Benzoate upper degradation pathway

A reusable bacterial aromatic-catabolism module for the upper benzoate degradation route that converts benzoate to catechol. The pathway begins with a multicomponent benzoate 1,2-dioxygenase system, represented here by BenA-like large oxygenase, BenB-like small oxygenase, and BenC-like reductase roles, and is followed by a BenD-like cis-diol dehydrogenase. Pseudomonas putida KT2440 benA/benB/benC/benD provide the local PSEPK exemplars for this module, but the module boundary is the conserved benzoate-to-catechol pathway segment rather than a PSEPK-specific locus definition.

MODULE:benzoate_upper_pathwayDRAFTCONCRETEMetabolic Pathwaymodules/benzoate_upper_pathway.yaml
benzoate catabolic process via hydroxylationGO:0043640
GO:0043640
benzoate catabolic process via hydroxylation
GO:0043640 grounds the module as benzoate catabolism by hydroxylation, covering dioxygenation of benzoate to a cis-dihydrodiol intermediate and dehydrogenation of that intermediate to catechol.
KEGG:ppu00622
Pseudomonas putida KT2440 xylene degradation
The PSEPK partition table assigns benA, benB, benC, and benD as the primary KT2440 genes in KEGG ppu00622 for this upper benzoate route.
KEGG:M00551
Benzoate degradation, benzoate to catechol
KEGG module M00551 captures the narrower benzoate-to-catechol pathway boundary implemented by benA, benB, benC, and benD; this is the preferred biochemical anchor for the module over the broader ppu00622 map label.
file:projects/P_PUTIDA/data/psepk_pathway_membership.tsv
PSEPK pathway membership table
The local membership table lists benA, benB, benC, and benD in ppu00622 and overlapping aromatic-catabolism maps, while PP_1791 and PP_2504 are ppu00621 lower-pathway spillover genes and are outside this module.
PMID:12534466
Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440
The KT2440 aromatic-catabolism map places the ben genes in a benzoate peripheral pathway feeding catechol into the beta-ketoadipate route.
PMID:11053377
BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida.
The BenR study identifies benABC as likely encoding the benzoate dioxygenase system and supports co-regulated benzoate-responsive expression.
file:PSEPK/benA/benA-ai-review.yaml
Curated benA review
The benA review accepts benzoate 1,2-dioxygenase activity and benzoate catabolism via hydroxylation as core functions of the large oxygenase subunit.
file:PSEPK/benB/benB-ai-review.yaml
Curated benB review
The benB review treats BenB as a beta subunit contributing to the BenABC dioxygenase complex and removes a propagated 3-phenylpropionate process assignment.
file:PSEPK/benC/benC-ai-review.yaml
Curated benC review
The benC review accepts ferredoxin-NAD+ reductase activity and contribution to benzoate 1,2-dioxygenase activity as the electron-transfer role for the pathway's first step.
file:PSEPK/benD/benD-ai-review.yaml
Curated benD review
The benD review accepts the exact cis-diol dehydrogenase activity and removes a propagated fatty-acid elongation process assignment.
file:modules/benzoate_upper_pathway-deep-research-openscientist.md
OpenScientist module research for benzoate upper degradation
OpenScientist module-level research supports the benzoate-to-catechol boundary, the obligatory ordering of BenABC dioxygenation before BenD dehydrogenation, and the exclusion of downstream catechol cleavage and CoA-dependent benzoate routes from this module.
file:projects/P_PUTIDA/deep-research/PSEPK__benzoate_upper_pathway__ppu00622-deep-research-openscientist.md
OpenScientist PSEPK ppu00622 benzoate upper-pathway review
OpenScientist concluded that the benzoate upper pathway is covered by benA/benB/benC/benD, that PP_1791 and PP_2504 are lower meta-cleavage spillover candidates, and that the ppu00622 xylene map label is broader than the endogenous KT2440 benzoate-to-catechol route.

First-pass PSEPK interpretation: benA/benB/benC/benD satisfy the upper benzoate degradation segment from benzoate to catechol. The broader KEGG ppu00622 "xylene degradation" bucket intersects several aromatic maps, but this module deliberately stops at catechol; catechol ring cleavage, 2-hydroxymuconate/4-oxalocrotonate steps, and the PP_1791/PP_2504 ppu00621 spillover genes belong in downstream catechol/meta-cleavage modules. The module also keeps the electron-transfer and oxygenase roles separate so that BenC is not represented as independently enabling the terminal oxygenase chemistry.

