Glucarate and galactarate catabolism to 2-oxoglutarate

A reusable three-stage aldarate catabolic route in which substrate-specific dehydratases convert D-glucarate or D-galactarate to the common intermediate 5-dehydro-4-deoxy-D-glucarate. A second dehydratase then forms 2,5-dioxopentanoate, which an aldehyde dehydrogenase-family enzyme oxidizes to 2-oxoglutarate. Organisms can encode either or both substrate-entry reactions.

MODULE:glucarate_galactarate_catabolismDRAFTCONCRETEMetabolic Pathwaymodules/glucarate_galactarate_catabolism.yaml
D-glucarate catabolic processGO:0042838 D-galactarate catabolic processGO:0046392
GO:0042838
D-glucarate catabolic process
GO:0042838 captures the D-glucarate branch represented by GudD and the common downstream reactions.
GO:0046392
D-galactarate catabolic process
GO:0046392 captures the D-galactarate branch represented by GarD and the common downstream reactions.
file:projects/P_PUTIDA/deep-research/PSEPK__glucarate_galactarate_catabolism__ppu00053-deep-research-openscientist.md
OpenScientist PSEPK glucarate and galactarate catabolism synthesis
Species-aware retrieval supports the three-stage boundary, distinguishes the aldarate-locus PP_3602 from other EC 1.2.1.26 paralogs, and treats transport and regulation as accessory context rather than reaction steps.
RHEA:14573
glucarate dehydratase reaction
Rhea 14573 defines dehydration of D-glucarate to 5-dehydro-4-deoxy-D-glucarate.
RHEA:16005
galactarate dehydratase reaction
Rhea 16005 defines dehydration of galactarate to the same common 5-dehydro-4-deoxy-D-glucarate intermediate.
RHEA:24608
5-dehydro-4-deoxyglucarate dehydratase reaction
Rhea 24608 defines conversion of the common intermediate to 2,5-dioxopentanoate, carbon dioxide, and water.
RHEA:11296
2,5-dioxovalerate dehydrogenase (NADP+) reaction
Rhea 11296 defines oxidation of 2,5-dioxopentanoate to 2-oxoglutarate with NADP+.
file:PSEPK/PP_3599/PP_3599-uniprot.txt
UniProtKB entry for PSEPK PP_3599
Reviewed Q88GW8 grounds the shared KDGDH reaction in Pseudomonas putida KT2440.

The boundary starts at the substrate-specific aldarate dehydratases and ends at 2-oxoglutarate. Aldarate uptake, upstream uronate production, and downstream central metabolism are outside the module. The two entry reactions are ONE_OR_MORE alternatives because a genome may support either substrate or both. The PSEPK OpenScientist synthesis supports this boundary but is treated as retrieval context; exact functions remain grounded in GO, Rhea, UniProt, PANTHER, and PAINT records. Molecular functions are confined to the reaction annotons; no generic cytoplasmic localization is asserted.

6Nodes
3Parts
1Variant Sets
2Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:glucarate_galactarate_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.

Reaction chaining (advisory)

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

  • glucarate_entry → kdgd_step [NOT_CHECKED]
    GudD produces the 5-dehydro-4-deoxy-D-glucarate consumed by KDGDH.
  • galactarate_entry → kdgd_step [NOT_CHECKED]
    GarD produces the 5-dehydro-4-deoxy-D-glucarate consumed by KDGDH.
  • kdgd_step → dioxovalerate_dehydrogenase_step [NOT_CHECKED]
    KDGDH produces the 2,5-dioxopentanoate consumed by the terminal dehydrogenase.

