UPB1 encodes beta-ureidopropionase (N-carbamoyl-beta-alanine amidohydrolase; beta-alanine synthase; EC 3.5.1.6), the third and final enzyme of the reductive pyrimidine catabolic pathway. It hydrolyses N-carbamoyl-beta-alanine (3-ureidopropanoate) to beta-alanine, ammonia and carbon dioxide, and likewise converts N-carbamoyl-beta-aminoisobutyrate (from thymine degradation) to beta-aminoisobutyrate, ammonia and CO2. It acts downstream of dihydropyrimidine dehydrogenase (DPYD) and dihydropyrimidinase (DPYS), and its product beta-alanine is a precursor for carnosine and other metabolites. The enzyme is a member of the nitrilase (carbon-nitrogen hydrolase) superfamily, using an active-site cysteine nucleophile (Cys233), and is cytosolic, highly expressed in liver. It assembles into homodimers, homotetramers, homooctamers and larger homooligomers, with substrate- and pH-dependent allosteric regulation of activity through oligomer state. Loss-of-function variants in UPB1 cause beta-ureidopropionase deficiency (UPB1D), an inborn error of pyrimidine degradation characterised by N-carbamyl-beta-amino aciduria and a highly variable phenotype ranging from neurological involvement (intellectual disability, seizures, hypotonia, microcephaly) to asymptomatic; the enzyme is also relevant to catabolism of fluoropyrimidine anticancer drugs.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003837 beta-ureidopropionase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) annotation of the core beta-ureidopropionase catalytic activity, concordant with direct experimental evidence in human. Reason: This is the defining molecular function of UPB1 and is supported by multiple experimental studies of the human enzyme; the IBA is at the correct level of specificity. Supporting Evidence: PMID:24526388 The third step, catalyzed by Ξ²-ureidopropionase (Ξ²UP) (EC 3.5.1.6), results in conversion of N-carbamyl-Ξ²-alanine and N-carbamyl-Ξ²-aminoisobutyric acid into Ξ²-alanine and Ξ²-aminoisobutyric acid, respectively, with concomitant production of ammonia and carbon dioxide. |
| GO:0019483 beta-alanine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic annotation to beta-alanine biosynthesis, the biological process in which UPB1 produces beta-alanine as the terminal step of pyrimidine catabolism. Reason: UPB1 generates beta-alanine directly from N-carbamoyl-beta-alanine; this is a correct and well-supported process annotation. Note that the UniProt DR line lists the more specific term GO:0033396 (beta-alanine biosynthetic process via 3-ureidopropionate), but that term is now obsolete, so GO:0019483 is the appropriate level. Supporting Evidence: PMID:22525402 Γ-ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyzes the conversion of N-carbamyl-Γ-alanine and N-carbamyl-Γ-aminoisobutyric acid to Γ-alanine and Γ-aminoisobutyric acid, ammonia and CO(2). |
| GO:0003837 beta-ureidopropionase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated (ARBA/RHEA/EC 3.5.1.6) inference of the core enzyme activity, identical to the experimentally supported molecular function. Reason: Redundant with the EXP/IDA/IBA annotations to GO:0003837 and correctly mapped from EC 3.5.1.6 / RHEA:11184. Supporting Evidence: PMID:29976570 Ξ²-Ureidopropionase (Ξ²UP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Automated subcellular-location mapping placing UPB1 in the cytoplasm, consistent with its cytosolic localization. Reason: Correct but general; the more precise cytosol term (GO:0005829) is supported by Reactome. Keeping the cytoplasm parent is acceptable. Supporting Evidence: file:human/UPB1/UPB1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. |
| GO:0001701 in utero embryonic development | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Developmental-process annotation transferred by Ensembl Compara orthology from rat; not supported by any direct evidence that UPB1 has a role in embryonic development beyond its metabolic function. Reason: This is an electronic orthology transfer (GO_REF:0000107) from rat Q03248, not evidence about human UPB1. UPB1 is a pyrimidine-catabolic enzyme; there is no literature support for a specific role in in utero embryonic development. The phenotype associated with loss of function is a metabolic/neurological inborn error, not an embryonic-development defect. Flagging as over-annotated rather than removing, as it is an automated inference rather than a clearly wrong mapping. Supporting Evidence: file:human/UPB1/UPB1-uniprot.txt Catalyzes a late step in pyrimidine degradation |
