Hydroxycinnamate and vanillate catabolism to protocatechuate

A four-step bacterial peripheral aromatic-catabolism route that funnels the hydroxycinnamate ferulate to protocatechuate by the non-beta-oxidative CoA-dependent pathway. A feruloyl-CoA synthetase (Fcs) activates ferulate to feruloyl-CoA; a crotonase-fold hydroxycinnamoyl-CoA hydratase-lyase (Ech/HCHL) hydrates the thioester and cleaves it to vanillin and acetyl-CoA; an NAD-dependent vanillin dehydrogenase (Vdh) oxidizes vanillin to vanillate; and the two-component Rieske oxygenase VanAB O-demethylates vanillate to protocatechuate and formaldehyde. Aromatic-acid uptake, formaldehyde detoxification, gallate catabolism and the downstream protocatechuate beta-ketoadipate pathway are separate modules.

MODULE:hydroxycinnamate_vanillate_catabolismCOMPLETECONCRETEMetabolic 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.
PMID:9461612
Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester.
The P. fluorescens hydratase-lyase gene establishes the feruloyl-CoA to vanillin step outside KT2440.
PMID:9098058
Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate.
HR199 vdh and vanAB convert vanillin via vanillate to protocatechuate and confer growth on vanillin when transferred.
PMID:10348863
Genetic analysis of a chromosomal region containing vanA and vanB, genes required for conversion of either ferulate or vanillate to protocatechuate in Acinetobacter.
Acinetobacter baylyi ADP1 mutants blocked in vanAB cannot catabolize ferulate or vanillate, extending the terminal step beyond Pseudomonas.

The route is anchored in Pseudomonas putida KT2440, where every step has target-strain genetic evidence, and is sampled in three further strains with experimental evidence: the P. fluorescens AN103 hydratase-lyase HCHL, the Pseudomonas sp. HR199 vanillin dehydrogenase, and the Acinetobacter baylyi ADP1 VanAB demethylase. The taxon context (Pseudomonadales) is the evidence-sampled envelope, not a claim of universality. Swiss-Prot-reviewed vanillin dehydrogenases of Corynebacterium glutamicum and Amycolatopsis and the Rhodococcus jostii RHA1 VanA (PTHR42986 and PTHR21266 member inventories) show the same enzymes in Actinomycetota, but no full-route exemplar outside Pseudomonadales is grounded here. Sphingomonad lignin catabolism uses a different, tetrahydrofolate-dependent vanillate demethylase and is not this module. Fcs, Ech, Vdh and VanA are grounded as reaction-qualified families without PANTHER identifiers: their PANTHER families (PTHR43201, PTHR42964, PTHR42986, PTHR21266) each mix substrate specificities within the subfamily that holds these enzymes, as recorded in the family reviews, so membership does not predict the reaction. Dedicated non-PANTHER signatures exist for the first two steps: NCBIfam NF006588 (p-hydroxycinnamoyl CoA hydratase/lyase), used as the Ech family term, and CDD cd05921 (FCS), matched by KT2440 Fcs. VanB is grounded to PTHR47354:SF1, which that family review includes in the scope of ferredoxin-NAD+ reductase activity (excluding only the SF7 flavin reductases). The Vdh exemplars differ in pathway entry point: the KT2440 evidence starts from ferulate and the HR199 evidence from vanillin, so the Vdh annoton carries both ferulate and vanillin catabolic process. The VanAB step uses aerobic phenol-containing compound catabolic process because GO has no vanillate catabolic process term; the KT2440 VanB gene review proposes one. GalA-dependent gallate cleavage is a parallel pathway and is excluded from this serial ferulate-to-protocatechuate module. Transport of ferulate and vanillate and handling of the formaldehyde released by VanAB are outside the module boundary.

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

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:hydroxycinnamate_vanillate_catabolism 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.

Function consistency and core coverage

9 gene-function check(s) reflected in core functions · 0 conflict(s) · 4 evidence or coverage gap(s) (14 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
fcs_activity fcs (PSEPK)
UniProtKB:Q88HK0
Family Representative 		trans-feruloyl-CoA synthase activity
GO:0050563 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ech_activity ech (PSEPK)
UniProtKB:Q88HJ8
Family Representative 		feruloyl-CoA hydratase/lyase activity
GO:0050547 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ech_activity HCHL (PSEFL)
UniProtKB:O69762
Family Representative 		feruloyl-CoA hydratase/lyase activity
GO:0050547 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vdh_activity vdh (PSEPK)
UniProtKB:Q88HJ9
Family Representative 		vanillin dehydrogenase (NAD+) activity
GO:0050608 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vdh_activity vdh (PSEUH)
UniProtKB:O05619
Family Representative 		vanillin dehydrogenase (NAD+) activity
GO:0050608 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vanA_oxygenase_activity vanA (PSEPK)
UniProtKB:Q88GI6
Family Representative 		vanillate monooxygenase activity
GO:0018489 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vanA_oxygenase_activity vanA (ACIAD)
UniProtKB:Q6FDI6
Family Representative 		vanillate monooxygenase activity
GO:0018489 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vanB_reductase_activity vanB (PSEPK)
UniProtKB:Q88GI5
Family Representative 		ferredoxin-NAD+ reductase activity
GO:0008860 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vanB_reductase_activity vanB (ACIAD)
UniProtKB:O24840
Family Representative 		ferredoxin-NAD+ reductase activity
GO:0008860 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
fcs_activity Feruloyl-CoA synthetases (Fcs)
Family 		trans-feruloyl-CoA synthase activity
GO:0050563 		Family Id Missing
The family has no identifier linking it to a curated family review.
ech_activity Hydroxycinnamoyl-CoA hydratase-lyases (Ech/HCHL)
NCBIfam:NF006588
Family 		feruloyl-CoA hydratase/lyase activity
GO:0050547 		Family Review Missing
No supported structured family review is available for NCBIfam:NF006588.
vdh_activity NAD-dependent vanillin dehydrogenases (Vdh)
Family 		vanillin dehydrogenase (NAD+) activity
GO:0050608 		Family Id Missing
The family has no identifier linking it to a curated family review.
vanA_oxygenase_activity VanA Rieske oxygenase subunits
Family 		vanillate monooxygenase activity
GO:0018489 		Family Id Missing
The family has no identifier linking it to a curated family review.
vanB_reductase_activity VanB reductases of PTHR47354:SF1
PANTHER:PTHR47354:SF1
Family 		ferredoxin-NAD+ reductase activity
GO:0008860 		Family Supported
Family review supports GO:0008860 for PANTHER:PTHR47354:SF1. The EC 1.18.1.3 reductase activity applies to the Rieske-system reductases that carry a [2Fe-2S] ferredoxin domain and reduce an iron-sulfur acceptor. It does not apply to the SF7 flavin reductases, which have no such domain and release reduced flavin instead.

