{"gene":"UMPS","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2010,"finding":"C. elegans UMPS-1 (ortholog of human UMPS) catalyzes the conversion of orotic acid to UMP in de novo pyrimidine biosynthesis and is cytoplasmically localized in intestinal cells. Loss of umps-1 function leads to enlargement of lysosome-related gut granules (up to 250× normal size) through build-up of orotic acid; this phenotype is suppressed by loss of pyr-1 (upstream de novo pyrimidine enzyme) and depends on the ABCG transporter WHT-2, which is proposed to transport orotic acid into gut granules to promote osmotic swelling.","method":"Genetic mutant screen, epistasis (umps-1/pyr-1 double mutant suppression; umps-1/gut granule biogenesis mutant synthetic lethality), fluorescence microscopy of UMPS-1::GFP, subcellular fractionation/localization","journal":"The FEBS journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal genetic and imaging methods in a single study; epistasis with pyr-1 and wht-2 clearly places UMPS-1 in a defined pathway","pmids":["20148972"],"is_preprint":false},{"year":2018,"finding":"QM/MM computational analysis of yeast OPRT (ortholog of human UMPS OPRT domain) established the sequential order of substrate binding: orotate (OA) binds first to OPRT, followed by the Mg2+-PRPP complex binding to the OA-OPRT complex; direct PRPP binding without Mg2+ is energetically unfavorable. The true substrate for the phosphoribosyl transfer reaction is the Mg2+-PRPP complex.","method":"Quantum mechanics/molecular mechanics (QM/MM) computational analysis of S. cerevisiae OPRT","journal":"Computational biology and chemistry","confidence":"Medium","confidence_rationale":"Tier 1 (mechanistic/computational) / Weak — single computational study, no experimental validation reported in this abstract; consistent with prior experimental observations cited therein","pmids":["29533816"],"is_preprint":false},{"year":2018,"finding":"QM/MM analysis of yeast OPRT confirmed the reaction pathway: Mg2+ complexes with PRPP, then Mg2+-PRPP and OA migrate to the active site, OA binds first, then Mg2+-PRPP binds to OA-OPRT. The identity of the divalent metal ion does not alter the reaction mechanism, but Co2+ inhibits the reaction due to large Co2+-PRPP binding and migration energies, explaining experimentally observed Co2+ inhibition.","method":"Quantum mechanics/molecular mechanics (QM/MM) computational analysis with multiple divalent metal ions (Mg2+, Ca2+, Mn2+, Co2+, Zn2+)","journal":"Computational biology and chemistry","confidence":"Low","confidence_rationale":"Tier 1 (computational) / Weak — single computational study; Co2+ inhibitory mechanism is a computational explanation of prior experimental data, not independently validated here","pmids":["29567489"],"is_preprint":false},{"year":2023,"finding":"QM/MM analysis of yeast OPRT with orotate-mimetic inhibitors identified that 4-hydroxy-6-methylpyridin-2(1H)-one competitively inhibits OPRT through a network of hydrogen bonds, hydrophobic contacts, and bridging water molecules at the active site; an ortho-methyl substituent increases π-electron density in the aromatic ring, enhancing binding.","method":"QM/MM computational analysis of S. cerevisiae OPRT with inhibitor binding energetics","journal":"Physical chemistry chemical physics : PCCP","confidence":"Low","confidence_rationale":"Tier 1 (computational) / Weak — single computational study with no experimental biochemical validation reported","pmids":["36637052"],"is_preprint":false},{"year":2020,"finding":"miR-185-5p directly represses UMPS protein expression; lncRNA SNORD3A acts as a competing endogenous RNA (ceRNA) that sequesters miR-185-5p, thereby de-repressing UMPS protein levels and sensitizing breast cancer cells to 5-FU. SNORD3A overexpression increased UMPS protein but not when miR-185-5p was co-overexpressed, establishing the SNORD3A→miR-185-5p⊣UMPS regulatory axis.","method":"ceRNA/sponge assay (luciferase reporter), overexpression and knockdown in vitro and in vivo (xenograft), immunoblot for UMPS protein","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — multiple orthogonal methods (reporter assay, gain/loss of function, in vivo), single lab; the UMPS-specific mechanistic finding (miR-185-5p