Hydroxycinnamate and vanillate catabolism to protocatechuate

A four-part bacterial peripheral aromatic-catabolism module in which Fcs activates ferulate to feruloyl-CoA, Ech cleaves the thioester to vanillin, Vdh oxidizes vanillin to vanillate, and the two-component VanAB enzyme O-demethylates vanillate to protocatechuate. Aromatic-acid uptake, formaldehyde detoxification, gallate catabolism, and the downstream protocatechuate beta-ketoadipate pathway are separate modules.

MODULE:hydroxycinnamate_vanillate_catabolismDRAFTCONCRETEMetabolic Pathwaymodules/hydroxycinnamate_vanillate_catabolism.yaml
ferulate catabolic processGO:1901067 aerobic phenol-containing compound catabolic processGO:0046191
GO:1901067
ferulate catabolic process
Defines the upper ferulate-catabolic context of the first three reactions.
RHEA:36251
trans-feruloyl-CoA synthase reaction
Defines ATP-dependent ferulate activation to feruloyl-CoA.
RHEA:62412
feruloyl-CoA hydratase/lyase reaction
Defines conversion of feruloyl-CoA and water to vanillin and acetyl-CoA.
RHEA:13309
vanillin dehydrogenase reaction
Defines NAD-dependent oxidation of vanillin to vanillate.
RHEA:13021
vanillate monooxygenase reaction
Defines VanAB conversion of vanillate to protocatechuate and formaldehyde.
file:projects/P_PUTIDA/deep-research/PSEPK__hydroxycinnamate-vanillate-catabolism__ppu00627-deep-research-openscientist.md
OpenScientist PSEPK hydroxycinnamate and vanillate catabolism synthesis
Species-aware retrieval identifies direct KT2440 evidence for every modeled reaction.
PMID:12764569
Functional analyses of genes involved in the metabolism of ferulic acid in Pseudomonas putida KT2440.
Separate fcs, ech, and vdh inactivation establishes the first three parts of the KT2440 route.
PMID:31809239
Biotransformation of corn bran derived ferulic acid to vanillic acid using engineered Pseudomonas putida KT2440.
A vanAB-nonfunctional KT2440 mutant establishes the terminal vanillate-metabolism part.

Ortholog selectors are used because current PANTHER subfamilies for these proteins visibly mix distinct acyl-CoA synthetase, hydratase, aldehyde dehydrogenase, and Rieske-oxygenase specificities. GalA-dependent gallate cleavage is a parallel pathway and is deliberately excluded from this serial ferulate-to-protocatechuate module.

5Nodes
4Parts
0Variant Sets
0Variants
5Annotons
3Connections

Derived QC

Recommended-field compliance

55.6% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)

Module deep research

✗ none found

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

Leaf nodes lacking representative members

4 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (3/5 grounded genes reviewed)

3 complete review(s) · 3 with deep research · 2 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
fcs Q88HK0 ✓ ✓ ✓
characterized Pseudomonas HR199 Vdh O05619 ✗ — —
characterized Pseudomonas fluorescens HCHL O69762 ✗ — —
vanA Q88GI6 ✓ ✓ ✓
vanB Q88GI5 ✓ ✓ ✓

Details

Hydroxycinnamate and vanillate catabolism to protocatechuateMetabolic Pathwayhydroxycinnamate_vanillate_catabolism
ferulate catabolic processGO:1901067 aerobic phenol-containing compound catabolic processGO:0046191

Connections

fcs_activation -> ech_cleavage Provides Input For
ech_cleavage -> vdh_oxidation Provides Input For
vdh_oxidation -> vanAB_demethylation Provides Input For
Part 1: ferulate activation
Feruloyl-CoA formationReactionfcs_activation

Annotons

Trans-feruloyl-CoA synthase
fcs_activity
Participant: Ortholog Of: PSEPK Fcs
Ortholog Of:
PSEPK FcsUniProtKB:Q88HK0
Orthologs retaining the characterized ferulate-activating EC 6.2.1.34 reaction.

Function

trans-feruloyl-CoA synthase activityGO:0050563
Substrates: (E)-ferulate ATP CoA
Products: (E)-feruloyl-CoA AMP diphosphate

Processes

ferulate catabolic processGO:1901067

ATP-dependent first committed step of the hydroxycinnamate route.

Part 2: feruloyl-CoA hydration and cleavage
Feruloyl-CoA hydratase/lyase reactionReactionech_cleavage

Annotons

Feruloyl-CoA hydratase/lyase
ech_activity
Participant: Ortholog Of: characterized Pseudomonas fluorescens HCHL
Ortholog Of:
characterized Pseudomonas fluorescens HCHLUniProtKB:O69762
Orthologs retaining the composite feruloyl-CoA hydration and retro-aldol cleavage reaction.

Function

feruloyl-CoA hydratase/lyase activityGO:0050547
Substrates: (E)-feruloyl-CoA water
Products: vanillin acetyl-CoA

Processes

ferulate catabolic processGO:1901067

Non-beta-oxidative two-carbon side-chain cleavage yielding vanillin.

Part 3: vanillin oxidation
Vanillin dehydrogenase reactionReactionvdh_oxidation

Annotons

Vanillin dehydrogenase
vdh_activity
Participant: Ortholog Of: characterized Pseudomonas HR199 Vdh
Ortholog Of:
characterized Pseudomonas HR199 VdhUniProtKB:O05619
Orthologs retaining NAD-dependent vanillin oxidation.

Function

vanillin dehydrogenase activityGO:0050608
Substrates: vanillin NAD+ water
Products: vanillate NADH

Processes

ferulate catabolic processGO:1901067

Oxidizes the vanillin intermediate to vanillate.

Part 4: vanillate O-demethylation
VanAB vanillate O-demethylaseProtein ComplexvanAB_demethylation

Annotons

VanA oxygenase subunit
vanA_oxygenase_activity
Participant: Ortholog Of: PSEPK VanA
Ortholog Of:
PSEPK VanAUniProtKB:Q88GI6
Orthologs retaining the Rieske oxygenase component of VanAB.

Function

vanillate monooxygenase activityGO:0018489
Substrates: vanillate oxygen
Products: protocatechuate formaldehyde

Processes

aerobic phenol-containing compound catabolic processGO:0046191

Rieske oxygenase subunit that performs substrate O-demethylation.

VanB electron-transfer subunit
vanB_reductase_activity
Participant: Ortholog Of: PSEPK VanB
Ortholog Of:
PSEPK VanBUniProtKB:Q88GI5
Orthologs retaining the FMN/2Fe-2S reductase component of VanAB.

Function

electron transfer activityGO:0009055
Substrates: NADH
Products: NAD+

Processes

aerobic phenol-containing compound catabolic processGO:0046191

Supplies reducing equivalents to VanA and contributes to complex-level vanillate monooxygenase activity.