Gene-review completeness (4/8 grounded genes reviewed)

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

Gene Review Complete Deep research
probable KDGDH (Arthrobacter sp. FB24) A0JQW8 ✗ — —
garD Q88GW6 ✓ ✓ ✗
gudD Q88DR6 ✓ ✓ ✗
GudD (Escherichia coli K-12) P0AES2 ✗ — —
GarD (Escherichia coli K-12) P39829 ✗ — —
PP_3599 Q88GW8 ✓ ✓ ✗
PP_3602 Q88GW5 ✓ ✓ ✗
KgsD (Acinetobacter baylyi ADP1) Q6FFQ0 ✗ — —

Details

Glucarate and galactarate catabolism to 2-oxoglutarateMetabolic Pathwayglucarate_galactarate_catabolism
D-glucarate catabolic processGO:0042838 D-galactarate catabolic processGO:0046392

Connections

Part 1: substrate-specific aldarate entry
Aldarate dehydration to the common intermediateMetabolic Pathwayaldarate_entry
Variant set: Aldarate substrate-entry reactions by substrate (One Or More)
D-glucarate entryReactionglucarate_entry

Annotons

GudD glucarate dehydratase activity
gudd_activity
Participant: Family: glucarate dehydratase subfamily
Family:
glucarate dehydratase subfamilyPANTHER:PTHR48080:SF4
Representative Members: GudD (Pseudomonas putida KT2440)UniProtKB:Q88DR6 GudD (Escherichia coli K-12)UniProtKB:P0AES2

Function

glucarate dehydratase activityGO:0008872
Substrates: D-glucarate
Products: 5-dehydro-4-deoxy-D-glucarate water

Processes

D-glucarate catabolic processGO:0042838

Commits D-glucarate to the common aldarate-catabolism intermediate.

D-galactarate entryReactiongalactarate_entry

Annotons

GarD galactarate dehydratase activity
gard_activity
Participant: Family: galactarate dehydratase subfamily
Family:
galactarate dehydratase subfamilyPANTHER:PTHR30536:SF1
Representative Members: GarD (Pseudomonas putida KT2440)UniProtKB:Q88GW6 GarD (Escherichia coli K-12)UniProtKB:P39829

Function

galactarate dehydratase activityGO:0008867
Substrates: D-galactarate
Products: 5-dehydro-4-deoxy-D-glucarate water

Processes

D-galactarate catabolic processGO:0046392

Commits D-galactarate to the common aldarate-catabolism intermediate.

Part 2: common-intermediate decarboxylation and dehydration
5-dehydro-4-deoxyglucarate to 2,5-dioxopentanoateReactionkdgd_step

Annotons

KDGDH activity
kdgd_activity
Participant: Family: 5-dehydro-4-deoxyglucarate dehydratase subfamily
Family:
5-dehydro-4-deoxyglucarate dehydratase subfamilyPANTHER:PTHR12128:SF19
Representative Members: KDGDH (Pseudomonas putida KT2440)UniProtKB:Q88GW8 probable KDGDH (Arthrobacter sp. FB24)UniProtKB:A0JQW8

Function

5-dehydro-4-deoxyglucarate dehydratase activityGO:0047448
Substrates: 5-dehydro-4-deoxy-D-glucarate proton
Products: 2,5-dioxopentanoate carbon dioxide water

Processes

D-glucarate catabolic processGO:0042838 D-galactarate catabolic processGO:0046392

Produces the aldehyde substrate for the terminal dehydrogenase after either entry reaction.

Part 3: terminal oxidation to central metabolism
2,5-dioxopentanoate to 2-oxoglutarateReactiondioxovalerate_dehydrogenase_step

Annotons

2,5-dioxovalerate dehydrogenase activity
dioxovalerate_dehydrogenase_activity
Participant: Family: alpha-ketoglutaric-semialdehyde dehydrogenase family
Family:
alpha-ketoglutaric-semialdehyde dehydrogenase familyInterPro:IPR044151
Representative Members: PP_3602 (Pseudomonas putida KT2440)UniProtKB:Q88GW5 KgsD (Acinetobacter baylyi ADP1)UniProtKB:Q6FFQ0

Function

2,5-dioxovalerate dehydrogenase (NADP+) activityGO:0047533
Substrates: 2,5-dioxopentanoate NADP+ water
Products: 2-oxoglutarate NADPH proton

Processes

D-glucarate catabolic processGO:0042838 D-galactarate catabolic processGO:0046392

Produces 2-oxoglutarate, completing the pathway and connecting aldarate carbon to central metabolism.