pydX

Gene Description

pydX (PP_4037) encodes the partner subunit of the bacterial heteromeric dihydropyrimidine dehydrogenase in reductive pyrimidine catabolism. PydX is an iron-sulfur- and flavin-associated redox protein that works with adjacent PydA to reduce uracil or thymine to 5,6-dihydrouracil or 5,6-dihydrothymine. Its primary role is NADH oxidation and internal electron transfer within the assembled PydXA enzyme, not an independently established whole-enzyme activity. Whether Q88FQ1 binds FAD or FMN has not been resolved directly.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004159 dihydropyrimidine dehydrogenase (NAD+) activity	IEA GO_REF:0000120	MODIFY	Summary: The term is correct for the assembled PydXA DPD, but PydX is the electron-input subunit rather than an independently active dihydropyrimidine dehydrogenase. Reason: Retain the term but change the relation from enables to contributes_to; PydX supplies reducing equivalents to the PydA pyrimidine-reduction site. Proposed replacements: dihydropyrimidine dehydrogenase (NAD+) activity Supporting Evidence: file:PSEPK/pydX/pydX-deep-research-openscientist.md The 455-amino-acid PydX polypeptide is not the catalytic centre itself; rather, it provides the pyridine-nucleotide oxidation and intramolecular electron-relay machinery that feeds reducing equivalents to the pyrimidine-reducing active site housed on its partner subunit, PydA.
GO:0016491 oxidoreductase activity	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: Generic oxidoreductase activity is true but does not identify the heteromeric DPD reaction. Reason: The specific DPD activity and iron-sulfur cofactor role are more informative.
GO:0003954 NADH dehydrogenase activity	IC file:PSEPK/pydX/pydX-deep-research-openscientist.md	NEW	Summary: PydX performs the NADH-oxidizing input half-reaction and relays reducing equivalents to the PydA catalytic subunit. Reason: GO:0003954 captures the catalytic NADH-to-acceptor reaction enabled by PydX, while GO:0004159 remains a contributes_to function of the assembled PydXA enzyme. Supporting Evidence: PMID:21169495 dihydropyrimidine dehydrogenase is the first member of a novel NADH-dependent subclass of iron-sulfur flavoenzymes file:PSEPK/pydX/pydX-deep-research-openscientist.md The 455-amino-acid PydX polypeptide is not the catalytic centre itself; rather, it provides the pyridine-nucleotide oxidation and intramolecular electron-relay machinery that feeds reducing equivalents to the pyrimidine-reducing active site housed on its partner subunit, PydA.
GO:0051536 iron-sulfur cluster binding	IEA GO_REF:0000002	ACCEPT	Summary: The PydX sequence carries the iron-sulfur-binding family signature used by the paired bacterial DPD electron-transfer system. Reason: Retain as a mechanistically informative cofactor-binding function of the subunit.
GO:0072529 pyrimidine-containing compound catabolic process	IC PMID:22782928 Pseudomonas putida PydR, a RutR-like transcriptional regulat...	NEW	Summary: PydX is the tandem partner of PydA in the reductive pyrimidine-catabolic DPD locus. Reason: The paired-enzyme architecture and locus assignment support the pathway role even though the reported KT2440 deletion phenotype is for pydA. Supporting Evidence: PMID:22782928 The putative DPD genes, pydX and pydA, are tandemly arranged in the Pseudomonas putida genome.

Core Functions

Pyridine-nucleotide/flavin and iron-sulfur electron-input subunit contributing to heteromeric PydXA dihydropyrimidine dehydrogenase in reductive pyrimidine catabolism.

Molecular Function:

NADH dehydrogenase activity

Directly Involved In:

pyrimidine-containing compound catabolic process

Supporting Evidence:

file:PSEPK/pydX/pydX-uniprot.txt
DR GO; GO:0051536; F:iron-sulfur cluster binding; IEA:InterPro.
file:PSEPK/pydX/pydX-notes.md
The putative DPD genes, pydX and pydA, are tandemly arranged in the Pseudomonas putida genome.
file:PSEPK/pydX/pydX-deep-research-openscientist.md
The 455-amino-acid PydX polypeptide is not the catalytic centre itself; rather, it provides the pyridine-nucleotide oxidation and intramolecular electron-relay machinery that feeds reducing equivalents to the pyrimidine-reducing active site housed on its partner subunit, PydA.

Gene Description

Existing Annotations Review

Core Functions

Pyridine-nucleotide/flavin and iron-sulfur electron-input subunit contributing to heteromeric PydXA dihydropyrimidine dehydrogenase in reductive pyrimidine catabolism.

References

Deep Research

OpenScientist

📚 Additional Documentation

Notes

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