urad encodes 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase (EC 4.1.1.97), the third and last enzyme of oxidative uricolysis. It converts the unstable intermediate OHCU, formed from urate by urate oxidase and 5-hydroxyisourate hydrolase, into (S)-allantoin with release of CO2, and does so stereoselectively: without the enzyme the reaction proceeds spontaneously to a racemic product. The protein is a homodimer with an all-alpha fold and no cofactor; His67 supplies the proton that fixes the (S) configuration and Glu87 destabilises the substrate carboxylate to promote CO2 loss. It acts with the other two uricolytic enzymes, which are peroxisomal, and carries a weak C-terminal PTS1 tripeptide. The pathway converts poorly soluble urate into soluble allantoin for nitrogen excretion; its genes were pseudogenised in hominoids, which is why humans accumulate urate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005777 peroxisome | IBA GO_REF:0000033 | ACCEPT | Summary: Peroxisome: animal uricolysis is a peroxisomal pathway and Urad's partner enzymes Uox and Urah are peroxisomal; the zebrafish protein carries only a weak C-terminal PTS1 (TKL) and UniProt's assignment is a curator inference (ECO:0000305), not a measurement. Reason: Accepted because the pathway context is compelling - the substrate OHCU is generated by peroxisomal Uox/Urah and is chemically unstable, so the decarboxylase must act where it is made - and because the reporter evidence summarised in the deep-research file indicates the weak TKL signal is functional. Noted honestly: there is no cached zebrafish immunolocalisation of endogenous Urad, and a partly cytosolic pool is plausible. The IBA and IEA rows make the same claim and are graded identically. Supporting Evidence: file:DANRE/urad/urad-uniprot.txt SUBCELLULAR LOCATION: Peroxisome {ECO:0000305}. file:DANRE/urad/urad-deep-research-falcon.md In animals, uricolysis is classically described as a **peroxisomal** p file:DANRE/urad/urad-deep-research-falcon.md D. rerio Urad** has a predicted weak PTS1 (**TKL**) and that EGFP repo |
| GO:0051997 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity | IBA GO_REF:0000033 | ACCEPT | Summary: OHCU decarboxylase activity inherited from the OHCU decarboxylase family node (PTN000044713), which includes the experimentally characterised zebrafish and mouse enzymes. Reason: The family is defined by this single reaction and the target is one of the descendants with direct evidence, so its own ZFIN entry appearing in the WITH/FROM list is the expected marker of experimental grounding rather than circularity. Node placement is not in question: zebrafish Urad retains the catalytic His67/Glu87 pair identified in the crystal structure of this very enzyme (PMID:17428786). Supporting Evidence: PMID:17428786 describe the 1.8A resolution crystal structure of the homodimeric PMID:17428786 which His-67 and Glu-87 appear to play a particularly significant role. Glu-87 file:DANRE/urad/urad-uniprot.txt FUNCTION: Catalyzes the stereoselective decarboxylation of 2-oxo-4- |
| GO:0000255 allantoin metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Allantoin metabolic process: Urad makes (S)-allantoin, so it is the enzyme that produces the metabolite the term is about. Reason: Correct participation - the gene product catalyses the reaction that forms allantoin - but it is a sibling framing of the same single step already captured more precisely by urate catabolic process, which places the reaction as step 3/3 of the pathway from urate. Retained rather than modified because allantoin production is a genuine and distinct aspect of this enzyme's output, but it is not an additional core function. Supporting Evidence: file:DANRE/urad/urad-uniprot.txt FUNCTION: Catalyzes the stereoselective decarboxylation of 2-oxo-4- file:DANRE/urad/urad-uniprot.txt carboxylate + H(+) = (S)-allantoin + CO2; Xref=Rhea:RHEA:26301, PMID:28508122 A combination of the three enzymes in an appropriate ratio allowed efficient conversion of urate to (S)-allantoin with no accumulation of intermediate metabolites. |
