purD

UniProt ID: Q88DK2
Organism: Pseudomonas putida KT2440
Review Status: DRAFT
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Gene Description

PurD is phosphoribosylamine--glycine ligase, the ATP-dependent enzyme that adds glycine to 5-phosphoribosylamine to form GAR in the second reaction of de novo IMP synthesis.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000117 		MODIFY
Summary: Correct but less informative than the enzyme-specific activity.
Reason: Replace the generic catalytic parent with phosphoribosylamine-glycine ligase activity.
GO:0004637 phosphoribosylamine-glycine ligase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Correct enzyme-specific molecular function.
Reason: The exact Phosphoribosylamine--glycine ligase product assignment supports this activity.
GO:0005524 ATP binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: Valid substrate binding, but not the core function of PurD.
Reason: ATP is consumed by the ligase reaction, while the enzyme-specific activity captures the core function.
GO:0006189 'de novo' IMP biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: Correct pathway assignment.
Reason: This enzyme catalyzes a required reaction between PRPP and IMP.
GO:0009113 purine nucleobase biosynthetic process
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: Nucleobase-process annotation does not match the nucleotide product of this pathway.
Reason: The PRPP-to-IMP pathway produces a purine nucleotide, not a free purine nucleobase; GO:0009113 is therefore not a broader parent of GO:0006189.
GO:0046872 metal ion binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: Valid cofactor binding, but not the core function of PurD.
Reason: Metal binding supports catalysis, while the enzyme-specific activity captures the core function.

Core Functions

Forms GAR in the second reaction of de novo IMP synthesis.

Molecular Function:
phosphoribosylamine-glycine ligase activity
Directly Involved In:
'de novo' IMP biosynthetic process
Supporting Evidence:
  • file:PSEPK/purD/purD-uniprot.txt
    Reaction=5-phospho-beta-D-ribosylamine + glycine + ATP = N(1)-(5-phospho-beta-D-ribosyl)glycinamide + ADP + phosphate + H(+);
  • file:PSEPK/purD/purD-uniprot.txt
    PATHWAY: Purine metabolism; IMP biosynthesis via de novo pathway;
  • file:PSEPK/purD/purD-uniprot.txt
    DR HAMAP; MF_00138; GARS; 1.

References

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Suggested Experiments

Experiment: Test a clean purD deletion for purine auxotrophy and rescue by the appropriate downstream purine intermediate or by gene complementation.

Deep Research

OpenScientist

(purD-deep-research-openscientist.md)

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📚 Additional Documentation

Notes

(purD-notes.md)

purD curation notes

  • UniProt identifies Q88DK2 as Phosphoribosylamine--glycine ligase [file:PSEPK/purD/purD-uniprot.txt "RecName: Full=Phosphoribosylamine--glycine ligase"].
  • Replace generic catalytic activity with GO:0004637. ATP and metal binding are valid
    supporting molecular functions, retained as non-core.
  • Mark purine nucleobase biosynthetic process as over-annotated because this route
    produces the nucleotide IMP rather than a free purine nucleobase; GO:0009113 is not
    a broad parent of GO:0006189.

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