targets UMPS) is directly supported","pmids":["32382150"],"is_preprint":false},{"year":2024,"finding":"A phosphotyrosine site on human UMPS inhibits its enzymatic activity; CRISPRi-rescue experiments with phospho-dead/phospho-mimetic mutations combined with stable isotope tracing demonstrated that phosphorylation at this site reduces UMPS activity in hepatic metabolism in an obesity model.","method":"CRISPRi-rescue with phospho-dead/phospho-mimetic mutants, stable isotope tracing, multiomics in high-fat diet mouse model","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPRi-rescue with mutagenesis and isotope tracing are orthogonal functional methods; preprint, not yet peer-reviewed","pmids":[],"is_preprint":true}],"current_model":"UMPS encodes a bifunctional enzyme (OPRT and OMP decarboxylase domains) that catalyzes the last two steps of de novo UMP synthesis from orotic acid, using Mg2+-PRPP as the true co-substrate in a sequentially ordered binding mechanism (orotate first, then Mg2+-PRPP); UMPS activity is negatively regulated by phosphorylation at a tyrosine site; its expression is post-transcriptionally repressed by miR-185-5p, which can itself be sequestered by lncRNA SNORD3A; and in C. elegans, cytoplasmic UMPS-1 links de novo pyrimidine flux (via orotic acid accumulation) to lysosome-related organelle size through the ABCG transporter WHT-2."},"narrative":{"mechanistic_narrative":"UMPS encodes the cytoplasmic bifunctional enzyme that catalyzes the final two steps of de novo pyrimidine biosynthesis, converting orotic acid to UMP, a role established through its C. elegans ortholog UMPS-1 in intestinal cells [PMID:20148972]. Loss of UMPS-1 causes accumulation of orotic acid that is channeled by the ABCG transporter WHT-2 into lysosome-related gut granules, driving their osmotic enlargement; this phenotype is suppressed by loss of the upstream de novo pyrimidine enzyme PYR-1, placing UMPS within a defined metabolic pathway whose flux controls organelle size [PMID:20148972]. Mechanistically, the orotate phosphoribosyltransferase (OPRT) activity proceeds by sequentially ordered substrate binding in which orotate binds first, followed by the Mg2+-PRPP complex as the true co-substrate [PMID:29533816]. UMPS activity is negatively regulated by tyrosine phosphorylation, which lowers enzymatic output in hepatic pyrimidine metabolism, and its protein expression is repressed post-transcriptionally by miR-185-5p, an effect relieved by the competing endogenous RNA SNORD3A and linked to 5-FU sensitivity in breast cancer cells [PMID:32382150].","teleology":[{"year":2010,"claim":"Established that UMPS converts orotic acid to UMP in vivo and that this de novo pyrimidine flux is coupled to organelle homeostasis, answering what cellular consequences follow from loss of the enzyme.","evidence":"Genetic mutant screen, epistasis, and UMPS-1::GFP imaging in C. elegans intestinal cells","pmids":["20148972"],"confidence":"High","gaps":["WHT-2-mediated orotic acid transport into granules is proposed but not directly demonstrated biochemically","Relevance of the gut-granule phenotype to mammalian UMPS function unaddressed","No structural characterization of the enzyme"]},{"year":2018,"claim":"Resolved the order of substrate binding in the OPRT reaction, establishing that orotate binds before the Mg2+-PRPP complex and that Mg2+-PRPP, not PRPP alone, is the catalytically competent co-substrate.","evidence":"QM/MM computational analysis of S. cerevisiae OPRT, including comparison across divalent metal ions","pmids":["29533816","29567489"],"confidence":"Medium","gaps":["Purely computational, no experimental kinetic validation in this work","Based on the yeast ortholog rather than human UMPS","Co2+ inhibition mechanism is a computational rationalization of prior data"]},{"year":2020,"claim":"Identified a post-transcriptional control circuit for UMPS, showing miR-185-5p directly represses UMPS protein and that lncRNA SNORD3A de-represses it by sponging the miRNA, linking UMPS dosage to chemosensitivity.","evidence":"Luciferase ceRNA/sponge assays, gain/loss-of-function in vitro and xenografts, UMPS immunoblot in breast cancer cells","pmids":["32382150"],"confidence":"Medium","gaps":["Single lab without independent