Beta-ketoadipate lower pathway from 3-oxoadipate to central metabolites

Species-neutral bacterial module for the shared lower beta-ketoadipate pathway that converts 3-oxoadipate and CoA to acetyl-CoA and succinate while recycling a succinyl-CoA CoA donor. A two-subunit PcaIJ-like CoA-transferase first transfers CoA from succinyl-CoA to 3-oxoadipate, producing 3-oxoadipyl-CoA and succinate. A PcaF-like thiolase then cleaves 3-oxoadipyl-CoA with CoA to acetyl-CoA and succinyl-CoA, regenerating the donor consumed in the first reaction. The module begins after catechol- and protocatechuate-derived upper branches converge at 3-oxoadipate and excludes those branch-specific ring-cleavage reactions. The same two-enzyme organization is conserved in aromatic-degrading Gammaproteobacteria of the orders Pseudomonadales and Moraxellales, represented here by biochemically and genetically characterized members from Pseudomonas putida and Acinetobacter baylyi.

Exemplars are Pseudomonas putida KT2440 PcaI/PP_3951/Q88FX5, PcaJ/PP_3952/P0A101 and PcaF-I/PP_1377/Q88N39, and Acinetobacter baylyi ADP1 PcaI/ACIAD1704/Q43973, PcaJ/ACIAD1705/Q59091 and PcaF/ACIAD1706/Q43974. The ADP1 proteins were added because the ADP1-lineage transferase was purified and shown to be an alpha2beta2 heteromer and all three carry Swiss-Prot protein-level evidence; they move the module beyond a single Pseudomonas instance without inflating member counts. The module stays scoped to Bacteria: fungal and actinobacterial routes to 3-oxoadipate exist but their lower-pathway enzymes were not used as exemplars here. Families are grounded with NCBIfam TIGR02429 (PcaI), TIGR02428 (PcaJ) and TIGR02430 (PcaF), which are specific to the pathway enzymes. The corresponding PANTHER families (PTHR13707 ketoacid-CoA transferase, which includes eukaryotic SCOT, and PTHR18919 acetyl-CoA C-acyltransferase, which includes all thiolases) are much broader and are deliberately not used as family terms. The PcaIJ reaction is a property of the heteromeric enzyme, so each subunit is modeled as contributing to, rather than independently enabling, 3-oxoadipate CoA-transferase activity. The catechol_ortho_cleavage and protocatechuate_ortho_cleavage modules represent separate upstream routes that feed this shared lower pathway.