3Nodes
2Parts
0Variant Sets
0Variants
4Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • benzoate_upper_pathway-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • benabc_dioxygenation → bend_dehydrogenation [NOT_CHECKED]

Gene-review completeness (4/4 grounded genes reviewed)

4 complete review(s) · 4 with deep research · 0 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
benA Q88I40 ✓ ✓ ✓
benB Q88I39 ✓ ✓ ✓
benC Q88I38 ✓ ✓ ✓
benD Q88I37 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
cytosolGO:0005829
Benzoate to catechol upper pathwayMetabolic Pathwaybenzoate_upper_pathway
benzoate catabolic process via hydroxylationGO:0043640
Context
bacteriaNCBITaxon:2
cytosolGO:0005829

Connections

The cis-dihydrodiol produced by BenABC is the substrate for BenD.
Part 1: benzoate dioxygenation to a cis-dihydrodiol
BenABC benzoate dioxygenationReactionbenabc_dioxygenation

A multicomponent benzoate 1,2-dioxygenase system introduces both atoms of dioxygen into benzoate, producing the cis-dihydrodiol intermediate used by the downstream dehydrogenase step.

Annotons

Benzoate 1,2-dioxygenase large oxygenase subunit
bena_large_oxygenase
Participant: Family: benzoate 1,2-dioxygenase large subunit family
Family:
benzoate 1,2-dioxygenase large subunit familyInterPro:IPR017639 BenA-like ring-hydroxylating dioxygenase alpha/large subunits containing the Rieske and catalytic oxygenase domains.
Representative Members: PSEPK benA exemplarUniProtKB:Q88I40

Function

benzoate 1,2-dioxygenase activityGO:0018623
Substrates: benzoate dioxygen NADH
Products: cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate NAD+
Cofactors: Rieske [2Fe-2S] clusterGO:0051537 non-heme ironGO:0005506

Processes

benzoate catabolic process via hydroxylationGO:0043640

Locations

cytosolGO:0005829

Terminal oxygenase large subunit that carries the Rieske electron-transfer cluster and catalytic non-heme iron site for benzoate cis-dihydroxylation.

Benzoate 1,2-dioxygenase small oxygenase subunit
benb_small_oxygenase
Participant: Family: benzoate 1,2-dioxygenase small subunit family
Family:
benzoate 1,2-dioxygenase small subunit familyInterPro:IPR017641 BenB-like ring-hydroxylating dioxygenase beta/small subunits that support the terminal oxygenase component.
Representative Members: PSEPK benB exemplarUniProtKB:Q88I39

Function

contributes to benzoate 1,2-dioxygenase activityGO:0018623
Substrates: benzoate dioxygen
Products: cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate

Processes

benzoate catabolic process via hydroxylationGO:0043640

Locations

cytosolGO:0005829

Small oxygenase subunit that contributes to the BenAB terminal oxygenase component rather than independently catalyzing the full dioxygenase reaction.

Benzoate dioxygenase reductase/electron-transfer component
benc_electron_transfer
Participant: Family: BenC-like FAD/NAD-binding reductase family
Family:
BenC-like FAD/NAD-binding reductase familyInterPro:IPR047683 BenC-like reductase components that provide electrons to the terminal benzoate dioxygenase oxygenase.
Representative Members: PSEPK benC exemplarUniProtKB:Q88I38

Function

ferredoxin-NAD+ reductase activityGO:0008860
Substrates: NADH oxidized BenC [2Fe-2S] center
Products: NAD+ reduced BenC [2Fe-2S] center
Cofactors: FADGO:0050660 [2Fe-2S] clusterGO:0051537

Processes

benzoate catabolic process via hydroxylationGO:0043640

Locations

cytosolGO:0005829

Reductase/electron-transfer component that supplies reducing equivalents needed by the BenAB oxygenase through a fused FAD/[2Fe-2S] electron-transfer chain; this is modeled as its own redox function plus contribution to the dioxygenase step.

Part 2: cis-dihydrodiol dehydrogenation to catechol
BenD cis-diol dehydrogenationReactionbend_dehydrogenation

BenD-like dehydrogenases oxidize the benzoate cis-dihydrodiol intermediate generated by BenABC, yielding catechol for downstream beta-ketoadipate or catechol-cleavage modules.

Annotons

Benzoate cis-dihydrodiol dehydrogenase
bend_cis_diol_dehydrogenase
Participant: Family: BenD dehydrogenase family
Family:
BenD dehydrogenase familyInterPro:IPR047686 BenD-like SDR-family enzymes catalyzing oxidation of the benzoate cis-dihydrodiol intermediate.
Representative Members: PSEPK benD exemplarUniProtKB:Q88I37

Function

1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase activityGO:0047116
Substrates: cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate NAD+
Products: catechol NADH carbon dioxide

Processes

benzoate catabolic process via hydroxylationGO:0043640

Locations

cytosolGO:0005829

Dehydrogenation step converting the BenABC product to catechol.