replication","Mechanism of 5-FU sensitization not dissected at the enzymatic level","Whether the axis operates outside breast cancer is untested"]},{"year":2024,"claim":"Demonstrated that tyrosine phosphorylation of UMPS is an inhibitory post-translational switch on its enzymatic activity, connecting UMPS regulation to metabolic state.","evidence":"CRISPRi-rescue with phospho-dead/phospho-mimetic mutants and stable isotope tracing in a high-fat diet mouse model (preprint)","pmids":[],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Responsible kinase/phosphatase not identified","Structural basis for activity inhibition unknown"]},{"year":null,"claim":"How enzymatic regulation (phosphorylation), transcript-level control (miRNA/lncRNA), and metabolic flux integrate to set UMPS output in human tissues remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model connecting the regulatory layers","No experimental structure of human bifunctional UMPS","Upstream signals controlling phosphorylation undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0016829","term_label":"lyase activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0]}],"complexes":[],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P11172","full_name":"Uridine 5'-monophosphate synthase","aliases":[],"length_aa":480,"mass_kda":52.2,"function":"Bifunctional enzyme catalyzing the last two steps of de novo pyrimidine biosynthesis, orotate phosphoribosyltransferase (OPRT), which converts orotate to orotidine-5'-monophosphate (OMP), and orotidine-5'-monophosphate decarboxylase (ODC), the terminal enzymatic reaction that decarboxylates OMP to uridine monophosphate (UMP)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/P11172/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UMPS","classification":"Not Classified","n_dependent_lines":601,"n_total_lines":1208,"dependency_fraction":0.49751655629139074},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/UMPS","total_profiled":1310},"omim":[{"mim_id":"613891","title":"URIDINE MONOPHOSPHATE SYNTHETASE; UMPS","url":"https://www.omim.org/entry/613891"},{"mim_id":"258900","title":"OROTIC ACIDURIA","url":"https://www.omim.org/entry/258900"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UMPS"},"hgnc":{"alias_symbol":["OPRT","ODC"],"prev_symbol":[]},"alphafold":{"accession":"P11172","domains":[{"cath_id":"3.40.50.2020","chopping":"1-211","consensus_level":"medium","plddt":89.0288,"start":1,"end":211},{"cath_id":"3.20.20.70","chopping":"226-477","consensus_level":"high","plddt":97.0267,"start":226,"end":477}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P11172","model_url":"https://alphafold.ebi.ac.uk/files/AF-P11172-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P11172-F1-predicted_aligned_error_v6.png","plddt_mean":92.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UMPS","jax_strain_url":"https://www.jax.org/strain/search?query=UMPS"},"sequence":{"accession":"P11172","fasta_url":"https://rest.uniprot.org/uniprotkb/P11172.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P11172/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P11172"}},"corpus_meta":[{"pmid":"32382150","id":"PMC_32382150","title":"LncRNA SNORD3A specifically sensitizes breast cancer cells to 5-FU by sponging miR-185-5p to enhance UMPS expression.","date":"2020","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/32382150","citation_count":41,"is_preprint":false},{"pmid":"31561592","id":"PMC_31561592","title":"Clinical Routine TERT Promoter Mutational Screening of Follicular Thyroid Tumors of Uncertain Malignant Potential (FT-UMPs): A Useful Predictor of Metastatic Disease.","date":"2019","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/31561592","citation_count":34,"is_preprint":false},{"pmid":"20148972","id":"PMC_20148972","title":"A Caenorhabditis elegans model of orotic aciduria reveals enlarged lysosome-related organelles in embryos lacking umps-1 function.","date":"2010","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/20148972","citation_count":17,"is_preprint":false},{"pmid":"28205048","id":"PMC_28205048","title":"Mild orotic aciduria in UMPS heterozygotes: a metabolic finding without clinical consequences.","date":"2017","source":"Journal of inherited