| GO:0005777 peroxisome | IEA GO_REF:0000044 | ACCEPT | Summary: Peroxisome: animal uricolysis is a peroxisomal pathway and Urad's partner enzymes Uox and Urah are peroxisomal; the zebrafish protein carries only a weak C-terminal PTS1 (TKL) and UniProt's assignment is a curator inference (ECO:0000305), not a measurement. Reason: Accepted because the pathway context is compelling - the substrate OHCU is generated by peroxisomal Uox/Urah and is chemically unstable, so the decarboxylase must act where it is made - and because the reporter evidence summarised in the deep-research file indicates the weak TKL signal is functional. Noted honestly: there is no cached zebrafish immunolocalisation of endogenous Urad, and a partly cytosolic pool is plausible. The IBA and IEA rows make the same claim and are graded identically. Supporting Evidence: file:DANRE/urad/urad-uniprot.txt SUBCELLULAR LOCATION: Peroxisome {ECO:0000305}. file:DANRE/urad/urad-deep-research-falcon.md In animals, uricolysis is classically described as a **peroxisomal** p file:DANRE/urad/urad-deep-research-falcon.md D. rerio Urad** has a predicted weak PTS1 (**TKL**) and that EGFP repo |
| GO:0051997 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity | IEA GO_REF:0000120 | ACCEPT | Summary: OHCU decarboxylase activity assigned automatically from EC 4.1.1.97 / RHEA:26301; the same reaction is demonstrated for this protein. Reason: The automated mapping reproduces UniProt's catalytic activity line, which is itself backed by direct experiment on the zebrafish enzyme (ECO:0000269|PubMed:17428786), so it is correct and maximally specific. Supporting Evidence: file:DANRE/urad/urad-uniprot.txt carboxylate + H(+) = (S)-allantoin + CO2; Xref=Rhea:RHEA:26301, file:DANRE/urad/urad-uniprot.txt FUNCTION: Catalyzes the stereoselective decarboxylation of 2-oxo-4- PMID:17428786 last step in the urate degradation pathway, for both ligand-free enzyme and |
| GO:0019628 urate catabolic process | IEA GO_REF:0000041 | ACCEPT | Summary: Urate catabolic process: Urad performs step 3 of 3 of the (S)-allantoin-from-urate pathway, acting on the OHCU produced from urate by Uox and Urah. Reason: The gene product itself catalyses a step of the pathway, so this is participation in the strict sense, and it is the most specific process term the reaction supports. The three zebrafish enzymes together convert urate to (S)-allantoin with no intermediate accumulation (PMID:28508122). Supporting Evidence: file:DANRE/urad/urad-uniprot.txt PATHWAY: Purine metabolism; urate degradation; (S)-allantoin from file:DANRE/urad/urad-uniprot.txt urate: step 3/3. PMID:28508122 A combination of the three enzymes in an appropriate ratio allowed efficient conversion of urate to (S)-allantoin with no accumulation of intermediate metabolites. PMID:17428786 last step in the urate degradation pathway, for both ligand-free enzyme and |
| GO:0051997 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity | IDA PMID:28508122 A Trivalent Enzymatic System for Uricolytic Therapy of HPRT ... | ACCEPT | Summary: OHCU decarboxylase activity measured on the recombinant zebrafish enzyme (DrUrad): it converts 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline to (S)-allantoin with loss of CO2, the third reaction of uricolysis. Reason: The zebrafish protein itself was produced and assayed, and in combination with DrUox and DrUrah it drove complete conversion of urate to (S)-allantoin without intermediate accumulation (PMID:28508122); the same enzyme's catalytic residues were defined structurally (PMID:17428786). The term states exactly this reaction. Supporting Evidence: PMID:28508122 three zebrafish enzymes required in the uricolytic pathway. PMID:28508122 A combination of the three enzymes in an appropriate ratio allowed efficient conversion of urate to (S)-allantoin with no accumulation of intermediate metabolites. PMID:28508122 decarboxylation of OHCU to give (S)-allantoin, catalyzed by OHCU decarboxylase (Urad) (Fig. file:DANRE/urad/urad-uniprot.txt carboxylate + H(+) = (S)-allantoin + CO2; Xref=Rhea:RHEA:26301, |
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Download this section (compressed HTML)Q: Is zebrafish Urad actually peroxisomal in vivo, given only a weak TKL PTS1 and a curator-inferred (ECO:0000305) UniProt location, or does a cytosolic pool exist?
Q: Does loss of urad in zebrafish cause accumulation of OHCU or racemic allantoin, and is that phenotype distinguishable from uox loss?
Experiment: Immunolocalise endogenous Urad, or knock in a tag, and compare with Uox and a peroxisomal marker in zebrafish liver.
Hypothesis: Urad co-localises with Uox in peroxisomes despite its weak PTS1, placing all three uricolytic steps in one compartment.
Experiment: Generate urad loss-of-function zebrafish and measure urate, OHCU-derived products and allantoin enantiomer ratio.
Hypothesis: Without Urad the pathway still consumes urate but yields racemic allantoin from spontaneous OHCU decay.
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