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.

MODULE:beta_ketoadipate_lower_pathwayDRAFTCONCRETEMetabolic Pathwaymodules/beta_ketoadipate_lower_pathway.yaml
beta-ketoadipate pathwayGO:0042952
GO:0042952
beta-ketoadipate pathway
GO:0042952 provides the process-level context for the shared reactions that channel 3-oxoadipate into central metabolism.
UniPathway:UPA00157
beta-ketoadipate pathway
UniPathway assigns PSEPK PcaI and PcaJ to step 1 of 2 in the conversion of 3-oxoadipate to acetyl-CoA and succinyl-CoA.
KEGG:ppu01220
Pseudomonas putida KT2440 degradation of aromatic compounds
The broad PSEPK aromatic-degradation map contains the lower-pathway enzymes, but the reusable biochemical boundary is the two-reaction sequence beginning at 3-oxoadipate.
PMID:1624453
Characterization of the genes encoding beta-ketoadipate:succinyl-coenzyme A transferase in Pseudomonas putida
The pcaI and pcaJ genes encode the two nonidentical subunits of the beta-ketoadipate:succinyl-CoA transferase that performs the penultimate reaction of the pathway.
file:PSEPK/pcaF/pcaF-ai-review.yaml
Curated PSEPK pcaF-I review
The review supports PcaF-I as the 3-oxoadipyl-CoA thiolase that completes conversion of the activated intermediate to acetyl-CoA and succinyl-CoA.

PSEPK exemplars are PcaI/PP_3951/Q88FX5, PcaJ/PP_3952/P0A101, and PcaF-I/PP_1377/Q88N39. 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.

3Nodes
2Parts
0Variant Sets
0Variants
2Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:beta_ketoadipate_lower_pathway deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (3/3 grounded genes reviewed)

3 complete review(s) · 3 with deep research · 0 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
pcaF-I Q88N39 ✓ ✓ ✓
pcaI Q88FX5 ✓ ✓ ✓
pcaJ P0A101 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
Beta-ketoadipate lower pathwayMetabolic Pathwaybeta_ketoadipate_lower_pathway
beta-ketoadipate pathwayGO:0042952
Context
bacteriaNCBITaxon:2

Connections

PcaIJ produces 3-oxoadipyl-CoA, the substrate cleaved by PcaF.
Part 1: 3-oxoadipate activation by CoA transfer
PcaIJ 3-oxoadipate CoA transferReactionpcaij_3_oxoadipate_coa_transfer

The PcaI- and PcaJ-like subunits form a heteromeric CoA-transferase that transfers CoA from succinyl-CoA to 3-oxoadipate.

Annotons

PcaIJ 3-oxoadipate CoA-transferase complex
pcaij_transferase_complex
Participant: Protein Complex: bacterial PcaIJ 3-oxoadipate CoA-transferase
Protein Complex:
bacterial PcaIJ 3-oxoadipate CoA-transferase Heteromeric CoA-transferase assembled from PcaI- and PcaJ-family subunits.
Active units:
PcaI CoA-transferase subunit
Participant: Family: PcaI 3-oxoadipate CoA-transferase subunit family
Family:
PcaI 3-oxoadipate CoA-transferase subunit familyNCBIfam:TIGR02429
Representative Members: PSEPK pcaI exemplarUniProtKB:Q88FX5
Role: Required alpha-like subunit that contributes to the heteromeric CoA-transferase reaction.
file:PSEPK/pcaI/pcaI-uniprot.txt
Q88FX5 records EC 2.8.3.6 and NCBIfam TIGR02429 for the PcaI subunit.
PcaJ CoA-transferase subunit
Participant: Family: PcaJ 3-oxoadipate CoA-transferase subunit family
Family:
PcaJ 3-oxoadipate CoA-transferase subunit familyNCBIfam:TIGR02428
Representative Members: PSEPK pcaJ exemplarUniProtKB:P0A101
Role: Required beta-like partner subunit that contributes to the heteromeric CoA-transferase reaction.
file:PSEPK/pcaJ/pcaJ-uniprot.txt
P0A101 records EC 2.8.3.6 and NCBIfam TIGR02428 for the PcaJ subunit.

Function

3-oxoadipate CoA-transferase activityGO:0047569
Substrates: 3-oxoadipate succinyl-CoA
Products: 3-oxoadipyl-CoA succinate

Processes

beta-ketoadipate pathwayGO:0042952

The molecular function is asserted for the assembled PcaIJ complex; the structured active units retain each subunit's exact family and PSEPK exemplar.

Part 2: 3-oxoadipyl-CoA thiolytic cleavage
PcaF 3-oxoadipyl-CoA thiolysisReactionpcaf_3_oxoadipyl_coa_thiolysis

A PcaF-like degradative thiolase cleaves 3-oxoadipyl-CoA with CoA, yielding acetyl-CoA and succinyl-CoA.

Annotons

PcaF 3-oxoadipyl-CoA thiolase
pcaf_thiolase
Participant: Family: PcaF 3-oxoadipyl-CoA thiolase family
Family:
PcaF 3-oxoadipyl-CoA thiolase familyNCBIfam:TIGR02430 Pathway-specific PcaF-like degradative thiolases of the bacterial beta-ketoadipate pathway.
Representative Members: PSEPK pcaF-I exemplarUniProtKB:Q88N39

Function

3-oxoadipyl-CoA thiolase activityGO:0033812
Substrates: 3-oxoadipyl-CoA coenzyme A
Products: acetyl-CoA succinyl-CoA

Processes

beta-ketoadipate pathwayGO:0042952

Completes the lower pathway by releasing two central-carbon thioesters from 3-oxoadipyl-CoA.