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
file:modules/bacterial_glucarate_and_galactarate_catabolism-deep-research-openscientist.md
OpenScientist review of bacterial glucarate and galactarate catabolism
Module-level retrieval supports the alternative substrate-entry branches, their convergence on a two-reaction route to 2-oxoglutarate, and exclusion of transport, regulation, and downstream central metabolism.
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 and identifies aldarate-locus PP_3602 as the leading terminal-enzyme candidate, while leaving its distinction from other EC 1.2.1.26 paralogs untested.
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+.
RHEA:47152
2,5-dioxovalerate dehydrogenase (NAD+) reaction
Rhea 47152 defines the corresponding oxidation with NAD+; the preferred cofactor of the KT2440 paralogs has not been measured.
PMID:17202142
alpha-ketoglutaric semialdehyde dehydrogenase isozymes involved in metabolic pathways of D-glucarate, D-galactarate, and hydroxy-L-proline. Molecular and metabolic convergent evolution.
Biochemical characterization in Azospirillum brasilense establishes high alphaKGSA specificity with pathway-linked NAD+- and NADP+-dependent KGSADH isozymes.
KGSADH-II and KGSADH-III showed similar high substrate specificity for alphaKGSA and different coenzyme specificity
PMID:16835232
A novel alpha-ketoglutaric semialdehyde dehydrogenase: evolutionary insight into an alternative pathway of bacterial L-arabinose metabolism.
Orthologous A. brasilense enzymology supports alphaKGSA as a preferred substrate of the KGSADH reaction class.
Higher catalytic efficiency of ALDH was found with alphaKGSA and succinic semialdehyde among the tested aldehyde substrates.
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. KT2440 encodes three KGSADH-family paralogs (Q88GW5, Q88NF5, and Q88JR4). Only the synteny-favored Q88GW5 is represented in the aldarate reaction leaf; Q88NF5 and Q88JR4 remain comparison paralogs rather than pathway members. NAD+ versus NADP+ preference has not been established for Q88GW5.

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.

Function consistency and core coverage

5 gene-function check(s) reflected in core functions · 0 conflict(s) · 6 evidence or coverage gap(s) (12 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
gudd_activity GudD (Pseudomonas putida KT2440)
UniProtKB:Q88DR6
Family Representative 		glucarate dehydratase activity
GO:0008872 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gudd_activity GudD (Escherichia coli K-12)
UniProtKB:P0AES2
Family Representative 		glucarate dehydratase activity
GO:0008872 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
gard_activity GarD (Pseudomonas putida KT2440)
UniProtKB:Q88GW6
Family Representative 		galactarate dehydratase activity
GO:0008867 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gard_activity GarD (Escherichia coli K-12)
UniProtKB:P39829
Family Representative 		galactarate dehydratase activity
GO:0008867 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
kdgd_activity KDGDH (Pseudomonas putida KT2440)
UniProtKB:Q88GW8
Family Representative 		5-dehydro-4-deoxyglucarate dehydratase activity
GO:0047448 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
kdgd_activity probable KDGDH (Arthrobacter sp. FB24)
UniProtKB:A0JQW8
Family Representative 		5-dehydro-4-deoxyglucarate dehydratase activity
GO:0047448 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dioxovalerate_dehydrogenase_activity PP_3602 (Pseudomonas putida KT2440)
UniProtKB:Q88GW5
Family Representative 		2,5-dioxovalerate aldehyde dehydrogenase activity with NAD+ or NADP+
GO:0004030 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dioxovalerate_dehydrogenase_activity KgsD (Acinetobacter baylyi ADP1)
UniProtKB:Q6FFQ0
Family Representative 		2,5-dioxovalerate aldehyde dehydrogenase activity with NAD+ or NADP+
GO:0004030 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gudd_activity glucarate dehydratase subfamily
PANTHER:PTHR48080:SF4
Family 		glucarate dehydratase activity
GO:0008872 		Family Scope Restricted
GO:0016836 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. Safe for the acid-sugar dehydratase subfamilies under PTN000350912; not for SF3, whose members are epimerases, an OSBS and a muconate cycloisomerase.
gard_activity galactarate dehydratase subfamily
PANTHER:PTHR30536:SF1
Family 		galactarate dehydratase activity
GO:0008867 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR30536:SF1.
kdgd_activity 5-dehydro-4-deoxyglucarate dehydratase subfamily
PANTHER:PTHR12128:SF19
Family 		5-dehydro-4-deoxyglucarate dehydratase activity
GO:0047448 		Family Supported
Family review supports GO:0047448 for PANTHER:PTHR12128:SF19. All 59 Swiss-Prot members of SF19 are named KDGDH, and the KT2440 member PP_3599 is the reviewed enzyme. No other subfamily carries this activity.
dioxovalerate_dehydrogenase_activity alpha-ketoglutaric-semialdehyde dehydrogenase family
InterPro:IPR044151
Family 		2,5-dioxovalerate aldehyde dehydrogenase activity with NAD+ or NADP+
GO:0004030 		Family Review Missing
No supported structured family review is available for InterPro:IPR044151.

Gene-review completeness (5/8 grounded genes reviewed)

4 complete review(s) · 0 with deep research · 3 missing review · 5 reviewed but lacking deep research

Gene Review Complete Deep research
probable KDGDH (Arthrobacter sp. FB24) A0JQW8 ✗ — —
ACIAD0131 Q6FFQ0 ✓ ✓ ✗
garD Q88GW6 ✓ ✓ ✗
gudD Q88DR6 ✓ ✓ ✗
GudD (Escherichia coli K-12) P0AES2 ✗ — —
GarD (Escherichia coli K-12) P39829 ✗ — —
PP_3599 Q88GW8 ✓ ✓ ✗
PP_3602 Q88GW5 ✓ 5/6 ✗

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 aldehyde dehydrogenase activity with NAD+ or NADP+GO:0004030
Substrates: 2,5-dioxopentanoate NAD+ or NADP+ water
Products: 2-oxoglutarate NADH or 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. PP_3602 is the synteny-favored KT2440 candidate. PP_1256 and PP_2585 are comparison paralogs outside this pathway leaf, and cofactor preference remains unresolved.