metabolic disease","url":"https://pubmed.ncbi.nlm.nih.gov/28205048","citation_count":16,"is_preprint":false},{"pmid":"17607371","id":"PMC_17607371","title":"Expression of orotate phosphoribosyltransferase (OPRT) in hepatobiliary and pancreatic carcinoma.","date":"2007","source":"Pathology oncology research : POR","url":"https://pubmed.ncbi.nlm.nih.gov/17607371","citation_count":13,"is_preprint":false},{"pmid":"33489760","id":"PMC_33489760","title":"Hereditary orotic aciduria (HOA): A novel uridine-5-monophosphate synthase (UMPS) mutation.","date":"2021","source":"Molecular genetics and metabolism reports","url":"https://pubmed.ncbi.nlm.nih.gov/33489760","citation_count":11,"is_preprint":false},{"pmid":"8069469","id":"PMC_8069469","title":"Localization of uridine monophosphate synthase (UMPS) gene to river buffalo chromosomes by FISH.","date":"1994","source":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","url":"https://pubmed.ncbi.nlm.nih.gov/8069469","citation_count":10,"is_preprint":false},{"pmid":"11915731","id":"PMC_11915731","title":"[Correlation between clinical pathophysiologic factors and expression of orotate phosphoribosyl transferase (OPRT), thymidylate synthase (TS), and dihydropyrimidine dehydrogenase (DPD) in colorectal cancer].","date":"2002","source":"Gan to kagaku ryoho. Cancer & chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/11915731","citation_count":6,"is_preprint":false},{"pmid":"15918566","id":"PMC_15918566","title":"[Preparation of anti-OPRT antibody for immunochemical detection].","date":"2005","source":"Gan to kagaku ryoho. Cancer & chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/15918566","citation_count":6,"is_preprint":false},{"pmid":"11265402","id":"PMC_11265402","title":"[Expression and pathophysiologic features of orotate phosphoribosyl transferase activity (OPRT) in gastric carcinoma].","date":"2001","source":"Gan to kagaku ryoho. Cancer & chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/11265402","citation_count":4,"is_preprint":false},{"pmid":"19851728","id":"PMC_19851728","title":"Overexpression of outer membrane protein OprT and increase of membrane permeability in phoU mutant of toluene-tolerant bacterium Pseudomonas putida GM730.","date":"2009","source":"Journal of microbiology (Seoul, Korea)","url":"https://pubmed.ncbi.nlm.nih.gov/19851728","citation_count":4,"is_preprint":false},{"pmid":"11383215","id":"PMC_11383215","title":"[Correlation between 5-fluorouracil (5-FU) sensitivity as measured by collagen gel droplet embedded culture drug sensitivity test (CD-DST) and expression of orotate phosphoribosyl transferase (OPRT), thymidylate synthase (TS), and dihydropyrimidine dehydrogenase (DPD) in colorectal cancer].","date":"2001","source":"Gan to kagaku ryoho. Cancer & chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/11383215","citation_count":4,"is_preprint":false},{"pmid":"21084814","id":"PMC_21084814","title":"[Four resected cases with basaloid carcinoma of esophagus--comparison of 5-FU-related enzymes (thymidylate synthase (TS), dihydropyrimidine dehydrogenase (DPD), orotate phosphoribosyl transferase (OPRT)) between basaloid carcinoma and squamous cell carcinoma].","date":"2010","source":"Gan to kagaku ryoho. Cancer & chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/21084814","citation_count":4,"is_preprint":false},{"pmid":"29533816","id":"PMC_29533816","title":"QM/MM reveals the sequence of substrate binding during OPRT action.","date":"2018","source":"Computational biology and chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29533816","citation_count":3,"is_preprint":false},{"pmid":"15272584","id":"PMC_15272584","title":"[Choice of chemotherapeutic drugs for colorectal cancers by DPD and OPRT activities in cancer tissues].","date":"2004","source":"Gan to kagaku ryoho. Cancer & chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/15272584","citation_count":3,"is_preprint":false},{"pmid":"27274438","id":"PMC_27274438","title":"Orotate phosphoribosyltransferase is overexpressed in malignant pleural mesothelioma: Dramatically responds one case in high OPRT expression.","date":"2016","source":"Rare diseases (Austin, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/27274438","citation_count":2,"is_preprint":false},{"pmid":"35356460","id":"PMC_35356460","title":"Case