Notes for DANRE uox

2026-05-09 review notes

• Core function is peroxisomal urate oxidase activity in urate catabolism [file:DANRE/uox/uox-uniprot.txt "Catalyzes the oxidation of uric acid to 5-hydroxyisourate"].
• Broad purine-catabolism and urate-metabolism annotations were modified to the specific urate catabolic process because Uox catalyzes the urate oxidation step [file:DANRE/uox/uox-uniprot.txt "urate degradation; (S)-allantoin from urate: step 1/3"].
• Protein homotetramerization is supported structurally but treated as non-core [file:DANRE/uox/uox-uniprot.txt "SUBUNIT: Homotetramer; dimer of dimers."].

Re-review 2026-09-29

Every review block was templated (the same two summaries and the same UniProt/PMID:27922051 quotes repeated under all rows, including rows whose own reference was a different paper). All four cited papers are cached with full text and were read; each row now cites the evidence that actually belongs to it.

• GO:0004846 urate oxidase activity has four experimental rows, now differentiated: PMID:27922051 (IDA+IMP) is the kinetic/structural characterisation of the purified zebrafish enzyme PMID:27922051, recorded by UniProt as [file:DANRE/uox/uox-uniprot.txt "KM=11 uM for urate {ECO:0000269|PubMed:27922051};"] and [file:DANRE/uox/uox-uniprot.txt "ACTIVITY REGULATION: Competitively inhibited by xanthine."]; PMID:26349049 (IDA) is an in vivo complementation in Agrobacterium fabrum PMID:26349049 with the peroxide by-product evidenced by PMID:26349049; PMID:28508122 (IDA) is recombinant DrUox in the PEGylated three-enzyme therapeutic system PMID:28508122. All ACCEPT.
• PENDING resolved: GO:0004846 IBA -> ACCEPT (PANTHER node PTN000044668 is the cofactorless uricase family; zebrafish uox is inside it and carries its own experimental evidence, so appearing in its own WITH/FROM is expected) and GO:0019628 IEA GO_REF:0000120 -> ACCEPT.
• GO:0005777 peroxisome no longer rests on the deep-research file alone: the zebrafish sequence itself carries the targeting signal PMID:27922051 and animal uricolysis is peroxisomal PMID:27922051. IBA/IEA/ISS rows all ACCEPT with one rationale.
• GO:0046415 urate metabolic process (IMP) stays MODIFY -> GO:0019628, now argued from the mutant's direction of effect PMID:36553446: urate accumulates on loss of the enzyme, so the gene acts in the catabolic branch, not in urate metabolism generally.
• GO:0006145 (IBA) keeps MODIFY -> GO:0019628 and gained the missing propagation_review (TERM_SCOPING_PROBLEM / GRANULARITY_MISMATCH; node PTN000044668 and donor UniProtKB:P33282 both act on urate, not on a purine nucleobase).
• GO:0051289 homotetramerization (IPI) stays KEEP_AS_NON_CORE, now with the measurement PMID:27922051 and [file:DANRE/uox/uox-uniprot.txt "SUBUNIT: Homotetramer; dimer of dimers. {ECO:0000269|PubMed:27922051}."].
• Two rows absent from the refreshed GOA were dropped (GO:0072523 IEA GO_REF:0000117 and GO:0019628 IEA GO_REF:0000041); the ARBA/UniPathway assignments are now carried under GO_REF:0000120, which is reviewed. 15 rows remain.
• Description rewritten with the chemistry, kinetics, assembly, targeting signal and pathway context; reference_review added to all four PMIDs; core_functions and suggested experiments refreshed. Validation: 0 errors, 0 warnings.