Prs4 (YBL068W) is one of five ribose-phosphate pyrophosphokinase (PRPP synthase) subunits in Saccharomyces cerevisiae. PRPP synthase forms 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from ribose 5-phosphate and ATP (EC 2.7.6.1). PRPP is the ribose-phosphate donor for de novo and salvage synthesis of purine, pyrimidine and pyridine nucleotides and for histidine and tryptophan biosynthesis. S. cerevisiae has five PRS genes, and none of their products is active alone. Co-expression in E. coli shows that active enzyme needs specific pairs (Prs1 with Prs2, Prs3 or Prs4; Prs5 with Prs2 or Prs4), and enzyme stable in vitro needs at least three subunits. The cytosolic PRPP synthase is therefore a hetero-oligomeric complex of Prs subunits. Prs4 is a canonical PRPP synthase polypeptide closely related to Prs2. It gives active enzyme with Prs1 or Prs5 and is a minor subunit: prs4 nulls grow normally, but prs2 prs4 is lethal when PRS1 or PRS3 is also lost.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro IPR000842/IPR005946 (PRPP synthase signatures) mapped to magnesium ion binding. PRS4 carries the conserved divalent-cation binding site (DCbs) motif of PRPP synthases, and the reaction uses Mg-ATP, so Mg2+ binding is expected; it has not been measured directly for the PRS4 subunit. Reason: Cofactor binding inferred from the conserved DCbs motif; correct for a PRPP synthase subunit but not the core function. Supporting Evidence: PMID:9829955 contains the characteristic motifs of PRS enzymes, the divalent cation binding site (DCbs) and the PRPP binding site (PRPPbs) file:yeast/PRS4/PRS4-uniprot.txt SIMILARITY: Belongs to the ribose-phosphate pyrophosphokinase family. |
| GO:0002189 ribose phosphate diphosphokinase complex | IDA PMID:15280369 Heterooligomeric phosphoribosyl diphosphate synthase of Sacc... | ACCEPT | Summary: Hove-Jensen co-expressed the five yeast PRS genes in a PRPP-less E. coli strain: no single subunit had activity, while PRS4 gave active enzyme only together with Prs1 or Prs5, and stable enzyme required at least three subunits. This shows that PRS4 acts as a subunit of a hetero-oligomeric PRPP synthase. Supporting Evidence: PMID:15280369 Expression of the five S. cerevisiae PRS genes individually in an Escherichia coli PRPP-less strain (Deltaprs) showed that a single PRS gene product had no PRPP synthase activity. PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. PMID:15280369 yeast PRPP synthase requires at least three different subunits to be stable in vitro |
| GO:0002189 ribose phosphate diphosphokinase complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA00026376 machine-learning rule assigning the ribose phosphate diphosphokinase complex. It is correct for PRS4: yeast PRPP synthase forms only as a multi-subunit Prs complex. Supporting Evidence: PMID:15280369 yeast PRPP synthase requires at least three different subunits to be stable in vitro file:yeast/PRS4/PRS4-uniprot.txt heteromultimeric complexes with other 5-phosphoribose 1-diphosphate |
| GO:0004749 ribose phosphate diphosphokinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 2.7.6.1 / RHEA:15609 and the InterPro PRPP-synthase signature mapped to ribose phosphate diphosphokinase activity. PRS4 has the PRPP-binding and DCbs motifs and is one of the five yeast PRPP synthase subunits. Caveat: no single yeast Prs subunit is active alone, so 'contributes_to' (as SGD uses in its IGI rows) is the more precise qualifier. Supporting Evidence: file:yeast/PRS4/PRS4-uniprot.txt Reaction=D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1- PMID:15280369 Expression of the five S. cerevisiae PRS genes individually in an Escherichia coli PRPP-less strain (Deltaprs) showed that a single PRS gene product had no PRPP synthase activity. |
| GO:0004749 ribose phosphate diphosphokinase activity | IGI PMID:15280369 Heterooligomeric phosphoribosyl diphosphate synthase of Sacc... | ACCEPT | Summary: Hove-Jensen showed in E. coli that PRS4 co-expressed with PRS1 gives active PRPP synthase, while neither subunit alone does. The 'contributes_to' qualifier fits a subunit that is inactive on its own. Supporting Evidence: PMID:15280369 Expression of the five S. cerevisiae PRS genes individually in an Escherichia coli PRPP-less strain (Deltaprs) showed that a single PRS gene product had no PRPP synthase activity. PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. |