Report: A Novel Missense Mutation c.517G>C in the UMPS Gene Associated With Mild Orotic Aciduria.","date":"2022","source":"Frontiers in neurology","url":"https://pubmed.ncbi.nlm.nih.gov/35356460","citation_count":2,"is_preprint":false},{"pmid":"37147901","id":"PMC_37147901","title":"Mobilization of a diatom mutator-like element (MULE) transposon inactivates the uridine monophosphate synthase (UMPS) locus in Phaeodactylum tricornutum.","date":"2023","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/37147901","citation_count":2,"is_preprint":false},{"pmid":"34344843","id":"PMC_34344843","title":"Novel mutation in UMPS gene leads to false positive result of DUMPS (genetic disorder) in buffaloes: need for gene sequencing before confirming results of RFLP in new species.","date":"2021","source":"Journal of genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34344843","citation_count":2,"is_preprint":false},{"pmid":"16770098","id":"PMC_16770098","title":"[Correlation between clinical pathologic factors and enzymatic activity of orotate Phosphoribosyl transferase (OPRT), Dihydropyrimidine dehydrogenase (DPD) and Thymidylate synthase (TS) in colorectal cancer].","date":"2006","source":"Gan to kagaku ryoho. Cancer & chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/16770098","citation_count":1,"is_preprint":false},{"pmid":"29567489","id":"PMC_29567489","title":"QM/MM analysis of effect of divalent metal ions on OPRT action.","date":"2018","source":"Computational biology and chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29567489","citation_count":1,"is_preprint":false},{"pmid":"36637052","id":"PMC_36637052","title":"Enzyme-substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis.","date":"2023","source":"Physical chemistry chemical physics : PCCP","url":"https://pubmed.ncbi.nlm.nih.gov/36637052","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.01.14.632917","title":"A highly stable engineered disulfide bond in the dimer interface of  <i>E. coli</i>  orotate phosphoribosyl transferase measures cytosolic redox conditions in yeast","date":"2025-01-15","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.14.632917","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.28.609894","title":"Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity","date":"2024-08-29","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.28.609894","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13685,"output_tokens":1830,"usd":0.034252,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8734,"output_tokens":1887,"usd":0.045422,"stage2_stop_reason":"end_turn"},"total_usd":0.079674,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"C. elegans UMPS-1 (ortholog of human UMPS) catalyzes the conversion of orotic acid to UMP in de novo pyrimidine biosynthesis and is cytoplasmically localized in intestinal cells. Loss of umps-1 function leads to enlargement of lysosome-related gut granules (up to 250× normal size) through build-up of orotic acid; this phenotype is suppressed by loss of pyr-1 (upstream de novo pyrimidine enzyme) and depends on the ABCG transporter WHT-2, which is proposed to transport orotic acid into gut granules to promote osmotic swelling.\",\n      \"method\": \"Genetic mutant screen, epistasis (umps-1/pyr-1 double mutant suppression; umps-1/gut granule biogenesis mutant synthetic lethality), fluorescence microscopy of UMPS-1::GFP, subcellular fractionation/localization\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal genetic and imaging methods in a single study; epistasis with pyr-1 and wht-2 clearly places UMPS-1 in a defined pathway\",\n      \"pmids\": [\"20148972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"QM/MM computational analysis of yeast OPRT (ortholog of human UMPS OPRT domain) established the sequential order of substrate binding: orotate (OA) binds first to OPRT, followed by the Mg2+-PRPP complex binding to the OA-OPRT complex; direct PRPP binding without Mg2+ is energetically unfavorable. The true substrate for the phosphoribosyl transfer reaction is the Mg2+-PRPP complex.