3-oxoadipate degradation

MetaCyc:PWY-2361

Complete two-reaction 3-oxoadipate degradation module in MetaCyc PWY-2361, with Pseudomonas putida catalyst context. CoA transfer from succinyl-CoA forms 3-oxoadipyl-CoA and succinate; thiolysis with CoA forms acetyl-CoA and regenerates succinyl-CoA. The native reactions are reversible, while this pathway selects CoA transfer followed by thiolysis. The upstream catechol and protocatechuate branches are distinct modules. Native catalyst assemblies retain source-scoped annotations and do not establish universal strain composition. Regulation edges describe expression of the pcaIJ and pcaF products in the PRS2000 experimental lineage, not direct activation of purified enzymes. Adipate is an experimental nonmetabolizable inducer analog. Q52154 matches the deposited pcaR translation, while alternative initiating methionines remain uncertain.

Pathway type

degradation

Organism scope

Pseudomonas putida NCBITaxon:303

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Pathway network

16 nodes · 22 asserted directed edges

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Reaction / activity
Chemical / cofactor
Protein / complex
Pathway
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Pseudomonas putida `NCBITaxon:303`	taxon
3-oxoadipate(2-) `CHEBI:15775`	small molecule
3-oxoadipyl-CoA(5-) `CHEBI:57348`	small molecule
succinyl-CoA(5-) `CHEBI:57292`	small molecule
succinate(2-) `CHEBI:30031`	small molecule
acetyl-CoA(4-) `CHEBI:57288`	small molecule
coenzyme A(4-) `CHEBI:57287`	small molecule
3-oxoadipate CoA-transferase `MetaCyc:CPLX-2722`	complex
α subunit of β-ketoadipate succinyl-CoA transferase `MetaCyc:MONOMER-3190`	protein
β subunit of β-ketoadipate succinyl-CoA transferase `MetaCyc:MONOMER-3191`	protein
β-ketoadipyl CoA thiolase `MetaCyc:CPLX-2746`	complex
subunit of β-ketoadipyl CoA thiolase `MetaCyc:MONOMER-3207`	protein
Pca regulon regulatory protein `UniProtKB:Q52154`	protein
adipate(2-) `CHEBI:17128`	small molecule
3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	molecular activity	left to right
3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	molecular activity	right to left

