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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004760 L-serine:pyruvate transaminase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Serine:pyruvate aminotransferase activity propagated from the AGT/SPT node PTN000475663. 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. Supporting Evidence: PMID:6697688 It was specific for L-alanine and L-serine with glyoxylate and for L-serine with pyruvate as amino acceptor. file:DANRE/agxta/agxta-bioinformatics/RESULTS.md Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. |
| GO:0004760 L-serine:pyruvate transaminase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Serine:pyruvate aminotransferase activity from EC 2.6.1.51. Reason: Same activity as the IBA row. Supporting Evidence: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. |
| GO:0004760 L-serine:pyruvate transaminase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Serine:pyruvate aminotransferase activity transferred by sequence similarity from rat Agxt (P09139). 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. Supporting Evidence: PMID:21558762 In addition, SPT contributes substantially to gluconeogenesis from serine in rabbit, human and dog livers, irrespective of its mitochondrial or peroxisomal localization. |
| GO:0005739 mitochondrion | ISS GO_REF:0000024 | ACCEPT | Summary: Mitochondrion transferred from rat Agxt (P09139), whose upstream-start product carries a cleavable MTS. 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. Supporting Evidence: PMID:35295584 Interestingly, zebrafish encode another putative AGT (agxtb, Q6PHK4_DANRE) which lacks a PTS1 but possesses an N-terminal MTS. PMID:21558762 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. file:DANRE/agxta/agxta-bioinformatics/RESULTS.md both have the positively charged, acid-poor composition of a mitochondrial targeting sequence. |
| GO:0005777 peroxisome | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Peroxisome propagated from node PTN000475539 (human AGXT, rat Agxt). 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. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000475539 SUPPORTS SOURCE BUT NOT TARGET Peroxisomal AGT is right for the node and for agxta; agxtb lost the C-terminal PTS1 and kept the MTS after the teleost duplication. UniProtKB:P21549 · AGXT (human) SUPPORTS SOURCE BUT NOT TARGET 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). RGD:2073 · Agxt (rat) SUPPORTS SOURCE BUT NOT TARGET Rat makes both forms from one gene by alternative start sites; the peroxisomal form uses the C-terminal PTS1 that agxtb lacks. Supporting Evidence: PMID:35295584 Interestingly, zebrafish encode another putative AGT (agxtb, Q6PHK4_DANRE) which lacks a PTS1 but possesses an N-terminal MTS. file:DANRE/agxta/agxta-bioinformatics/RESULTS.md agxtb kept the extension and its C-terminus became SKA, which does not fit the PTS1 consensus. PMID:15911627 Peroxisomal import of human alanine:glyoxylate aminotransferase requires ancillary targeting information remote from its C terminus. |
| GO:0005777 peroxisome | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Peroxisome transferred by sequence similarity from human AGXT (P21549). 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. Supporting Evidence: PMID:41781394 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. PMID:35295584 Interestingly, zebrafish encode another putative AGT (agxtb, Q6PHK4_DANRE) which lacks a PTS1 but possesses an N-terminal MTS. |
| GO:0006545 glycine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Glycine biosynthetic process propagated from PTN000475663. 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. Supporting Evidence: PMID:41781394 The enzyme alanine:glyoxylate aminotransferase (AGT) converts glyoxylate to glycine, preventing the formation of harmful calcium oxalate crystals. |
| GO:0008453 L-alanine:glyoxylate transaminase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Alanine:glyoxylate aminotransferase activity from PTN000475663; the defining activity of AGXT. Reason: Core activity, measured for purified fish liver AGT and for mammalian AGXT; catalytic residues conserved in agxtb. Supporting Evidence: PMID:6697688 Alanine:glyoxylate aminotransferase was highly purified and characterized from mackerel liver. file:DANRE/agxta/agxta-bioinformatics/RESULTS.md Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. |
| GO:0008453 L-alanine:glyoxylate transaminase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Alanine:glyoxylate aminotransferase activity from EC 2.6.1.44. Reason: Same activity as the IBA row. Supporting Evidence: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. |
| GO:0008453 L-alanine:glyoxylate transaminase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Alanine:glyoxylate aminotransferase activity transferred from mouse Agxt (O35423). Reason: Same activity as the IBA row; the mouse enzyme, like agxtb, carries an N-terminal MTS in its upstream-start form. Supporting Evidence: file:DANRE/agxta/agxta-bioinformatics/RESULTS.md Both copies keep the PLP-binding lysine (human K209) and the substrate-binding arginine (human R360), so both are predicted to be active aminotransferases. |
| GO:0009436 glyoxylate catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Glyoxylate catabolic process from PTN000475663. 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. Supporting Evidence: PMID:21558762 In carnivores, its mitochondrial localization appears to be needed to metabolize glyoxylate formed from L-hydroxyproline in mitochondria. |
| GO:0042866 pyruvate biosynthetic process | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Pyruvate biosynthetic process transferred from rat Agxt (P09139). 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. Supporting Evidence: PMID:35295584 Mitochondrial AGT can transaminate alanine and serine to pyruvate and hydroxypyruvate for gluconeogenesis. |
| GO:0046487 glyoxylate metabolic process | ISS GO_REF:0000024 | ACCEPT | Summary: Glyoxylate metabolic process transferred from human AGXT. Reason: Correct and general; parent of the more specific glyoxylate catabolic process accepted above. Supporting Evidence: PMID:41781394 The enzyme alanine:glyoxylate aminotransferase (AGT) converts glyoxylate to glycine, preventing the formation of harmful calcium oxalate crystals. |
| GO:0071391 cellular response to estrogen stimulus | IDA PMID:18618001 Zebrafish whole-adult-organism chemogenomics for large-scale... | MARK AS OVER ANNOTATED | 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. 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. Supporting Evidence: PMID:18618001 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. PMID:18618001 Alanine-glyoxylate aminotransferase−1.47NS−0.80−0.85−1.82NSNS−1.014# |
Loading supporting content…
Download this section (compressed HTML)Q: Is Agxtb imported into mitochondria in zebrafish liver and kidney, and is its N-terminal extension cleaved as an MTS?
Q: Does the SKA C-terminus of Agxtb really abolish peroxisomal import, or can internal signals still bring some Agxtb into peroxisomes?
Q: 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?
Experiment: 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.
Hypothesis: Agxtb is mitochondrial and Agxta peroxisomal.
Type: subcellular localization
Experiment: Compare oxalate and glycolate excretion of agxtb and agxta mutant larvae after a hydroxyproline load versus a glycolate load.
Hypothesis: Mitochondrial Agxtb handles glyoxylate from hydroxyproline catabolism.
Type: knockout phenotyping
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)