\",\n      \"method\": \"Quantum mechanics/molecular mechanics (QM/MM) computational analysis of S. cerevisiae OPRT\",\n      \"journal\": \"Computational biology and chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 (mechanistic/computational) / Weak — single computational study, no experimental validation reported in this abstract; consistent with prior experimental observations cited therein\",\n      \"pmids\": [\"29533816\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"QM/MM analysis of yeast OPRT confirmed the reaction pathway: Mg2+ complexes with PRPP, then Mg2+-PRPP and OA migrate to the active site, OA binds first, then Mg2+-PRPP binds to OA-OPRT. The identity of the divalent metal ion does not alter the reaction mechanism, but Co2+ inhibits the reaction due to large Co2+-PRPP binding and migration energies, explaining experimentally observed Co2+ inhibition.\",\n      \"method\": \"Quantum mechanics/molecular mechanics (QM/MM) computational analysis with multiple divalent metal ions (Mg2+, Ca2+, Mn2+, Co2+, Zn2+)\",\n      \"journal\": \"Computational biology and chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 (computational) / Weak — single computational study; Co2+ inhibitory mechanism is a computational explanation of prior experimental data, not independently validated here\",\n      \"pmids\": [\"29567489\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"QM/MM analysis of yeast OPRT with orotate-mimetic inhibitors identified that 4-hydroxy-6-methylpyridin-2(1H)-one competitively inhibits OPRT through a network of hydrogen bonds, hydrophobic contacts, and bridging water molecules at the active site; an ortho-methyl substituent increases π-electron density in the aromatic ring, enhancing binding.\",\n      \"method\": \"QM/MM computational analysis of S. cerevisiae OPRT with inhibitor binding energetics\",\n      \"journal\": \"Physical chemistry chemical physics : PCCP\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 (computational) / Weak — single computational study with no experimental biochemical validation reported\",\n      \"pmids\": [\"36637052\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"miR-185-5p directly represses UMPS protein expression; lncRNA SNORD3A acts as a competing endogenous RNA (ceRNA) that sequesters miR-185-5p, thereby de-repressing UMPS protein levels and sensitizing breast cancer cells to 5-FU. SNORD3A overexpression increased UMPS protein but not when miR-185-5p was co-overexpressed, establishing the SNORD3A→miR-185-5p⊣UMPS regulatory axis.\",\n      \"method\": \"ceRNA/sponge assay (luciferase reporter), overexpression and knockdown in vitro and in vivo (xenograft), immunoblot for UMPS protein\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — multiple orthogonal methods (reporter assay, gain/loss of function, in vivo), single lab; the UMPS-specific mechanistic finding (miR-185-5p targets UMPS) is directly supported\",\n      \"pmids\": [\"32382150\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"A phosphotyrosine site on human UMPS inhibits its enzymatic activity; CRISPRi-rescue experiments with phospho-dead/phospho-mimetic mutations combined with stable isotope tracing demonstrated that phosphorylation at this site reduces UMPS activity in hepatic metabolism in an obesity model.\",\n      \"method\": \"CRISPRi-rescue with phospho-dead/phospho-mimetic mutants, stable isotope tracing, multiomics in high-fat diet mouse model\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPRi-rescue with mutagenesis and isotope tracing are orthogonal functional methods; preprint, not yet peer-reviewed\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"UMPS encodes a bifunctional enzyme (OPRT and OMP decarboxylase domains) that catalyzes the last two steps of de novo UMP synthesis from orotic acid, using Mg2+-PRPP as the true co-substrate in a sequentially ordered binding mechanism (orotate first, then Mg2+-PRPP); UMPS activity is negatively regulated by phosphorylation at a tyrosine site; its expression is post-transcriptionally repressed by miR-185-5p, which can itself be sequestered by lncRNA SNORD3A; and in C. elegans, cytoplasmic UMPS-1 links de novo pyrimidine flux (via orotic acid accumulation) to lysosome-related organelle size through the ABCG transporter WHT-2.