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	part_of The complete native pathway contains this reaction. Native reaction reversibility is distinct from the selected pathway traversal.	`MetaCyc:PWY-2361`	MetaCyc:PWY-2361 Source assertion: The native reaction-list contains 3-OXOADIPATE-COA-TRANSFERASE-RXN; its layout selects L2R. Source location `/ptools-xml/Pathway/reaction-list/Reaction[@frameid="3-OXOADIPATE-COA-TRANSFERASE-RXN"]; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid="3-OXOADIPATE-COA-TRANSFERASE-RXN"]/direction` MetaCyc:3-OXOADIPATE-COA-TRANSFERASE-RXN Source assertion: The native reaction cross-reference identifies RHEA:12049; the complete reaction direction is REVERSIBLE. Source location `/ptools-xml/Reaction/dblink[dblink-db="RHEA"]; /ptools-xml/Reaction/reaction-direction`
3-oxoadipate(2-) `CHEBI:15775`	consumes Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	RHEA:12049 Source assertion: RHEA:12049 lists CHEBI:15775 as a substrate with coefficient 1. Source location `RHEA:12049/rh:substrates -> http://rdf.rhea-db.org/12048_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_12048_compound_1219/rh:compound -> http://rdf.rhea-db.org/Compound_1219/rh:chebi`
succinyl-CoA(5-) `CHEBI:57292`	consumes Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	RHEA:12049 Source assertion: RHEA:12049 lists CHEBI:57292 as a substrate with coefficient 1. Source location `RHEA:12049/rh:substrates -> http://rdf.rhea-db.org/12048_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_12048_compound_4684/rh:compound -> http://rdf.rhea-db.org/Compound_4684/rh:chebi`
3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	produces Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	3-oxoadipyl-CoA(5-) `CHEBI:57348`	RHEA:12049 Source assertion: RHEA:12049 lists CHEBI:57348 as a product with coefficient 1. Source location `RHEA:12049/rh:products -> http://rdf.rhea-db.org/12048_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_12048_compound_2553/rh:compound -> http://rdf.rhea-db.org/Compound_2553/rh:chebi`
3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	produces Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	succinate(2-) `CHEBI:30031`	RHEA:12049 Source assertion: RHEA:12049 lists CHEBI:30031 as a product with coefficient 1. Source location `RHEA:12049/rh:products -> http://rdf.rhea-db.org/12048_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_12048_compound_2501/rh:compound -> http://rdf.rhea-db.org/Compound_2501/rh:chebi`
3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	part_of The complete native pathway contains this reaction. Native reaction reversibility is distinct from the selected pathway traversal.	`MetaCyc:PWY-2361`	MetaCyc:PWY-2361 Source assertion: The native reaction-list contains RXN-3641; its layout selects R2L. Source location `/ptools-xml/Pathway/reaction-list/Reaction[@frameid="RXN-3641"]; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid="RXN-3641"]/direction` MetaCyc:RXN-3641 Source assertion: The native reaction cross-reference identifies RHEA:19483; the complete reaction direction is REVERSIBLE. Source location `/ptools-xml/Reaction/dblink[dblink-db="RHEA"]; /ptools-xml/Reaction/reaction-direction`
3-oxoadipyl-CoA(5-) `CHEBI:57348`	consumes Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	RHEA:19483 Source assertion: RHEA:19483 lists CHEBI:57348 as a substrate with coefficient 1. Source location `RHEA:19483/rh:substrates -> http://rdf.rhea-db.org/19481_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_19481_compound_2553/rh:compound -> http://rdf.rhea-db.org/Compound_2553/rh:chebi`
coenzyme A(4-) `CHEBI:57287`	consumes Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	RHEA:19483 Source assertion: RHEA:19483 lists CHEBI:57287 as a substrate with coefficient 1. Source location `RHEA:19483/rh:substrates -> http://rdf.rhea-db.org/19481_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_19481_compound_1264/rh:compound -> http://rdf.rhea-db.org/Compound_1264/rh:chebi`
3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	produces Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	succinyl-CoA(5-) `CHEBI:57292`	RHEA:19483 Source assertion: RHEA:19483 lists CHEBI:57292 as a product with coefficient 1. Source location `RHEA:19483/rh:products -> http://rdf.rhea-db.org/19481_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_19481_compound_4684/rh:compound -> http://rdf.rhea-db.org/Compound_4684/rh:chebi`
