pyrE (PA5331, P50587) review notes

No deep-research provider was available. Sources: reviewed UniProt record (HAMAP MF_01208),
cached abstracts of PMID:25917504 (P. aeruginosa pyrE deletion) and PMID:9222315 (E. coli
OPRTase purification, title only). PubMed and Europe PMC searches failed on 2026-11-05.

Function

Orotate phosphoribosyltransferase: PRPP + orotate to OMP, step 1 of UMP synthesis from orotate
[file:PSEAE/pyrE/pyrE-uniprot.txt "Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)."].
Deletion of pyrE in PAO1 causes orotate accumulation and altered virulence-factor output
PMID:25917504.
Orotate accumulation is the direct metabolic signature of losing OPRTase; the virulence changes
are downstream effects of the accumulated orotate.

GO term choices

GO:0044205 'de novo' UMP biosynthetic process (IEA, UniPathway) is the specific process; it is_a
pyrimidine nucleotide biosynthetic process (GO:0006221), so the GO:0006221 rows are TOO_GENERAL.
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process and GO:0046132 pyrimidine
ribonucleoside biosynthetic process (IBA, from yeast URA5/URA10 seeds) do not describe the OPRTase
step: orotate is already the nucleobase and the product is a nucleotide, not a nucleoside. Both
are modified to GO:0044205 at the leaf; neither is a seed from this gene.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN002928258	GO:0004588 orotate phosphoribosyltransferase activity	5	26 (25 taxa)	GO:0004588, IMP, PMID:25917504 (PseudoCAP)	SOUND	The deletion accumulates orotate, the OPRTase substrate; together with the HAMAP family assignment this supports the activity.	E. coli PyrE P0A7E3, S. cerevisiae URA5 and URA10 (SGD:S000004574, S000004884), A. nidulans Q5B0P6	Yes; E. coli PyrE and the yeast enzymes are biochemically characterised. No GO_CENTRAL defect.
PTN002928258	GO:0006221 pyrimidine nucleotide biosynthetic process	2	26 (25 taxa)	GO:0006221, IMP, PMID:25917504 (PseudoCAP)	SOUND	Correct (general) process for an enzyme of de novo UMP synthesis; the mutant blocks the pathway at orotate.	E. coli PyrE P0A7E3	Yes, on E. coli PyrE. The term is general (leaf rows judged TOO_GENERAL given GO:0044205) but true for the clade. No GO_CENTRAL defect.

Defects recorded: PSEUDOCAP 0; GO_CENTRAL 0.