id: Q6PHK4 gene_symbol: agxtb product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: agxtb (alanine--glyoxylate aminotransferase b) is one of two zebrafish co-orthologs of vertebrate AGXT, retained from the teleost-specific genome duplication; its paralog is agxta. 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. Vertebrate AGT removes glyoxylate before it is oxidized to oxalate and, in the mitochondrial form, also acts on glyoxylate from hydroxyproline breakdown and on serine and alanine for gluconeogenesis. agxtb keeps the catalytic lysine and substrate-binding arginine and has a 32-residue arginine-rich N-terminal extension that matches the mitochondrial targeting sequence of the spotted gar and tetrapod orthologs, but its C-terminus (SKA) no longer fits the peroxisomal targeting signal; it is therefore predicted to be the mitochondrial copy, while agxta is the peroxisomal one. agxtb is expressed mainly in liver, kidney, intestine and spleen and rises strongly in larvae. 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. action: ACCEPT reason: Vertebrate AGT is also serine:pyruvate aminotransferase, and fish liver AGT uses L-serine with pyruvate. agxtb keeps the catalytic residues of human AGXT and is the copy closest to gar AGXT. The serine:pyruvate reaction is the one tied to gluconeogenesis in the mitochondrial form of the enzyme, which this copy is predicted to be. 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 from EC 2.6.1.51. 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:0004760 label: L-serine:pyruvate transaminase activity evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: enables supporting_entities: - UniProtKB:P09139 review: summary: Serine:pyruvate aminotransferase activity transferred by sequence similarity from rat Agxt (P09139). action: ACCEPT reason: Rat SPT/AGT is the enzyme whose mitochondrial and peroxisomal forms were characterized biochemically; transfer to agxtb is sound (conserved catalytic residues). Duplicates the IBA row. supported_by: - reference_id: PMID:21558762 supporting_text: In addition, SPT contributes substantially to gluconeogenesis from serine in rabbit, human and dog livers, irrespective of its mitochondrial or peroxisomal localization. - term: id: GO:0005739 label: mitochondrion evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: located_in supporting_entities: - UniProtKB:P09139 review: summary: Mitochondrion transferred from rat Agxt (P09139), whose upstream-start product carries a cleavable MTS. action: ACCEPT reason: agxtb begins with a 32-residue arginine-rich, acid-poor extension that aligns with the MTS-like extension of spotted gar AGXT and is homologous in position to the MTS of the mouse and rat upstream-start products. This extension is present in the agxtb orthologues of every teleost in the panel examined. A survey of the zebrafish peroxisomal proteome also predicted an N-terminal MTS for agxtb. Mitochondrial location is the best-supported prediction for this copy, though it has not been tested in zebrafish. supported_by: - reference_id: PMID:35295584 supporting_text: Interestingly, zebrafish encode another putative AGT (agxtb, Q6PHK4_DANRE) which lacks a PTS1 but possesses an N-terminal MTS. - reference_id: PMID:21558762 supporting_text: Transcription from the upstream start site generates the 1900-nucleotide mRNA for a 45-kDa precursor for SPTm containing a cleavable N-terminal mitochondrial targeting signal of 22 amino acids. - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: both have the positively charged, acid-poor composition of a mitochondrial targeting sequence. - 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 (human AGXT, rat Agxt). action: MARK_AS_OVER_ANNOTATED reason: The node correctly carries peroxisome for the family, and the zebrafish paralog agxta keeps a C-terminal PTS1-like end. agxtb does not. Its C-terminus is SKA, which does not fit the PTS1 consensus and which is shared by most agxtb orthologues across teleosts, while it keeps the ancestral N-terminal MTS-like extension. After the duplication the two copies appear to have divided the ancestral targeting signals, and same-node IBA propagation cannot see this. Not removed, because peroxisomal import of AGT can also use internal signals and neither zebrafish protein has been localized experimentally. supported_by: - reference_id: PMID:35295584 supporting_text: Interestingly, zebrafish encode another putative AGT (agxtb, Q6PHK4_DANRE) which lacks a PTS1 but possesses an N-terminal MTS. - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: agxtb kept the extension and its C-terminus became SKA, which does not fit the PTS1 consensus. - reference_id: PMID:15911627 supporting_text: Peroxisomal import of human alanine:glyoxylate aminotransferase requires ancillary targeting information remote from its C terminus. propagation_review: root_cause: PROPAGATION_BAD failure_modes: - COMPARTMENT_OR_COMPLEX_MISMATCH source_entities: - source_id: PANTHER:PTN000475539 source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: Peroxisomal AGT is right for the node and for agxta; agxtb lost the C-terminal PTS1 and kept the MTS after the teleost duplication. - source_id: UniProtKB:P21549 source_label: AGXT (human) source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: Human AGT is exclusively peroxisomal because it lost the upstream start codon for its MTS; agxtb is in the opposite state (MTS kept, PTS1 lost). - source_id: RGD:2073 source_label: Agxt (rat) source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: Rat makes both forms from one gene by alternative start sites; the peroxisomal form uses the C-terminal PTS1 that agxtb lacks. residue_claims_not_applicable: A C-terminal tripeptide signal and an N-terminal extension, not single catalytic residues; the argument is the presence or absence of targeting motifs. - term: id: GO:0005777 label: peroxisome evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: located_in supporting_entities: - UniProtKB:P21549 review: summary: Peroxisome transferred by sequence similarity from human AGXT (P21549). action: MARK_AS_OVER_ANNOTATED reason: Human AGT is peroxisomal because it lacks the MTS start codon and has a C-terminal PTS1 (KKL) with an ancillary internal signal. agxtb is in the opposite state, with an N-terminal MTS-like extension and a C-terminus (SKA) that does not fit the PTS1 consensus, so location does not transfer from the human enzyme to this copy. The zebrafish paralog agxta is the copy for which peroxisome is predicted. supported_by: - reference_id: PMID:41781394 supporting_text: The human AGT protein lacks a functional MTS start codon and has been shown to exclusively target the peroxisome27,60, whereas the Xenopus protein exclusively targets the mitochondria61. - reference_id: PMID:35295584 supporting_text: Interestingly, zebrafish encode another putative AGT (agxtb, Q6PHK4_DANRE) which lacks a PTS1 but possesses an N-terminal MTS. - 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 PTN000475663. action: ACCEPT reason: Glycine is the direct product of the AGT reaction, whichever organelle the enzyme is in. The obsolete GO:0019265 (glycine formation by transamination of glyoxylate) cannot be used instead. 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 from PTN000475663; the defining activity of AGXT. action: ACCEPT reason: Core activity, measured for purified fish liver AGT and for mammalian AGXT; catalytic residues conserved in agxtb. 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:0008453 label: L-alanine:glyoxylate transaminase activity evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: enables supporting_entities: - UniProtKB:O35423 review: summary: Alanine:glyoxylate aminotransferase activity transferred from mouse Agxt (O35423). action: ACCEPT reason: Same activity as the IBA row; the mouse enzyme, like agxtb, carries an N-terminal MTS in its upstream-start form. 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 from PTN000475663. action: ACCEPT reason: Glyoxylate removal is the role of AGT in both organelles; in the mitochondrial form it handles glyoxylate made from hydroxyproline. Core process for this copy as well. supported_by: - reference_id: PMID:21558762 supporting_text: In carnivores, its mitochondrial localization appears to be needed to metabolize glyoxylate formed from L-hydroxyproline in mitochondria. - term: id: GO:0042866 label: pyruvate biosynthetic process evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: acts_upstream_of_or_within supporting_entities: - UniProtKB:P09139 review: summary: Pyruvate biosynthetic process transferred from rat Agxt (P09139). action: KEEP_AS_NON_CORE reason: Pyruvate is a product of the alanine:glyoxylate reaction (alanine is the amino donor), and mitochondrial AGT transaminates alanine and serine for gluconeogenesis. The term is correct chemistry but describes a by-product of glyoxylate detoxification rather than the purpose of the enzyme, so it is kept as non-core. supported_by: - reference_id: PMID:35295584 supporting_text: Mitochondrial AGT can transaminate alanine and serine to pyruvate and hydroxypyruvate for gluconeogenesis. - term: id: GO:0046487 label: glyoxylate metabolic process evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: acts_upstream_of_or_within supporting_entities: - UniProtKB:P21549 review: summary: Glyoxylate metabolic process transferred from human AGXT. action: ACCEPT reason: Correct and general; parent of the more specific glyoxylate catabolic process accepted above. 