PyrE (PA5331) is the orotate phosphoribosyltransferase (OPRTase, EC 2.4.2.10) of Pseudomonas aeruginosa PAO1, a 213-residue Mg2+-dependent homodimeric type I phosphoribosyltransferase. It transfers the ribose 5-phosphate group of 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to orotate, forming orotidine 5'-monophosphate (OMP), the first of the two steps that convert orotate to UMP in de novo pyrimidine nucleotide synthesis. Deleting pyrE causes orotate to accumulate and lowers production of hemolysin, casein protease and elastase while raising pyocyanin and pyoverdine, effects that the accumulated orotate partly reproduces in wild-type cells.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: UniRule (HAMAP MF_01208) Mg2+ cofactor binding. Reason: Correct cofactor binding for an OPRTase, peripheral to the catalytic function. Supporting Evidence: file:PSEAE/pyrE/pyrE-uniprot.txt Name=Mg(2+); Xref=ChEBI:CHEBI:18420 |
| GO:0004588 orotate phosphoribosyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002928258, seeded by E. coli PyrE, yeast URA5 and URA10, A. nidulans Q5B0P6 and PyrE itself (expected self-seed). Reason: Core catalytic activity, consistent with the HAMAP family assignment and the mutant phenotype. Supporting Evidence: 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). |
| GO:0004588 orotate phosphoribosyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined electronic OPRTase annotation (HAMAP, InterPro, EC, Rhea). Reason: Agrees with the experimental and phylogenetic rows. Supporting Evidence: file:PSEAE/pyrE/pyrE-uniprot.txt HAMAP; MF_01208; PyrE; 1. |
| GO:0004588 orotate phosphoribosyltransferase activity | IMP PMID:25917504 Accumulation of Pyrimidine Intermediate Orotate Decreases Vi... | ACCEPT | Summary: PseudoCAP row and a seed of the PTN002928258 OPRTase IBD. The pyrE deletion accumulates orotate, the enzyme's substrate. Reason: Sound seed: substrate accumulation on deletion is the direct metabolic consequence of losing OPRTase, and the activity is certain from family membership. Supporting Evidence: PMID:25917504 The pyrE mutant accumulated orotate and exhibited decreased production of hemolysin, casein protease, and elastase. |
| GO:0004588 orotate phosphoribosyltransferase activity | ISS PMID:9222315 A rapid purification by affinity chromatography of orotate p... | ACCEPT | Summary: ISS from E. coli PyrE (P0A7E3). Reason: Correct transfer from the characterised E. coli orthologue. Supporting Evidence: file:PSEAE/pyrE/pyrE-uniprot.txt NCBIfam; TIGR00336; pyrE; 1. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA cytoplasm from PTN002928258 (seed E. coli PyrE). Reason: Soluble enzyme of de novo pyrimidine synthesis with no signal peptide or transmembrane segment. |
| GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN002928258 (seeds E. coli PyrE, yeast URA5/URA10, S. pombe and A. nidulans OPRTases). PyrE is not a seed of this node term. Reason: OPRTase acts after the pyrimidine nucleobase orotate is made: it converts orotate to the nucleotide OMP. The step belongs to de novo UMP synthesis, GO:0044205, which the gene already carries by IEA. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002928258 · PTN002928258 SUPPORTS TRANSFER Correct OPRTase clade; the process term chosen (nucleobase synthesis) does not describe the OPRTase step, which forms a nucleotide. Long-standing convention across MOD seeds, so no defect is raised. UniProtKB:P0A7E3 · E. coli PyrE SUPPORTS TRANSFER Characterised OPRTase. Proposed replacements: 'de novo' UMP biosynthetic process Supporting Evidence: file:PSEAE/pyrE/pyrE-uniprot.txt PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway; |
| GO:0006221 pyrimidine nucleotide biosynthetic process | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN002928258, seeded by E. coli PyrE and PyrE itself. Reason: True, but entailed by the accepted GO:0044205 'de novo' UMP biosynthetic process, which is_a pyrimidine nucleotide biosynthetic process. |
| GO:0006221 pyrimidine nucleotide biosynthetic process | IEA GO_REF:0000120 | TOO GENERAL | Summary: Electronic pyrimidine nucleotide biosynthesis from the OPRT signature. Reason: Entailed by the accepted GO:0044205 'de novo' UMP biosynthetic process. |
| GO:0006221 pyrimidine nucleotide biosynthetic process | IMP PMID:25917504 Accumulation of Pyrimidine Intermediate Orotate Decreases Vi... | TOO GENERAL | Summary: PseudoCAP row and a seed of the PTN002928258 IBD for this term. The deletion blocks the pathway at orotate. Reason: Sound but general; entailed by the accepted GO:0044205 'de novo' UMP biosynthetic process. Supporting Evidence: PMID:25917504 responsible for converting orotate into orotate monophosphate within the de novo pyrimidine synthesis pathway |
| GO:0044205 'de novo' UMP biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: UniRule/UniPathway de novo UMP biosynthesis; OPRTase is step 1 of UMP formation from orotate. Reason: The specific process in which PyrE performs a step. Supporting Evidence: file:PSEAE/pyrE/pyrE-uniprot.txt PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway; |
| GO:0046132 pyrimidine ribonucleoside biosynthetic process | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN002928258, seeded by yeast URA5 and URA10. PyrE is not a seed of this node term. Reason: OPRTase forms a nucleotide (OMP), not a nucleoside; the step is part of de novo UMP synthesis, GO:0044205, which the gene already carries by IEA. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002928258 · PTN002928258 SUPPORTS TRANSFER Correct OPRTase clade; the nucleoside term carried over from the yeast seeds does not describe the OPRTase product. Not raised as a defect, since the yeast seed rows were not examined. SGD:S000004574 · S. cerevisiae URA5 UNRESOLVED Seed row not examined in this review. Proposed replacements: 'de novo' UMP biosynthetic process Supporting Evidence: file:PSEAE/pyrE/pyrE-uniprot.txt PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway; |
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Download this section (compressed HTML)Q: How does orotate accumulation lower protease and elastase production in P. aeruginosa: through quorum-sensing regulators, or through nucleotide pool imbalance?
Experiment: Measure quorum-sensing signal levels and las/rhl regulon transcription in the pyrE mutant with and without uracil supplementation, to separate orotate effects from pyrimidine limitation.
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