Bacterial purine base oxidation to urate

A reusable bacterial pathway realization in which xanthine is supplied by either zinc-dependent guanine deamination or NAD+-dependent hypoxanthine oxidation and is then oxidized to urate. In the two-subunit realization, the same XdhAB molybdo-flavo-iron-sulfur complex performs both NAD+-dependent oxidation reactions.

MODULE:bacterial_purine_base_oxidation_to_urateCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_purine_base_oxidation_to_urate.yaml
purine nucleobase catabolic processGO:0006145
GO:0006145
purine nucleobase catabolic process
GO:0006145 captures the purine-base degradation boundary represented by the convergent guanine and hypoxanthine routes.
RHEA:14665
guanine deaminase reaction
Rhea 14665 defines hydrolytic conversion of guanine to xanthine and ammonium.
RHEA:24670
NAD+-dependent hypoxanthine dehydrogenase reaction
Rhea 24670 defines oxidation of hypoxanthine to xanthine with NAD+ as electron acceptor.
RHEA:16669
NAD+-dependent xanthine dehydrogenase reaction
Rhea 16669 defines oxidation of xanthine to urate with NAD+ as electron acceptor.
PMID:11341925
Xanthine dehydrogenase from Pseudomonas putida 86: specificity, oxidation-reduction potentials of its redox-active centers, and first EPR characterization.
A characterized two-subunit Pseudomonas XDH oxidizes both hypoxanthine and xanthine, prefers NAD+, and contains molybdenum, FAD, and two iron-sulfur centers.
PMID:26355499
Identification of a chemoreceptor that specifically mediates chemotaxis toward metabolizable purine derivatives.
Pseudomonas putida KT2440 uses guanine, hypoxanthine, xanthine, and uric acid as sole nitrogen sources, providing direct organism-level evidence that purine-base catabolic flux operates in this genome.
file:modules/bacterial_purine_base_oxidation_to_urate-deep-research-openscientist.md
OpenScientist generic-module research report
The report independently supports the convergent two-part boundary and emphasizes that one XdhAB performing both oxidations is specific to this realization rather than a universal bacterial rule.
file:PSEPK/guaD/guaD-ai-review.yaml
PSEPK guaD gene review
Q88F18 is the guanine-deaminase candidate for the guanine entry route.
file:PSEPK/xdhA/xdhA-ai-review.yaml
PSEPK xdhA gene review
Q88F21 is the FAD- and iron-sulfur-containing XdhAB subunit.
file:PSEPK/xdhB/xdhB-ai-review.yaml
PSEPK xdhB gene review
Q88F20 is the molybdenum-cofactor-binding XdhAB subunit.

This is a species-neutral module for the bacterial two-subunit XdhAB realization, not a Pseudomonas-specific pathway. Pseudomonas putida KT2440, P. putida 86, and Rhodobacter capsulatus are included only as genome or biochemical exemplars. Fused eukaryotic XDH proteins, bacterial three-subunit systems, and Moco-independent hypoxanthine routes are outside this realization's participant architecture. Purine nucleotide hydrolysis and salvage are upstream alternatives, while urate oxidation and downstream allantoin degradation are separate modules. Xdh cofactor maturation is required for activity but belongs to molybdenum-cofactor biogenesis rather than this catalytic reaction-chain boundary. No Xdh-specific PAINT node is asserted for XdhA or XdhB. XdhA is classified in PTHR45444:SF3 and XdhB in PTHR11908:SF132 (both reviewed in interpro/panther/), but the exact xanthine-dehydrogenase PAINT nodes reached from either family sit on the animal fused-enzyme clades of the PTHR11908 tree, and SF132 mixes XdhB with CO dehydrogenase, caffeine dehydrogenase, 4-hydroxybenzoyl-CoA reductase and plant aldehyde-oxidase subunits. The subunit roles are therefore grounded to the narrower InterPro xanthine-dehydrogenase small-subunit (IPR014307, NCBIfam TIGR02963) and molybdopterin-subunit (IPR014309, TIGR02965) families rather than to a PANTHER family. GuaD is grounded to PTHR11271:SF6, whose family review scopes guanine deaminase activity to that subfamily. The two-subunit XdhAB architecture is characterized in alphaproteobacteria (R. capsulatus) and gammaproteobacteria (Pseudomonas). The E. coli and B. subtilis molybdenum subunits (E. coli XdhA Q46799, B. subtilis PucD O32144) belong to multi-subunit systems with a different partner architecture and no reviewed exemplar here, so they are not used as XdhAB exemplars; E. coli GuaD is the experimentally characterized guanine-deaminase exemplar.

5Nodes
2Parts
1Variant Sets
2Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_purine_base_oxidation_to_urate-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.

  • guanine_deamination_route → xanthine_oxidation_to_urate [NOT_CHECKED]
    Xanthine produced by GuaD is the substrate of XdhAB.
  • hypoxanthine_oxidation_route → xanthine_oxidation_to_urate [NOT_CHECKED]
    Xanthine produced from hypoxanthine is the substrate of XdhAB.