| GO:0004749 ribose phosphate diphosphokinase activity | IGI PMID:15280369 Heterooligomeric phosphoribosyl diphosphate synthase of Sacc... | ACCEPT | Summary: Hove-Jensen showed in E. coli that PRS4 co-expressed with PRS5 gives active PRPP synthase, while neither subunit alone does. The 'contributes_to' qualifier fits a subunit that is inactive on its own. Supporting Evidence: PMID:15280369 Expression of the five S. cerevisiae PRS genes individually in an Escherichia coli PRPP-less strain (Deltaprs) showed that a single PRS gene product had no PRPP synthase activity. PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. |
| GO:0004749 ribose phosphate diphosphokinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from the superpathway of histidine, purine and pyrimidine biosynthesis (PRPP-PWY-1), assigning ribose-5-phosphate + ATP -> PRPP + AMP (EC 2.7.6.1) to PRS4. Correct for this PRPP synthase subunit. The yeast enzyme is hetero-oligomeric, so the activity belongs to Prs subunit combinations and not to PRS4 alone. Supporting Evidence: file:yeast/PRS4/PRS4-uniprot.txt Reaction=D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1- PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. |
| GO:0004749 ribose phosphate diphosphokinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from PRPP biosynthesis (PWY0-662), assigning ribose-5-phosphate + ATP -> PRPP + AMP (EC 2.7.6.1) to PRS4. Correct for this PRPP synthase subunit. The yeast enzyme is hetero-oligomeric, so the activity belongs to Prs subunit combinations and not to PRS4 alone. Supporting Evidence: file:yeast/PRS4/PRS4-uniprot.txt Reaction=D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1- PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. |
| GO:0005515 protein binding | IPI PMID:11283351 A comprehensive two-hybrid analysis to explore the yeast pro... | REMOVE | Summary: PRS4-Prs5 association detected in the Ito et al. 2001 comprehensive yeast two-hybrid screen. It reflects assembly of the hetero-oligomeric PRPP synthase from Prs subunits, as shown independently by two-hybrid and co-expression studies. The interaction is real, but 'protein binding' adds nothing; complex membership is already captured by GO:0002189. Reason: Uninformative 'protein binding'. The Prs-Prs subunit association is represented by part_of ribose phosphate diphosphokinase complex (GO:0002189), and no more specific MF term applies. Supporting Evidence: PMID:11283351 Here we have completed the comprehensive analysis using this system to identify 4,549 two-hybrid interactions among 3,278 proteins. PMID:10212224 Specifically PRS1 and PRS3 polypeptides interact strongly with each other, and there are significant interactions between the PRS5 polypeptide and either the PRS2 or PRS4 polypeptides. |
| GO:0005515 protein binding | IPI PMID:17892321 Structure-templated predictions of novel protein interaction... | REMOVE | Summary: PRS4-Prs1 association detected in the Betel et al. 2007 D-MIST structure-templated interaction predictions, validated by IP. It reflects assembly of the hetero-oligomeric PRPP synthase from Prs subunits, as shown independently by two-hybrid and co-expression studies. The interaction is real, but 'protein binding' adds nothing; complex membership is already captured by GO:0002189. Reason: Uninformative 'protein binding'. The Prs-Prs subunit association is represented by part_of ribose phosphate diphosphokinase complex (GO:0002189), and no more specific MF term applies. Supporting Evidence: PMID:17892321 Among the experimentally confirmed predictions were interactions between the five components of the PRS complex, which together compose the 5-phosphoribosyl-1(a)-pyrophosphate synthetase enzyme (EC number 2.7.6.1). PMID:10212224 Specifically PRS1 and PRS3 polypeptides interact strongly with each other, and there are significant interactions between the PRS5 polypeptide and either the PRS2 or PRS4 polypeptides. |