3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	produces Coefficient 1 in the selected directional Rhea equation; all charged chemical side participants are retained.	acetyl-CoA(4-) `CHEBI:57288`	RHEA:19483 Source assertion: RHEA:19483 lists CHEBI:57288 as a product with coefficient 1. Source location `RHEA:19483/rh:products -> http://rdf.rhea-db.org/19481_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_19481_compound_4271/rh:compound -> http://rdf.rhea-db.org/Compound_4271/rh:chebi`
3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	provides_input_for CoA transfer supplies 3-oxoadipyl-CoA to the subsequent thiolysis step. Succinyl-CoA is consumed by the first step and regenerated by the second.	3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	MetaCyc:PWY-2361 Source assertion: RXN-3641 follows 3-OXOADIPATE-COA-TRANSFERASE-RXN; the pathway layouts share 3-KETO-ADIPYL-COA. Source location `/ptools-xml/Pathway/reaction-ordering[Reaction/@frameid="RXN-3641"]/predecessor-reactions; /ptools-xml/Pathway/reaction-layout`
3-oxoadipate CoA-transferase `MetaCyc:CPLX-2722`	catalyzes Native purified-protein annotation, citing PMID:6780551. The separate native complex comment saying the enzyme was not purified conflicts with this annotation and the primary report.	3-oxoadipate + succinyl-CoA => 3-oxoadipyl-CoA + succinate `RHEA:12049`	MetaCyc:ENZRXN-3369 Source assertion: The activity links CPLX-2722 to 3-OXOADIPATE-COA-TRANSFERASE-RXN and carries native evidence code EV-EXP-IDA-PURIFIED-PROTEIN. Source location `/ptools-xml/Enzymatic-Reaction/enzyme; /ptools-xml/Enzymatic-Reaction/reaction; /ptools-xml/Enzymatic-Reaction/evidence`
β-ketoadipyl CoA thiolase `MetaCyc:CPLX-2746`	catalyzes Native mutant-phenotype annotation, citing PMID:7961399; this does not assert purification of the P. putida thiolase or direct measurement of its native oligomerization.	3-oxoadipyl-CoA + CoA => succinyl-CoA + acetyl-CoA `RHEA:19483`	MetaCyc:ENZRXN-5295 Source assertion: The activity links CPLX-2746 to RXN-3641 and carries native evidence code EV-EXP-IMP. Source location `/ptools-xml/Enzymatic-Reaction/enzyme; /ptools-xml/Enzymatic-Reaction/reaction; /ptools-xml/Enzymatic-Reaction/evidence`
3-oxoadipate CoA-transferase `MetaCyc:CPLX-2722`	has_part The native complex annotates 2 copies of this component. The native alpha2beta2 assignment follows the historical oligomer measurements; current UniProt subunit entries instead say heterodimer, a retained source disagreement.	α subunit of β-ketoadipate succinyl-CoA transferase `MetaCyc:MONOMER-3190`	MetaCyc:CPLX-2722 Source assertion: The component list assigns coefficient 2 to MONOMER-3190. Source location `/ptools-xml/Protein/component[Protein/@frameid="MONOMER-3190"]/coefficient` MetaCyc:MONOMER-3190 Source assertion: The native monomer has a reciprocal component-of reference to CPLX-2722. Source location `/ptools-xml/Protein/component-of/Protein` UniProtKB:Q01103 Source assertion: The issuing SUBUNIT annotation says Heterodimer. This is retained as a conflicting assembly annotation, not substituted for the native historical alpha2beta2 model. Source location `$.comments[commentType="SUBUNIT"].texts`
3-oxoadipate CoA-transferase `MetaCyc:CPLX-2722`	has_part The native complex annotates 2 copies of this component. The native alpha2beta2 assignment follows the historical oligomer measurements; current UniProt subunit entries instead say heterodimer, a retained source disagreement.	β subunit of β-ketoadipate succinyl-CoA transferase `MetaCyc:MONOMER-3191`	MetaCyc:CPLX-2722 Source assertion: The component list assigns coefficient 2 to MONOMER-3191. Source location `/ptools-xml/Protein/component[Protein/@frameid="MONOMER-3191"]/coefficient` MetaCyc:MONOMER-3191 Source assertion: The native monomer has a reciprocal component-of reference to CPLX-2722. Source location `/ptools-xml/Protein/component-of/Protein` UniProtKB:P0A102 Source assertion: The issuing SUBUNIT annotation says Heterodimer. This is retained as a conflicting assembly annotation, not substituted for the native historical alpha2beta2 model. Source location `$.comments[commentType="SUBUNIT"].texts`