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:0071391 label: cellular response to estrogen stimulus evidence_type: IDA original_reference_id: PMID:18618001 qualifier: acts_upstream_of_or_within review: summary: Cellular response to estrogen stimulus, from a whole-adult zebrafish microarray study of estrogenic and aromatic-hydrocarbon compounds in which an alanine-glyoxylate aminotransferase probe was down-regulated. action: MARK_AS_OVER_ANNOTATED reason: The evidence is a change in mRNA level of a probe in tissues of fish exposed to estrogenic compounds (listed among discriminatory biomarker genes). A transcript change says the gene is estrogen-responsive; it does not show that the enzyme takes part in a cellular response to estrogen. Nothing else links AGT to estrogen signalling. The row can stay as a record of regulation, but it is not a function of the gene. supported_by: - reference_id: PMID:18618001 supporting_text: Focusing on two classes of compounds with wide implications to human health, polycyclic (halogenated) aromatic hydrocarbons [P(H)AHs] and estrogenic compounds (ECs), we generated robust prediction models that can discriminate compounds of the same class from those of different classes in two large independent experiments. - reference_id: PMID:18618001 supporting_text: Alanine-glyoxylate aminotransferase−1.47NS−0.80−0.85−1.82NSNS−1.014# core_functions: - description: PLP-dependent alanine:glyoxylate and serine:pyruvate aminotransferase predicted to act in mitochondria; the MTS-bearing copy of the zebrafish pair (32-residue N-terminal extension shared with gar AGXT; C-terminal PTS1 lost). Converts glyoxylate to glycine and transaminates serine and alanine. 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:0005739 label: mitochondrion supported_by: - reference_id: PMID:35295584 supporting_text: Interestingly, zebrafish encode another putative AGT (agxtb, Q6PHK4_DANRE) which lacks a PTS1 but possesses an N-terminal MTS. - reference_id: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md supporting_text: agxtb kept the extension and its C-terminus became SKA, which does not fit the PTS1 consensus. - description: Serine:pyruvate aminotransferase activity of the same enzyme, the reaction linked to gluconeogenesis from serine in the mitochondrial form of vertebrate AGT. molecular_function: id: GO:0004760 label: L-serine:pyruvate transaminase activity locations: - id: GO:0005739 label: mitochondrion supported_by: - reference_id: PMID:35295584 supporting_text: Mitochondrial AGT can transaminate alanine and serine to pyruvate and hydroxypyruvate for gluconeogenesis. references: - id: GO_REF:0000003 title: Gene Ontology annotation based on Enzyme Commission mapping findings: [] - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: PMID:18618001 title: Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Full text. Microarray biomarker study; an AGT probe is down-regulated by estrogenic compounds. Supports transcriptional responsiveness only. - id: PMID:35295584 title: Insights Into the Peroxisomal Protein Inventory of Zebrafish. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text. Bioinformatic prediction that agxtb has an MTS and no PTS1, and agxta a weak PTS1. - id: PMID:21558762 title: Studies on a unique organelle localization of a liver enzyme, serine:pyruvate (or alanine:glyoxylate) aminotransferase. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full-text review of rat/mammalian SPT/AGT dual targeting by alternative start sites. - id: PMID:15911627 title: Peroxisomal import of human alanine:glyoxylate aminotransferase requires ancillary targeting information remote from its C terminus. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; internal ancillary PTS1A in mammalian AGTs, absent from Xenopus AGT. - 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; human peroxisomal and Xenopus mitochondrial controls. - 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. - 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 Agxtb imported into mitochondria in zebrafish liver and kidney, and is its N-terminal extension cleaved as an MTS? - question: Does the SKA C-terminus of Agxtb really abolish peroxisomal import, or can internal signals still bring some Agxtb into peroxisomes? - question: Why is agxtb about three times more highly expressed than agxta in larvae (E-ERAD-475), and does the mitochondrial copy carry most of the glyoxylate load from hydroxyproline in a carnivorous fish? suggested_experiments: - hypothesis: Agxtb is mitochondrial and Agxta peroxisomal. description: Co-localize tagged Agxtb (tag at the C-terminus, leaving the N-terminal extension free) with mitochondrial and peroxisomal markers in zebrafish hepatocytes or fish cell lines; delete the N-terminal extension and add a canonical PTS1 (SKL) to test whether the targeting difference is carried by these signals alone. experiment_type: subcellular localization - hypothesis: Mitochondrial Agxtb handles glyoxylate from hydroxyproline catabolism. description: Compare oxalate and glycolate excretion of agxtb and agxta mutant larvae after a hydroxyproline load versus a glycolate load. experiment_type: knockout phenotyping