| GO:0005515 protein binding | IPI PMID:17892321 Structure-templated predictions of novel protein interaction... | REMOVE | Summary: PRS4-Prs3 association detected in the Betel et al. 2007 D-MIST structure-templated interaction predictions, validated by IP. It reflects assembly of the hetero-oligomeric PRPP synthase from Prs subunits, as shown independently by two-hybrid and co-expression studies. The interaction is real, but 'protein binding' adds nothing; complex membership is already captured by GO:0002189. Reason: Uninformative 'protein binding'. The Prs-Prs subunit association is represented by part_of ribose phosphate diphosphokinase complex (GO:0002189), and no more specific MF term applies. Supporting Evidence: PMID:17892321 Among the experimentally confirmed predictions were interactions between the five components of the PRS complex, which together compose the 5-phosphoribosyl-1(a)-pyrophosphate synthetase enzyme (EC number 2.7.6.1). PMID:10212224 Specifically PRS1 and PRS3 polypeptides interact strongly with each other, and there are significant interactions between the PRS5 polypeptide and either the PRS2 or PRS4 polypeptides. |
| GO:0005515 protein binding | IPI PMID:17892321 Structure-templated predictions of novel protein interaction... | REMOVE | Summary: PRS4-Prs5 association detected in the Betel et al. 2007 D-MIST structure-templated interaction predictions, validated by IP. It reflects assembly of the hetero-oligomeric PRPP synthase from Prs subunits, as shown independently by two-hybrid and co-expression studies. The interaction is real, but 'protein binding' adds nothing; complex membership is already captured by GO:0002189. Reason: Uninformative 'protein binding'. The Prs-Prs subunit association is represented by part_of ribose phosphate diphosphokinase complex (GO:0002189), and no more specific MF term applies. Supporting Evidence: PMID:17892321 Among the experimentally confirmed predictions were interactions between the five components of the PRS complex, which together compose the 5-phosphoribosyl-1(a)-pyrophosphate synthetase enzyme (EC number 2.7.6.1). PMID:10212224 Specifically PRS1 and PRS3 polypeptides interact strongly with each other, and there are significant interactions between the PRS5 polypeptide and either the PRS2 or PRS4 polypeptides. |
| GO:0005515 protein binding | IPI PMID:18467557 An in vivo map of the yeast protein interactome. | REMOVE | Summary: PRS4-Prs1 association detected in the Tarassov et al. 2008 genome-wide DHFR protein-fragment complementation (PCA) screen. It reflects assembly of the hetero-oligomeric PRPP synthase from Prs subunits, as shown independently by two-hybrid and co-expression studies. The interaction is real, but 'protein binding' adds nothing; complex membership is already captured by GO:0002189. Reason: Uninformative 'protein binding'. The Prs-Prs subunit association is represented by part_of ribose phosphate diphosphokinase complex (GO:0002189), and no more specific MF term applies. Supporting Evidence: PMID:18467557 We have performed a genome-wide in vivo screen for protein-protein interactions in Saccharomyces cerevisiae by means of a protein-fragment complementation assay (PCA). PMID:10212224 Specifically PRS1 and PRS3 polypeptides interact strongly with each other, and there are significant interactions between the PRS5 polypeptide and either the PRS2 or PRS4 polypeptides. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: PRS4-Prs3 association detected in the Michaelis et al. 2023 proteome-wide affinity-enrichment MS interactome. It reflects assembly of the hetero-oligomeric PRPP synthase from Prs subunits, as shown independently by two-hybrid and co-expression studies. The interaction is real, but 'protein binding' adds nothing; complex membership is already captured by GO:0002189. Reason: Uninformative 'protein binding'. The Prs-Prs subunit association is represented by part_of ribose phosphate diphosphokinase complex (GO:0002189), and no more specific MF term applies. Supporting Evidence: PMID:37968396 Affinity purification coupled to mass spectrometry is an ideal tool for such mapping PMID:10212224 Specifically PRS1 and PRS3 polypeptides interact strongly with each other, and there are significant interactions between the PRS5 polypeptide and either the PRS2 or PRS4 polypeptides. |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Huh et al. genome-wide GFP-tagging localized PRS4-GFP to the cytoplasm. This is consistent with a soluble PRPP synthase subunit. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000025022) placing PRPP synthases as active in the cytoplasm. Correct for PRS4, which GFP tagging places in the cytoplasm. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0086 Cytoplasm), itself based on the Huh et al. GFP data for PRS4. Correct. Supporting Evidence: file:yeast/PRS4/PRS4-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (PRPP-PWY-1) placing the PRPP synthase reaction in the cytosol. This is consistent with cytoplasmic localization of PRS4-GFP and with the soluble, non-organellar nature of the PRPP synthase complex. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories file:yeast/PRS4/PRS4-uniprot.txt Reaction=D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1- |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (PWY0-662) placing the PRPP synthase reaction in the cytosol. This is consistent with cytoplasmic localization of PRS4-GFP and with the soluble, non-organellar nature of the PRPP synthase complex. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories file:yeast/PRS4/PRS4-uniprot.txt Reaction=D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1- |
| GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000025022) for PRPP biosynthesis; PRS4 is one of the experimentally grounded yeast donors. This is the core process. Supporting Evidence: PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. PMID:10212224 These data suggest that yeast phosphoribosyl pyrophosphate synthetase exists in vivo as multimeric complex(es). |
| GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: UniPathway UPA00087 / ARBA00027291 mapping to PRPP biosynthesis (route I, step 1/1). Correct for PRS4. Supporting Evidence: file:yeast/PRS4/PRS4-uniprot.txt PATHWAY: Metabolic intermediate biosynthesis; 5-phospho-alpha-D-ribose |
| GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process | IGI PMID:15280369 Heterooligomeric phosphoribosyl diphosphate synthase of Sacc... | ACCEPT | Summary: Co-expression of PRS4 with PRS1 in a PRPP-less E. coli prs mutant restored PRPP synthesis in growing cells, while either gene alone did not. This directly shows PRS4 taking part in PRPP biosynthesis as a subunit. Supporting Evidence: PMID:15280369 Expression of the five S. cerevisiae PRS genes individually in an Escherichia coli PRPP-less strain (Deltaprs) showed that a single PRS gene product had no PRPP synthase activity. PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. |
| GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process | IGI PMID:15280369 Heterooligomeric phosphoribosyl diphosphate synthase of Sacc... | ACCEPT | Summary: Co-expression of PRS4 with PRS5 in a PRPP-less E. coli prs mutant restored PRPP synthesis in growing cells, while either gene alone did not. This directly shows PRS4 taking part in PRPP biosynthesis as a subunit. Supporting Evidence: PMID:15280369 Expression of the five S. cerevisiae PRS genes individually in an Escherichia coli PRPP-less strain (Deltaprs) showed that a single PRS gene product had no PRPP synthase activity. PMID:15280369 These combinations were PRS1 PRS2, PRS1 PRS3, and PRS1 PRS4, as well as PRS5 PRS2 and PRS5 PRS4. |
| GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process | IMP PMID:10212224 Genetic analysis and enzyme activity suggest the existence o... | ACCEPT | Summary: Hernando et al. built all combinations of prs disruptions and measured PRPP synthase activity, growth and nucleotide pools. Loss of PRS4 lowers PRPP-synthesizing capacity, and combinations with other prs nulls are lethal or slow-growing. Prs4 is a minor subunit: prs4 null mutants grow like wild type, but prs2 prs4 is lethal in combination with loss of PRS1 or PRS3. Supporting Evidence: PMID:10212224 a lethal phenotype that corresponds to strains containing a double disruption in PRS2 and PRS4 in combination with a disruption in either PRS1 or PRS3 PMID:10212224 Deletions of PRS2, PRS4, and PRS5 or combinations thereof cause this phenotype. |
| GO:0006164 purine nucleotide biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA (PTN000025022; donors are rat Prps1/2 and human PRPS1/2) for purine nucleotide biosynthesis. PRPP made by the Prs complex is the ribose-phosphate donor for de novo and salvage purine nucleotide synthesis, so PRS4 supplies an essential precursor. In GO, PRPP biosynthesis is not part_of purine nucleotide biosynthesis, and the same PRPP also feeds pyrimidine, NAD, histidine and tryptophan synthesis. Reason: Upstream precursor supply shared by several pathways. It is acceptable, but the core process is GO:0006015. Supporting Evidence: PMID:9829955 PRPP is required for the production of purine, pyrimidine, and pyridine nucleotides and the amino acids histidine and tryptophan PMID:10514564 an enzyme which catalyses the first step in a variety of biosynthetic pathways, including purine and pyrimidine biosynthesis |
| GO:0009156 ribonucleoside monophosphate biosynthetic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro IPR000842 (PRPP synthase conserved site) mapped to ribonucleoside monophosphate biosynthetic process. PRPP is the ribose-phosphate donor for phosphoribosyltransferases that make IMP, UMP and other NMPs, but PRS4 itself makes PRPP and not a nucleoside monophosphate. Reason: Indirect: describes the downstream use of PRPP. Retained as non-core. Supporting Evidence: PMID:9829955 PRPP is required for the production of purine, pyrimidine, and pyridine nucleotides and the amino acids histidine and tryptophan |
| GO:0009165 nucleotide biosynthetic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro IPR005946 (ribose-phosphate diphosphokinase) mapped to nucleotide biosynthetic process. This is correct in the broad sense that PRPP from the Prs complex is required for nucleotide synthesis; deletion of PRS1 or PRS3 lowers nucleotide pools. The step PRS4 catalyses is PRPP synthesis. Reason: Broad downstream process; the core process is PRPP biosynthesis. Supporting Evidence: PMID:9829955 PRPP is required for the production of purine, pyrimidine, and pyridine nucleotides and the amino acids histidine and tryptophan PMID:9108276 disruption of PRS1 or PRS3 has a significant effect on cell metabolism, whereas disruption of PRS2 or PRS4 has little measurable effect |
| GO:0009165 nucleotide biosynthetic process | RCA GO_REF:0000123 | TOO GENERAL | Summary: YeastPathways RCA inherited from the superpathway PRPP-PWY-1 (histidine, purine and pyrimidine biosynthesis). PRS4 catalyses only the PRPP-forming entry step, so the superpathway BP is a generalisation; PRPP is a genuine precursor of all nucleotides. Reason: Superpathway-inherited BP. The precise process is GO:0006015 PRPP biosynthesis. Supporting Evidence: PMID:10514564 an enzyme which catalyses the first step in a variety of biosynthetic pathways, including purine and pyrimidine biosynthesis PMID:9829955 PRPP is required for the production of purine, pyrimidine, and pyridine nucleotides and the amino acids histidine and tryptophan |
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Download this section (compressed HTML)Q: Does Prs4 contribute catalytic residues to the hetero-oligomer, or does it act mainly as a stabilising/regulatory subunit?
5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase, synthesizes PRPP; which is required for nucleotide, histidine, and tryptophan biosynthesis; one of five related enzymes, which are active as heteromultimeric complexes; PRS4 has a paralog, PRS2, that arose from the whole genome duplication; a missense mutation in the conserved residue R196 of its human homolog PRPS1 is pathogenic
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