| GO:0001889 liver development | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Liver-development annotation transferred by Ensembl Compara orthology from rat; UPB1 is highly expressed in liver but there is no evidence it participates in liver morphogenesis/development. Reason: Electronic orthology transfer from rat (GO_REF:0000107). High hepatic expression reflects where pyrimidine catabolism occurs, not a role in the developmental process of the liver. No experimental evidence links UPB1 to liver development. Marked as over-annotated rather than removed since it is an automated inference. Supporting Evidence: file:human/UPB1/UPB1-uniprot.txt TISSUE SPECIFICITY: Detected in liver (at protein level). |
| GO:0019483 beta-alanine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Automated (UniPathway UPA00131 / orthology) annotation to beta-alanine biosynthesis, redundant with the experimental and IBA annotations. Reason: Correct process annotation supported by UniPathway (beta-alanine biosynthesis) and by the experimental IDA annotations to the same term. Supporting Evidence: file:human/UPB1/UPB1-uniprot.txt PATHWAY: Amino-acid biosynthesis; beta-alanine biosynthesis. |
| GO:0019483 beta-alanine biosynthetic process | IDA PMID:22525402 Γ-ureidopropionase deficiency: phenotype, genotype and prote... | ACCEPT | Summary: Direct experimental evidence that UPB1 produces beta-alanine as the terminal step of the pyrimidine degradation pathway. Reason: Experimental study of the human enzyme and disease mutants establishes its role in converting N-carbamyl-beta-alanine to beta-alanine. Supporting Evidence: PMID:22525402 Γ-ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyzes the conversion of N-carbamyl-Γ-alanine and N-carbamyl-Γ-aminoisobutyric acid to Γ-alanine and Γ-aminoisobutyric acid, ammonia and CO(2). |
| GO:0019483 beta-alanine biosynthetic process | IDA PMID:29976570 Crystal structure and pH-dependent allosteric regulation of ... | ACCEPT | Summary: Direct experimental evidence (biochemical/structural characterisation of the human enzyme) for beta-alanine production from N-carbamoyl-beta-alanine. Reason: The crystal-structure paper biochemically characterises the human enzyme's conversion of N-carbamoyl-beta-alanine, the reaction that generates beta-alanine. Supporting Evidence: PMID:29976570 Ξ²-Ureidopropionase (Ξ²UP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. |
| GO:0003837 beta-ureidopropionase activity | EXP PMID:10415095 A radiochemical assay for beta-ureidopropionase using radiol... | ACCEPT | Summary: Experimental radiochemical assay measuring human beta-ureidopropionase activity on N-carbamyl-beta-alanine. Reason: Direct enzymatic assay of the human protein with kinetic characterisation (Km 15.5 uM), establishing the core molecular function. Supporting Evidence: PMID:10415095 Human beta-ureidopropionase obeyed Michaelis-Menten kinetics with an apparent Km for N-carbamyl-beta-alanine of 15.5 +/- 1.9 microM. |
| GO:0003837 beta-ureidopropionase activity | EXP PMID:10542323 cDNA cloning, genomic structure and chromosomal localization... | ACCEPT | Summary: Experimental confirmation that the cloned human UPB1 cDNA encodes an active beta-ureidopropionase. Reason: Heterologous expression of the human cDNA yielded high beta-ureidopropionase activity, confirming the enzyme's molecular function. Supporting Evidence: PMID:10542323 Expression of the human cDNA in an Escherichia coli and eukaryotic COS-7 expression system revealed a very high beta-ureidopropionase enzymatic activity, thus confirming the identity of the cDNA. |