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UMPS encodes the cytoplasmic bifunctional enzyme that catalyzes the final two steps of de novo pyrimidine biosynthesis, converting orotic acid to UMP, a role established through its C. elegans ortholog UMPS-1 in intestinal cells [#0]. Loss of UMPS-1 causes accumulation of orotic acid that is channeled by the ABCG transporter WHT-2 into lysosome-related gut granules, driving their osmotic enlargement; this phenotype is suppressed by loss of the upstream de novo pyrimidine enzyme PYR-1, placing UMPS within a defined metabolic pathway whose flux controls organelle size [#0]. Mechanistically, the orotate phosphoribosyltransferase (OPRT) activity proceeds by sequentially ordered substrate binding in which orotate binds first, followed by the Mg2+-PRPP complex as the true co-substrate [#1]. UMPS activity is negatively regulated by tyrosine phosphorylation, which lowers enzymatic output in hepatic pyrimidine metabolism [#5], and its protein expression is repressed post-transcriptionally by miR-185-5p, an effect relieved by the competing endogenous RNA SNORD3A and linked to 5-FU sensitivity in breast cancer cells [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established that UMPS converts orotic acid to UMP in vivo and that this de novo pyrimidine flux is coupled to organelle homeostasis, answering what cellular consequences follow from loss of the enzyme.\",\n      \"evidence\": \"Genetic mutant screen, epistasis, and UMPS-1::GFP imaging in C. elegans intestinal cells\",\n      \"pmids\": [\"20148972\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"WHT-2-mediated orotic acid transport into granules is proposed but not directly demonstrated biochemically\", \"Relevance of the gut-granule phenotype to mammalian UMPS function unaddressed\", \"No structural characterization of the enzyme\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Resolved the order of substrate binding in the OPRT reaction, establishing that orotate binds before the Mg2+-PRPP complex and that Mg2+-PRPP, not PRPP alone, is the catalytically competent co-substrate.\",\n      \"evidence\": \"QM/MM computational analysis of S. cerevisiae OPRT, including comparison across divalent metal ions\",\n      \"pmids\": [\"29533816\", \"29567489\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Purely computational, no experimental kinetic validation in this work\", \"Based on the yeast ortholog rather than human UMPS\", \"Co2+ inhibition mechanism is a computational rationalization of prior data\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified a post-transcriptional control circuit for UMPS, showing miR-185-5p directly represses UMPS protein and that lncRNA SNORD3A de-represses it by sponging the miRNA, linking UMPS dosage to chemosensitivity.\",\n      \"evidence\": \"Luciferase ceRNA/sponge assays, gain/loss-of-function in vitro and xenografts, UMPS immunoblot in breast cancer cells\",\n      \"pmids\": [\"32382150\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab without independent replication\", \"Mechanism of 5-FU sensitization not dissected at the enzymatic level\", \"Whether the axis operates outside breast cancer is untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated that tyrosine phosphorylation of UMPS is an inhibitory post-translational switch on its enzymatic activity, connecting UMPS regulation to metabolic state.\",\n      \"evidence\": \"CRISPRi-rescue with phospho-dead/phospho-mimetic mutants and stable isotope tracing in a high-fat diet mouse model (preprint)\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Responsible kinase/phosphatase not identified\", \"Structural basis for activity inhibition unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How enzymatic regulation (phosphorylation), transcript-level control (miRNA/lncRNA), and metabolic flux integrate to set UMPS output in human tissues remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model connecting the regulatory layers\", \"No experimental structure of human bifunctional UMPS\", \"Upstream signals controlling phosphorylation undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0016829\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":2,"faith_total":4,"faith_pct":50.0}}