Function consistency and core coverage

2 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (5 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
guad_activity GuaD (Pseudomonas putida KT2440)
UniProtKB:Q88F18
Family Representative 		guanine deaminase activity
GO:0008892 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
guad_activity GuaD (Escherichia coli K-12)
UniProtKB:P76641
Family Representative 		guanine deaminase activity
GO:0008892 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
xdhab_hypoxanthine_activity PROTEIN_COMPLEX
Gene 		hypoxanthine dehydrogenase activity
GO:0070674 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
xdhab_xanthine_activity PROTEIN_COMPLEX
Gene 		xanthine dehydrogenase activity
GO:0004854 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
guad_activity guanine deaminase family
PANTHER:PTHR11271:SF6
Family 		guanine deaminase activity
GO:0008892 		Family Supported
Family review supports GO:0008892 for PANTHER:PTHR11271:SF6. SF6, as bacterial_purine_base_oxidation_to_urate and purine_salvage_and_catabolism select; purine_nucleotide_catabolism uses the base family, which also takes in HutF.

Gene-review completeness (6/6 grounded genes reviewed)

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

Gene Review Complete Deep research
guaD P76641 ✓ ✓ ✗
guaD Q88F18 ✓ ✓ ✓
xdhA O54050 ✓ ✓ ✗
xdhA Q88F21 ✓ ✓ ✓
xdhB O54051 ✓ ✓ ✗
xdhB Q88F20 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
Bacterial purine base oxidation to urateMetabolic Pathwaybacterial_purine_base_oxidation_to_urate
purine nucleobase catabolic processGO:0006145
Context
bacteriaNCBITaxon:2

Connections

The guanine branch converges on the terminal xanthine oxidation step.
The hypoxanthine branch proceeds through xanthine to urate.
Part 1: alternative xanthine supply
Alternative purine-base routes to xanthineMetabolic Pathwayxanthine_supply_routes

Guanine deamination and hypoxanthine oxidation are alternative entry routes that converge on xanthine; one or both can be present in a bacterial genome.

Variant set: Xanthine supply variants by purine base substrate (One Or More)
Guanine deamination to xanthineReactionguanine_deamination_route

Annotons

Guanine deaminase activity
guad_activity
Participant: Family: guanine deaminase family
Family:
guanine deaminase familyPANTHER:PTHR11271:SF6
Representative Members: GuaD (Pseudomonas putida KT2440)UniProtKB:Q88F18 GuaD (Escherichia coli K-12)UniProtKB:P76641
Required Function:
guanine deaminase activityGO:0008892

Function

guanine deaminase activityGO:0008892
Substrates: guanine water proton
Products: xanthine ammonium

Processes

guanine catabolic processGO:0006147

Supplies xanthine by hydrolytic guanine deamination.

Hypoxanthine oxidation to xanthineReactionhypoxanthine_oxidation_route

Annotons

XdhAB hypoxanthine dehydrogenase activity
xdhab_hypoxanthine_activity
Participant: Protein Complex: two-subunit bacterial XdhAB complex
Protein Complex:
two-subunit bacterial XdhAB complex
Active units:
XdhA FAD and iron-sulfur subunit
Participant: Family: xanthine dehydrogenase small-subunit family
Family:
xanthine dehydrogenase small-subunit familyInterPro:IPR014307
Representative Members: XdhA (Pseudomonas putida KT2440)UniProtKB:Q88F21 XdhA (Rhodobacter capsulatus)UniProtKB:O54050
Role: Binds FAD and two [2Fe-2S] centers that relay electrons from the molybdenum center to NAD+.
XdhB molybdenum-binding subunit
Participant: Family: xanthine dehydrogenase molybdopterin-binding family
Family:
xanthine dehydrogenase molybdopterin-binding familyInterPro:IPR014309
Representative Members: XdhB (Pseudomonas putida KT2440)UniProtKB:Q88F20 XdhB (Rhodobacter capsulatus)UniProtKB:O54051
Role: Binds the molybdenum cofactor where purine-base hydroxylation occurs.

Function

hypoxanthine dehydrogenase activityGO:0070674
Substrates: hypoxanthine NAD+ water
Products: xanthine NADH proton

Processes

hypoxanthine catabolic processGO:0009114

Supplies xanthine by NAD+-dependent hypoxanthine oxidation.

Part 2: terminal xanthine oxidation to urate
XdhAB-dependent xanthine oxidation to urateReactionxanthine_oxidation_to_urate

Annotons

XdhAB xanthine dehydrogenase activity
xdhab_xanthine_activity
Participant: Protein Complex: two-subunit bacterial XdhAB complex
Protein Complex:
two-subunit bacterial XdhAB complex
Active units:
XdhA FAD and iron-sulfur subunit
Participant: Family: xanthine dehydrogenase small-subunit family
Family:
xanthine dehydrogenase small-subunit familyInterPro:IPR014307
Representative Members: XdhA (Pseudomonas putida KT2440)UniProtKB:Q88F21 XdhA (Rhodobacter capsulatus)UniProtKB:O54050
Role: Binds FAD and two [2Fe-2S] centers that relay electrons from the molybdenum center to NAD+.
XdhB molybdenum-binding subunit
Participant: Family: xanthine dehydrogenase molybdopterin-binding family
Family:
xanthine dehydrogenase molybdopterin-binding familyInterPro:IPR014309
Representative Members: XdhB (Pseudomonas putida KT2440)UniProtKB:Q88F20 XdhB (Rhodobacter capsulatus)UniProtKB:O54051
Role: Binds the molybdenum cofactor where purine-base hydroxylation occurs.

Function

xanthine dehydrogenase activityGO:0004854
Substrates: xanthine NAD+ water
Products: urate NADH proton

Processes

xanthine catabolic processGO:0009115

Produces urate from the convergent xanthine pool.