| GO:0003837 beta-ureidopropionase activity | EXP PMID:11508704 Expression and properties of human liver beta-ureidopropiona... | ACCEPT | Summary: Experimental characterisation of purified recombinant human liver beta-ureidopropionase, including cooperativity toward its substrate. Reason: Purification and biochemical assay of the human enzyme directly establish the beta-ureidopropionase activity. Supporting Evidence: PMID:11508704 exhibited positive cooperativity with N-carbamoyl-beta-alanine as the substrate with a Hill coefficient 2.0 |
| GO:0003837 beta-ureidopropionase activity | EXP PMID:24526388 Clinical, biochemical and molecular analysis of 13 Japanese ... | ACCEPT | Summary: Experimental activity measurements of wild-type and mutant human UPB1, confirming beta-ureidopropionase catalytic activity. Reason: Functional assays of human UPB1 (EC 3.5.1.6) catalysing the third catabolic step directly support this molecular function. Supporting Evidence: PMID:24526388 The third step, catalyzed by Ξ²-ureidopropionase (Ξ²UP) (EC 3.5.1.6), results in conversion of N-carbamyl-Ξ²-alanine and N-carbamyl-Ξ²-aminoisobutyric acid into Ξ²-alanine and Ξ²-aminoisobutyric acid, respectively, with concomitant production of ammonia and carbon dioxide. |
| GO:0003837 beta-ureidopropionase activity | IDA PMID:22525402 Γ-ureidopropionase deficiency: phenotype, genotype and prote... | ACCEPT | Summary: Direct assay evidence that human UPB1 has beta-ureidopropionase activity, with disease mutants showing reduced activity. Reason: Experimental measurement of enzyme activity in wild-type and mutant human UPB1 directly supports this molecular function. Supporting Evidence: PMID:22525402 Heterologous expression of the 6 mutant enzymes in Escherichia coli showed that all mutations yielded mutant Γ-ureidopropionase proteins with significantly decreased activity. |
| GO:0003837 beta-ureidopropionase activity | IDA PMID:29976570 Crystal structure and pH-dependent allosteric regulation of ... | ACCEPT | Summary: Direct biochemical/structural evidence for human beta-ureidopropionase activity, including catalytic residue and kinetic characterisation. Reason: The crystal-structure study biochemically characterises the catalytic activity of recombinant human UPB1. Supporting Evidence: PMID:29976570 Ξ²-Ureidopropionase (Ξ²UP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. |
| GO:0008270 zinc ion binding | IDA NOT PMID:29976570 Crystal structure and pH-dependent allosteric regulation of ... | ACCEPT | Summary: NOT annotation correctly asserting that human UPB1 does not bind zinc, refuting an earlier sequence-based prediction. Reason: Although early work reported ~0.5 zinc atoms/subunit and predicted a zinc site, the crystal structure shows no bound zinc and that the predicted residues are too far apart to form a site. The negated annotation is correct and should be retained to prevent erroneous propagation of a zinc-binding function. Supporting Evidence: file:human/UPB1/UPB1-uniprot.txt The crystal structure indicates a lack of bound zinc ions, and shows that the residues that were predicted to bind zinc are too far apart in space to form a zinc binding site |
| GO:0042803 protein homodimerization activity | IDA PMID:29976570 Crystal structure and pH-dependent allosteric regulation of ... | KEEP AS NON CORE | Summary: UPB1 forms homodimers, the basic building block of its higher-order oligomeric assemblies. Reason: Homodimerization is experimentally established and structurally important, but it is a means of assembling the active oligomer rather than the core catalytic function of the enzyme. Retained as non-core supporting activity. Supporting Evidence: PMID:29976570 Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. |