β-ketoadipyl CoA thiolase `MetaCyc:CPLX-2746`	has_part The native complex annotates 4 copies of this component. The homotetramer is a source annotation, not an oligomer measurement established by the cited P. putida mutant-phenotype experiment.	subunit of β-ketoadipyl CoA thiolase `MetaCyc:MONOMER-3207`	MetaCyc:CPLX-2746 Source assertion: The component list assigns coefficient 4 to MONOMER-3207. Source location `/ptools-xml/Protein/component[Protein/@frameid="MONOMER-3207"]/coefficient` MetaCyc:MONOMER-3207 Source assertion: The native monomer has a reciprocal component-of reference to CPLX-2746. Source location `/ptools-xml/Protein/component-of/Protein`
Pca regulon regulatory protein `UniProtKB:Q52154`	regulates PcaR is required for inducer-dependent pcaIJ expression in the PRS2000 lineage. The quoted pcaI-lacZ reporter measures the promoter of the independently established pcaIJ operon. This is transcriptional regulation, not binding to or direct activation of the transferase.	3-oxoadipate CoA-transferase `MetaCyc:CPLX-2722`	PMID:8376330 PcaR is required for pcaI induction Source location `p. 5836, text immediately below Table 3; pcaI reporter assay and pcaIJ operon context` UniProtKB:Q52154 Source assertion: The reviewed FUNCTION annotation describes positive regulation of pcaBDC, pcaIJ and pcaF; its sequence reference identifies strain PRS2000. Source location `$.comments[commentType="FUNCTION"]; $.references[0].referenceComments[type="STRAIN"]`
3-oxoadipate(2-) `CHEBI:15775`	regulates 3-Oxoadipate induces synthesis of the transferase under the source-described conditions, with PcaR-dependent pcaIJ expression. The edge represents expression induction; neither direct inducer binding to PcaR nor catalytic activation of the transferase is asserted.	3-oxoadipate CoA-transferase `MetaCyc:CPLX-2722`	MetaCyc:ENZRXN-3369 Source assertion: The native comment states that synthesis of the P. putida transferase is induced by beta-ketoadipate and cites Parales 1993 and Harwood 1996. Source location `/ptools-xml/Enzymatic-Reaction/comment`
adipate(2-) `CHEBI:17128`	regulates Adipate is a nonmetabolizable experimental inducer analog. In the PRS2000-derived PRS4050 chromosomal pcaI-lacZ reporter, 20 mM adipate with 10 mM glucose increased beta-galactosidase activity. This is promoter induction rather than a transferase reaction substrate or direct catalytic activation.	3-oxoadipate CoA-transferase `MetaCyc:CPLX-2722`	PMID:8376330 Growth with adipate, β-ketoadipate, or aromatic compounds caused a 10- to 20-fold induction Source location `p. 5836, chromosomal pcaI-lacZ fusion results and Fig. 6; reporter strain PRS4050`
Pca regulon regulatory protein `UniProtKB:Q52154`	regulates PcaR is required for pcaF expression. This is supported by the later 1995 author abstract and reviewed regulatory annotation; the full 1995 paper was inaccessible here. It supersedes the 1994 paper's explicit uncertainty and does not assert direct PcaR binding to the thiolase.	β-ketoadipyl CoA thiolase `MetaCyc:CPLX-2746`	PMID:8522507 is required for expression of both pcaF and pcaK Source location `Author abstract, sentence beginning PcaR; abstract-only primary inspection` UniProtKB:Q52154 Source assertion: The reviewed FUNCTION annotation includes positive regulation of pcaF within the pca regulon. Source location `$.comments[commentType="FUNCTION"].texts`
3-oxoadipate(2-) `CHEBI:15775`	regulates 3-Oxoadipate induces pcaF expression as reported in the 1995 author abstract. Full-paper methods and data were inaccessible here. This is expression induction of the terminal thiolase in the source context, not direct ligand binding or activation of purified PcaF.	β-ketoadipyl CoA thiolase `MetaCyc:CPLX-2746`	PMID:8522507 the pathway intermediate beta-ketoadipate induces both genes Source location `Author abstract, pcaF/pcaK expression sentence; abstract-only primary inspection`
adipate(2-) `CHEBI:17128`	regulates PRS2000 cell extracts showed thiolase activity of 16.1 on 10 mM glucose versus 111.0 nmol/min/mg on glucose plus 20 mM adipate. The pcaF mutant retained only low activity. This supports inducer-dependent expression in the experimental lineage, not direct activation of the purified enzyme.	β-ketoadipyl CoA thiolase `MetaCyc:CPLX-2746`	PMID:7961399 Thiolase activity for PRS2000 was 16.1 and 111.0 nmol of β-ketoadipyl-CoA disappeared per min per mg of protein Source location `p. 6485, first paragraph; conditions in p. 6483, pcaF mutant characterization, continued across Fig. 4`

