallographic soaking conditions; that in vitro promiscuity does not establish a physiological lipid-metabolism role. Supporting Evidence: file:PSEPK/pcaF/pcaF-uniprot.txt PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway; PMID:32647822 a tetrameric degradative thiolase from Pseudomonas putida KT2440 annotated as PcaF |
| GO:0019619 3,4-dihydroxybenzoate catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: Appropriate biological-process annotation because PcaF-I acts in the shared beta-ketoadipate segment used to complete protocatechuate/3,4-dihydroxybenzoate degradation. Reason: Proteomics and classical pca pathway genetics support participation of PcaF in the protocatechuate branch of aromatic compound catabolism. Supporting Evidence: PMID:16470664 beta-Ketoadipyl CoA thiolase (PcaF) and 3-oxoadipate enol-lactone hydrolase (PcaD) were induced by benzoate, p-hydroxybenzoate and vanilline, suggesting that benzoate, p-hydroxybenzoate and vanilline were degraded by different dioxygenases and then converged in the same beta-ketoadipate degradation pathway. |
| GO:0042952 beta-ketoadipate pathway | TAS file:PSEPK/pcaF/pcaF-uniprot.txt | NEW | Summary: PcaF-I performs the terminal reaction of the shared lower beta-ketoadipate pathway. Reason: This branch-neutral process annotation is missing from GOA. UniProt places PcaF-I at step 2 of 2 after aromatic ring-cleavage branches converge, and KT2440 proteomics detects PcaF induction by substrates entering through both catechol- and protocatechuate-derived routes. Supporting Evidence: file:PSEPK/pcaF/pcaF-uniprot.txt beta-ketoadipate pathway; acetyl-CoA and succinyl-CoA from 3-oxoadipate: step 2/2. PMID:16470664 beta-Ketoadipyl CoA thiolase (PcaF) and 3-oxoadipate enol-lactone hydrolase (PcaD) were induced by benzoate, p-hydroxybenzoate and vanilline |
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Download this section (compressed HTML)Q: Is PcaF-I dedicated to beta-ketoadipate turnover in vivo, or can it efficiently process alternative CoA thioesters under physiological conditions?
Q: How is pcaF-I coordinated transcriptionally with the rest of the protocatechuate branch in KT2440 under mixed aromatic substrates?
Experiment: Construct a clean pcaF-I deletion in KT2440 and test growth plus metabolite accumulation on protocatechuate, p-hydroxybenzoate, vanillate, and benzoate to confirm the pathway block at the 3-oxoadipyl-CoA cleavage step.
Hypothesis: Loss of pcaF-I will prevent efficient flux through the beta-ketoadipate pathway and cause accumulation of upstream protocatechuate-branch intermediates.
Experiment: Purify PcaF-I and compare catalytic efficiency for 3-oxoadipyl-CoA versus alternative acyl-CoA substrates to quantify whether the enzyme is pathway-specialized or broadly permissive like other degradative thiolases.
Hypothesis: PcaF-I will show clear catalytic preference for 3-oxoadipyl-CoA despite sharing general thiolase-family chemistry with broader acyltransferases.
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