UniProt accession Q88N39 corresponds to pcaF-I / PP_1377 in Pseudomonas putida KT2440 and is annotated as beta-ketoadipyl-CoA thiolase (EC 2.3.1.174), the enzyme that catalyzes thiolytic cleavage of beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA in the beta-ketoadipate pathway [file:PSEPK/pcaF/pcaF-uniprot.txt "Name=pcaF-I"; "Catalyzes thiolytic cleavage of beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA"; "beta-ketoadipate pathway; acetyl-CoA and succinyl-CoA from 3-oxoadipate: step 2/2."].
KT2440 proteomics supports placement of PcaF in convergent aromatic catabolism: PcaF was induced during growth on benzoate, p-hydroxybenzoate, and vanillin, consistent with use in the shared beta-ketoadipate degradation pathway [PMID:16470664 Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis, "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."].
Older genetics in P. putida PRS2000 identifies pcaF as the terminal thiolase step of the pathway [PMID:7961399 Identification of the pcaRKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate, "pcaF encodes beta-ketoadipyl-coenzyme A thiolase, the last enzyme in the pathway."].
pcaF expression is coordinated with the protocatechuate branch regulator PcaR and induced by beta-ketoadipate [PMID:8522507 Repression of 4-hydroxybenzoate transport and degradation by benzoate: a new layer of regulatory control in the Pseudomonas putida beta-ketoadipate pathway, "PcaR, a transcriptional activator of several genes of the beta-ketoadipate pathway, is required for expression of both pcaF and pcaK, and the pathway intermediate beta-ketoadipate induces both genes."].
The KT2440 structural paper treats PcaF as a degradative thiolase model and shows features expected for degradative rather than biosynthetic thiolases [PMID:32647822 Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase, "we exploit, a tetrameric degradative thiolase from Pseudomonas putida KT2440 annotated as PcaF, as a model system"; "Degradative thiolases have different active site architecture when compared to biosynthetic thiolases"].
The same structural study reports a tunnel capable of accommodating acyl-CoA
chains longer than C8 PMID:32647822. These ligand-trapping experiments used active-site
mutants and crystallographic soaking, so they demonstrate in vitro substrate
accommodation rather than a physiological role in lipid metabolism. The
paper separately states that beta-ketoadipyl-CoA is the natural substrate
PMID:32647822.
Current GOA for Q88N39 is entirely automated and contains six annotations. The most specific molecular function term is GO:0033812 3-oxoadipyl-CoA thiolase activity; the two generic acyltransferase terms are redundant umbrella labels, and GO:0006629 lipid metabolic process looks like a family-level over-annotation rather than a pathway-specific assignment for this aromatic catabolic enzyme [file:PSEPK/pcaF/pcaF-goa.tsv "GO:0033812"; "GO:0016746"; "GO:0016747"; "GO:0006629"; "GO:0019619"].
This curation adds GO:0042952 beta-ketoadipate pathway as a proposed NEW
annotation because UniProt places PcaF-I at step 2 of 2 in the shared lower
pathway [file:PSEPK/pcaF/pcaF-uniprot.txt "beta-ketoadipate pathway;
acetyl-CoA and succinyl-CoA from 3-oxoadipate: step 2/2."]. The term is not
placed in proposed_new_terms, which is reserved for ontology terms that do
not yet exist.