Gene-review completeness (9/9 grounded genes reviewed)

9 complete review(s) · 3 with deep research · 0 missing review · 6 reviewed but lacking deep research

Gene Review Complete Deep research
ech Q88HJ8 ✓ ✓ ✗
fcs Q88HK0 ✓ ✓ ✓
O69762 O69762 ✓ ✓ ✗
vanA Q6FDI6 ✓ ✓ ✗
vanA Q88GI6 ✓ ✓ ✓
vanB O24840 ✓ ✓ ✗
vanB Q88GI5 ✓ ✓ ✓
vdh O05619 ✓ ✓ ✗
vdh Q88HJ9 ✓ ✓ ✗

Details

Context
Pseudomonadales with the CoA-dependent ferulate routeNCBITaxon:72274
Hydroxycinnamate and vanillate catabolism to protocatechuateMetabolic Pathwayhydroxycinnamate_vanillate_catabolism
ferulate catabolic processGO:1901067 aerobic phenol-containing compound catabolic processGO:0046191
Context
Pseudomonadales with the CoA-dependent ferulate routeNCBITaxon:72274

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: Family: Feruloyl-CoA synthetases (Fcs)
Family:
Feruloyl-CoA synthetases (Fcs) ATP-dependent ANL-superfamily acid-CoA ligases that activate ferulate, matched by the CDD feruloyl-CoA synthetase model cd05921. PANTHER places KT2440 Fcs in PTHR43201:SF32 beside o-succinylbenzoate-CoA ligases, so no PANTHER identifier is asserted for this role.
Representative Members: fcs (PSEPK)UniProtKB:Q88HK0

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: Family: Hydroxycinnamoyl-CoA hydratase-lyases (Ech/HCHL)
Family:
Hydroxycinnamoyl-CoA hydratase-lyases (Ech/HCHL)NCBIfam:NF006588 Crotonase-fold enzymes that hydrate feruloyl-CoA and cleave it by retro-aldol to vanillin and acetyl-CoA. Their PANTHER subfamily PTHR42964:SF1 also holds FabM isomerases, PksH dehydratases and LiuC, so the NCBIfam PRK09120 model, which both representatives match, is used instead of a PANTHER identifier.
Representative Members: ech (PSEPK)UniProtKB:Q88HJ8 HCHL (PSEFL)UniProtKB:O69762

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: Family: NAD-dependent vanillin dehydrogenases (Vdh)
Family:
NAD-dependent vanillin dehydrogenases (Vdh) Aldehyde dehydrogenases that oxidize vanillin to vanillate. Their PANTHER subfamily PTHR42986:SF1 also holds benzaldehyde, salicylaldehyde and 4-hydroxybenzaldehyde dehydrogenases, so no PANTHER identifier is asserted.
Representative Members: vdh (PSEPK)UniProtKB:Q88HJ9 vdh (PSEUH)UniProtKB:O05619

Function

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

Processes

ferulate catabolic processGO:1901067 vanillin catabolic processGO:0042190

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: Family: VanA Rieske oxygenase subunits
Family:
VanA Rieske oxygenase subunits Rieske non-heme iron oxygenase alpha subunits with a VanA_C catalytic domain that partner with VanB. Their PANTHER subfamily PTHR21266:SF60 also holds KshA, NdmA/NdmB and DdmC, so no PANTHER identifier is asserted.
Representative Members: vanA (PSEPK)UniProtKB:Q88GI6 vanA (ACIAD)UniProtKB:Q6FDI6

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 reductase subunit
vanB_reductase_activity
Participant: Family: VanB reductases of PTHR47354:SF1
Family:
VanB reductases of PTHR47354:SF1PANTHER:PTHR47354:SF1 PDR-type flavin/[2Fe-2S] reductases that pass electrons from NADH to VanA. The subfamily also holds phthalate dioxygenase and carnitine monooxygenase reductases, so the VanA partner, not membership, defines the role.
Representative Members: vanB (PSEPK)UniProtKB:Q88GI5 vanB (ACIAD)UniProtKB:O24840

Function

ferredoxin-NAD+ reductase activityGO:0008860
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.