urad notes

2026-05-09 review notes

Reviewed GOA, UniProt A1L259, PMID:28508122, and PANTHER family cache. On 2026-05-09, a falcon deep-research attempt for DANRE urad timed out after 600 seconds, so this review used the cached publication, UniProt, GOA, and family evidence instead. The core function is peroxisomal OHCU decarboxylase activity in urate catabolism/allantoin metabolism.

Re-review 2026-09-29

Every summary opened with the same "X is reviewed for zebrafish urad" boilerplate and most rows leaned on the deep-research file. Both cited papers were re-read and each row now cites evidence that belongs to it.

• GO:0051997 OHCU decarboxylase activity (IDA, IBA, IEA) all ACCEPT, with distinct rationales. The IDA rests on the recombinant zebrafish enzyme PMID:28508122 and the fact that the three-enzyme mixture ran to completion PMID:28508122. The structural work on this enzyme identifies the catalytic pair PMID:17428786. That paper's cached record is abstract-only and does not name the species, but UniProt cites it with ECO:0000269 for this entry's FUNCTION, catalytic activity and homodimer, so it is the zebrafish enzyme and the curator judgment is deferred to.
• GO:0019628 urate catabolic process ACCEPT: participation is direct, step 3/3 [file:DANRE/urad/urad-uniprot.txt "PATHWAY: Purine metabolism; urate degradation; (S)-allantoin from"] [file:DANRE/urad/urad-uniprot.txt "urate: step 3/3."].
• GO:0000255 allantoin metabolic process ACCEPT -> KEEP_AS_NON_CORE. The enzyme does make allantoin, so the annotation stands, but it restates the same single reaction that urate catabolic process already places precisely in the pathway; it is not a second core function, and it was removed from core_functions.directly_involved_in accordingly.
• GO:0005777 peroxisome (IBA, IEA) ACCEPT but with the uncertainty stated rather than hidden: UniProt's location is a curator inference [file:DANRE/urad/urad-uniprot.txt "SUBCELLULAR LOCATION: Peroxisome {ECO:0000305}."], the zebrafish PTS1 is the weak TKL tripeptide, and no zebrafish immunolocalisation is cached. The argument for accepting is pathway logic: OHCU is unstable and is generated by peroxisomal Uox/Urah, so the decarboxylase must act where the substrate is made. A localisation experiment is listed in suggested_experiments.
• Description rewritten as standalone biology (reaction, stereoselectivity, catalytic residues, dimer, pathway position, hominoid pseudogenisation); reference_review added to both PMIDs with the species caveat on PMID:17428786; findings, core_functions, suggested questions and experiments added. No new PMIDs were needed beyond the two already cited: PubMed has no zebrafish urad loss-of-function study.
• 7 GOA rows, 0 PENDING, no rows dropped. Validation: 0 errors, 0 warnings.