id: Q6DG86 gene_symbol: agxta product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: agxta (alanine--glyoxylate aminotransferase a) is one of two zebrafish co-orthologs of vertebrate AGXT, retained from the teleost-specific genome duplication; its paralog is agxtb. It encodes a pyridoxal 5'-phosphate dependent class-V aminotransferase that is predicted to transaminate glyoxylate with L-alanine to glycine and pyruvate, and L-serine with pyruvate to hydroxypyruvate and L-alanine. In vertebrates this enzyme detoxifies glyoxylate, the precursor of oxalate, and its organelle location (peroxisomes, mitochondria or both) varies between species through an N-terminal mitochondrial targeting sequence and a C-terminal peroxisomal targeting signal. agxta keeps the catalytic lysine and substrate-binding arginine, ends in a C-terminal tripeptide (SRV) that resembles a weak peroxisomal targeting signal, and has no N-terminal extension or upstream start codon, so it is predicted to be the peroxisomal copy; agxtb carries the mitochondrial-type N-terminal signal instead. agxta is expressed in larval and adult liver, pronephric duct and kidney, intestine and spleen. No functional study of the zebrafish protein has been published. existing_annotations: - term: id: GO:0004760 label: L-serine:pyruvate transaminase activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - AGI_LocusCode:AT2G13360 - FB:FBgn0014031 - PANTHER:PTN000475663 - RGD:2073 - UniProtKB:P21549 - UniProtKB:Q9X1C0 review: summary: Serine:pyruvate aminotransferase activity propagated from the AGT/SPT node PTN000475663 (human AGXT, rat Agxt, Arabidopsis AGT1, fly Spat and others). action: ACCEPT reason: The vertebrate AGT is the same enzyme as serine:pyruvate aminotransferase, and purified fish liver AGT uses L-serine with pyruvate. agxta is inside the AGT clade and keeps the PLP-binding lysine and substrate-binding arginine of human AGXT. Nothing suggests loss of this sub-activity. Accepted, as for agxtb. supported_by: - reference_id: PMID:6697688 supporting_text: It was specific for L-alanine and L-serine with glyoxylate and for L-serine with pyruvate as amino acceptor. - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. - term: id: GO:0004760 label: L-serine:pyruvate transaminase activity evidence_type: IEA original_reference_id: GO_REF:0000003 qualifier: enables supporting_entities: - EC:2.6.1.51 review: summary: Serine:pyruvate aminotransferase activity mapped from EC 2.6.1.51 on the UniProt record. action: ACCEPT reason: Same activity as the IBA row; the EC assignment comes from the PIRNR family rule, which fits a full-length AGT with conserved catalytic residues. supported_by: - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. - term: id: GO:0005777 label: peroxisome evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - PANTHER:PTN000475539 - RGD:2073 - UniProtKB:P21549 review: summary: Peroxisome propagated from node PTN000475539, seeded by human AGXT and rat Agxt. action: ACCEPT reason: Of the two zebrafish copies, agxta is the one that fits this location. It ends in SRV, which a survey of the zebrafish peroxisomal proteome classed as a weak PTS1, and it has no N-terminal extension; its transcript has an in-frame stop 16 codons upstream of the start, so it cannot make an MTS-bearing isoform. Freshwater-fish liver AGT is found partly in peroxisomes. The call is a prediction from sequence; zebrafish Agxta has not been localized, and C-terminal tripeptides of this kind (SRV) have not been tested as PTS1 in fish. supported_by: - reference_id: PMID:35295584 supporting_text: Zebrafish also contains a putative peroxisomal alanine:glyoxylate aminotransferase (AGT) (Agxta, F1QY24 _DANRE) with a weak PTS1 (SRV), a key enzyme to prevent oxalate accumulation (Table 1 and Supplementary Table S3). - reference_id: PMID:8954944 supporting_text: The present report describes that hepatic alanine:glyoxylate aminotransferase is located both in the peroxisomes and in the mitochondria in fresh water fish - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: agxta therefore cannot make an MTS-bearing isoform from this locus. - term: id: GO:0006545 label: glycine biosynthetic process evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - PANTHER:PTN000475663 - RGD:2073 - SGD:S000001864 - UniProtKB:P21549 - WB:WBGene00011767 review: summary: Glycine biosynthetic process propagated from the AGT node PTN000475663. action: ACCEPT reason: The AGT reaction forms glycine from glyoxylate and alanine, so the enzyme catalyses a step of glycine formation. This is the direct product of the conserved activity and applies to both zebrafish copies. The more specific term for glycine formation by transamination of glyoxylate (GO:0019265) is obsolete, so this term is the appropriate one. supported_by: - reference_id: PMID:41781394 supporting_text: The enzyme alanine:glyoxylate aminotransferase (AGT) converts glyoxylate to glycine, preventing the formation of harmful calcium oxalate crystals. - term: id: GO:0008453 label: L-alanine:glyoxylate transaminase activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - AGI_LocusCode:AT2G13360 - FB:FBgn0014031 - MGI:MGI:1329033 - PANTHER:PTN000475663 - RGD:2073 - SGD:S000001864 - UniProtKB:P21549 - UniProtKB:Q7PRG3 - WB:WBGene00011767 review: summary: Alanine:glyoxylate aminotransferase activity propagated from PTN000475663; the defining activity of AGXT. action: ACCEPT reason: Core activity of the family, measured for purified fish liver AGT (mackerel and other species) and for mammalian AGXT. agxta keeps the catalytic residues. Core function. supported_by: - reference_id: PMID:6697688 supporting_text: Alanine:glyoxylate aminotransferase was highly purified and characterized from mackerel liver. - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. - term: id: GO:0008453 label: L-alanine:glyoxylate transaminase activity evidence_type: IEA original_reference_id: GO_REF:0000003 qualifier: enables supporting_entities: - EC:2.6.1.44 review: summary: Alanine:glyoxylate aminotransferase activity from EC 2.6.1.44. action: ACCEPT reason: Same activity as the IBA row. supported_by: - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. - term: id: GO:0009436 label: glyoxylate catabolic process evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0014031 - PANTHER:PTN000475663 - UniProtKB:P21549 - UniProtKB:Q7PRG3 review: summary: Glyoxylate catabolic process propagated from PTN000475663. action: ACCEPT reason: Removing glyoxylate before it is oxidized to oxalate is the physiological role of AGT. In fish, glyoxylate is also the end product of hepatic purine breakdown in peroxisomes, which fits a peroxisomal copy. Core process, shared with agxtb (which would act on mitochondrial glyoxylate). supported_by: - reference_id: PMID:8954944 supporting_text: The end products of purine degradation are urea and glyoxylate in fish. - reference_id: PMID:35295584 supporting_text: This prevents the conversion of glyoxylate into oxalate, which is toxic. core_functions: - description: PLP-dependent alanine:glyoxylate (and serine:pyruvate) aminotransferase predicted to act in peroxisomes, converting glyoxylate to glycine and so preventing oxalate formation; the peroxisomal-signal copy of the zebrafish pair (C-terminal SRV, no N-terminal targeting sequence). Location and activity are inferred from sequence and orthology; not measured in zebrafish. molecular_function: id: GO:0008453 label: L-alanine:glyoxylate transaminase activity directly_involved_in: - id: GO:0009436 label: glyoxylate catabolic process locations: - id: GO:0005777 label: peroxisome supported_by: - reference_id: PMID:35295584 supporting_text: Zebrafish also contains a putative peroxisomal alanine:glyoxylate aminotransferase (AGT) (Agxta, F1QY24 _DANRE) with a weak PTS1 (SRV), a key enzyme to prevent oxalate accumulation (Table 1 and Supplementary Table S3). - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: agxta kept a C-terminal PTS1-like end and lost the extension (and any upstream start) - description: Serine:pyruvate aminotransferase activity of the same enzyme (L-serine + pyruvate to hydroxypyruvate + L-alanine), shared by vertebrate AGTs. molecular_function: id: GO:0004760 label: L-serine:pyruvate transaminase activity supported_by: - reference_id: PMID:6697688 supporting_text: It was specific for L-alanine and L-serine with glyoxylate and for L-serine with pyruvate as amino acceptor. references: - id: GO_REF:0000003 title: Gene Ontology annotation based on Enzyme Commission mapping findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: PMID:35295584 title: Insights Into the Peroxisomal Protein Inventory of Zebrafish. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text. Bioinformatic survey of zebrafish PTS1/MTS proteins; names Agxta (as deleted entry F1QY24, same sequence as Q6DG86 except one residue) as weak-PTS1 and agxtb as MTS-bearing. Predictions only. - id: PMID:8954944 title: Metabolism of glyoxylate, the end product of purin degradation, in liver peroxisomes of fresh water fish. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; dual peroxisomal/mitochondrial hepatic AGT in freshwater fish (species not named in the abstract). - id: PMID:6697688 title: 'Enzymatic and immunological comparison of alanine: glyoxylate aminotransferases from different fish and mammalian livers.' findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; purified mackerel liver AGT substrate specificity (AGT1-like). - id: PMID:41781394 title: Convergent evolutionary shifts in AGT targeting between mitochondria and peroxisomes across mammal transitions to herbivory. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Mammal-wide MTS/PTS1 evolution with cell assays; background for the ancestral dual-signal state. - id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md title: agxta / agxtb protein, targeting-signal, expression and synteny comparison reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Local pair analysis directly supports PLP-site and substrate-binding residue retention in both agxt copies and the post-duplication split in predicted N-terminal mitochondrial versus C-terminal peroxisomal targeting signals; the report explicitly treats the localization calls as sequence predictions, not direct import assays. findings: [] suggested_questions: - question: Is Agxta peroxisomal in zebrafish hepatocytes, and is the C-terminal SRV sufficient for import by zebrafish Pex5, or does it need internal ancillary signals as human AGT does? - question: Did the split of targeting signals between agxta (PTS1-like end only) and agxtb (MTS only) happen once before the teleost radiation, or several times? The arowana agxta orthologue still has an Arg-rich N-terminal extension. - question: Does loss of agxta cause hyperoxaluria or kidney calcium oxalate deposits in zebrafish, and does agxtb compensate? suggested_experiments: - hypothesis: The two copies are targeted to different organelles. description: Express GFP-tagged Agxta (C-terminal tag left free by tagging at the N-terminus) and Agxtb (tag at the C-terminus) in zebrafish liver or cultured fish cells with peroxisomal (SKL) and mitochondrial markers; swap the C-terminal tripeptides and N-terminal extensions between the copies. experiment_type: subcellular localization - hypothesis: Peroxisomal Agxta is needed to prevent oxalate formation. description: Generate agxta, agxtb and double mutants (preferably promoter-deletion alleles to avoid transcriptional adaptation) and measure urinary/whole-larva oxalate, glycolate and glycine, and kidney crystal deposition after a glycolate or hydroxyproline load. experiment_type: knockout phenotyping