| GO:0046135 pyrimidine nucleoside catabolic process | IMP PMID:22525402 Γ-ureidopropionase deficiency: phenotype, genotype and prote... | MODIFY | Summary: Annotation to pyrimidine catabolism based on disease-mutation analysis, but the chosen term (nucleoside catabolism) is inaccurate: UPB1 acts on N-carbamoyl-beta-alanine, a nucleobase-degradation intermediate, not a nucleoside. Reason: The gene is genuinely involved in pyrimidine catabolism (loss of function causes accumulation of N-carbamyl-beta-amino acids), so the essence is correct, but nucleoside catabolism is the wrong branch. UPB1 acts downstream of base ring-opening on the ureido acid, so the appropriate terms are uracil catabolic process (GO:0006212) and, more generally, pyrimidine nucleobase catabolic process (GO:0006208). Proposed replacements: uracil catabolic process pyrimidine nucleobase catabolic process Supporting Evidence: PMID:22525402 markedly elevated levels of N-carbamyl-Γ-alanine and N-carbamyl-Γ-aminoisobutyric acid in urine and plasma. |
| GO:0051260 protein homooligomerization | IDA PMID:22525402 Γ-ureidopropionase deficiency: phenotype, genotype and prote... | KEEP AS NON CORE | Summary: UPB1 assembles into higher-order homooligomers, which underlies its substrate/pH-dependent allosteric regulation. Reason: Homooligomerization is experimentally supported and mechanistically relevant to activity regulation, but it is a supporting structural property rather than the core biological function (pyrimidine catabolism / beta-alanine biosynthesis). Supporting Evidence: PMID:29976570 Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. |
| GO:0051289 protein homotetramerization | IDA PMID:29976570 Crystal structure and pH-dependent allosteric regulation of ... | KEEP AS NON CORE | Summary: UPB1 forms homotetramers as part of its progression from dimers to larger oligomeric states. Reason: Homotetramerization is part of the experimentally observed oligomerization series; retained as a non-core supporting property rather than the core function. Supporting Evidence: PMID:29976570 Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | KEEP AS NON CORE | Summary: High-throughput detection of UPB1 in urinary exosomes; a real proteomic observation but not the site of catalytic function. Reason: This is a large-scale mass-spectrometry detection in urinary exosomes, not evidence for the functional localization of the enzyme, which is cytosolic. Retained as non-core to reflect the proteomic observation without implying an extracellular functional role. Supporting Evidence: PMID:19056867 Normal human urine contains large numbers of exosomes |
| GO:0005829 cytosol | TAS Reactome:R-HSA-73591 | ACCEPT | Summary: Cytosolic localization inferred from the Reactome reaction for conversion of 3-ureidopropionate to beta-alanine. Reason: Consistent with UniProt (Cytoplasm) and the known cytosolic site of pyrimidine catabolism; this is the functionally relevant location. Supporting Evidence: Reactome:R-HSA-73591 Cytosolic 3-ureidopropionase catalyzes the reaction of 3-ureidopropionate and water to form beta-alanine, CO2, and NH3 |
| GO:0005829 cytosol | TAS Reactome:R-HSA-73620 | ACCEPT | Summary: Cytosolic localization inferred from the Reactome reaction for conversion of 3-ureidoisobutyrate to 3-aminoisobutyrate (thymine branch). Reason: Consistent with the cytosolic function of UPB1 in both the uracil- and thymine-derived branches of pyrimidine catabolism. Supporting Evidence: Reactome:R-HSA-73620 Cytosolic UPB1 (beta-ureidopropionase) catalyzes the reaction of 3-ureidoisobutyrate and H2O to form (R)-3-aminoisobutyrate, CO2, and NH3 |
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Download this section (compressed HTML)Q: Does the substrate/pH-dependent oligomerization of human UPB1 regulate flux through pyrimidine catabolism in vivo, or is it primarily an in vitro phenomenon?
Q: To what extent does reduced UPB1 activity modulate systemic fluoropyrimidine (e.g. 5-fluorouracil) catabolism and toxicity, given that its substrates derive from these antimetabolites?
Experiment: Determine a substrate- or product-bound crystal/cryo-EM structure of human UPB1 to define the catalytic mechanism and the basis of allosteric activation by oligomer assembly.
Experiment: Metabolomic profiling of UPB1-deficient patient cells or knockout models to quantify accumulation of N-carbamyl-beta-alanine / N-carbamyl-beta-aminoisobutyrate and depletion of beta-alanine and downstream carnosine.
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