References

MetaCyc:PWY-2361 MetaCyc PWY-2361: complete native object (source version: META PGDB 27.0)
MetaCyc:CPLX-2722 MetaCyc CPLX-2722: complete native object (source version: META PGDB 27.0)
MetaCyc:MONOMER-3190 MetaCyc MONOMER-3190: complete native object (source version: META PGDB 27.0)
MetaCyc:MONOMER-3191 MetaCyc MONOMER-3191: complete native object (source version: META PGDB 27.0)
MetaCyc:CPLX-2746 MetaCyc CPLX-2746: complete native object (source version: META PGDB 27.0)
MetaCyc:MONOMER-3207 MetaCyc MONOMER-3207: complete native object (source version: META PGDB 27.0)
MetaCyc:3-OXOADIPATE-COA-TRANSFERASE-RXN MetaCyc 3-OXOADIPATE-COA-TRANSFERASE-RXN: complete native object (source version: META PGDB 27.0)
RHEA:12049 Rhea 12049: complete directional reaction and participant RDF (source version: Rhea 142 (2026-09-02), complete RDF; directional family identity retained)
MetaCyc:RXN-3641 MetaCyc RXN-3641: complete native object (source version: META PGDB 27.0)
RHEA:19483 Rhea 19483: complete directional reaction and participant RDF (source version: Rhea 142 (2026-09-02), complete RDF; directional family identity retained)
MetaCyc:ENZRXN-3369 MetaCyc ENZRXN-3369: complete native object (source version: META PGDB 27.0)
MetaCyc:ENZRXN-5295 MetaCyc ENZRXN-5295: complete native object (source version: META PGDB 27.0)
PMID:8376330 Regulation of the pcaIJ genes for aromatic acid degradation in Pseudomonas putida (source version: Original archived page 5836 scan, 1993; digest covers this quoted page, not the complete paper. All ten pages were inspected separately.)
PMID:7961399 Identification of the pcaRKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate (source version: Original archived page 6485 scan, 1994; digest covers this quoted page. Assay conditions are on separately retained page 6483; all ten pages were inspected.)
PMID:8522507 Repression of 4-hydroxybenzoate transport and degradation by benzoate: a new layer of regulatory control in the Pseudomonas putida beta-ketoadipate pathway (source version: Author abstract in the original PMC HTML, 1995; full paper, tables and figures were not accessible in this retrieval.)
UniProtKB:Q52154 Pca regulon regulatory protein (source version: Reviewed UniProtKB JSON retrieved 2026-10-14; entry 100, sequence 1)
UniProtKB:Q01103 3-oxoadipate CoA-transferase subunit A (source version: Reviewed UniProtKB JSON retrieved 2026-10-14; entry 86, sequence 2)
UniProtKB:P0A102 3-oxoadipate CoA-transferase subunit B (source version: Reviewed UniProtKB JSON retrieved 2026-10-14; entry 70, sequence 2)

Curation history

2026-10-14T10:05:38Z codex
- CREATE — Add the complete two-step 3-oxoadipate degradation module
  Curated MetaCyc PWY-2361 with exact Rhea and ChEBI chemistry, native Pseudomonas putida catalyst assemblies, and source-scoped pcaIJ/pcaF expression regulation. Retained wrong native citation, oligomer annotation, PcaR sequence-length, and inaccessible-primary-paper limitations. All prior authority terms and source owners are preserved. Evidence and validation results belong to research/pathway_additions/2026-10-14-next-249/oxoadipate; full raw originals remain external. Independent scientific review and required full gates follow this author curation event.
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