cpt2 encodes carnitine O-palmitoyltransferase 2 (EC 2.3.1.21), a peripheral protein of the matrix face of the mitochondrial inner membrane and the second enzyme of the carnitine shuttle. After Cpt1 converts long-chain acyl-CoA to acylcarnitine at the outer membrane and the carnitine/acylcarnitine translocase moves it across the inner membrane, Cpt2 catalyses the reverse transesterification, regenerating long-chain acyl-CoA in the matrix and releasing free carnitine, so that the fatty acyl group can enter the beta-oxidation spiral. It is active on medium-chain (C8-C12) as well as long-chain (C14-C18) acyl esters. In zebrafish, morpholino knockdown causes abnormal lipid utilization and deposition, reduced body size and abnormal brain development, reflecting the dependence of the early embryo on fatty acid oxidation for energy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Mitochondrion: correct but less specific than the mitochondrial inner membrane, where Cpt2 sits as a peripheral protein on the matrix side. The IBA node PTN000501944 is seeded by mouse, rat and human CPT2. Reason: The enzyme is mitochondrial in every characterized ortholog and in the zebrafish knockdown study, but the informative location is the inner membrane facing the matrix, which is annotated separately and is where the acylcarnitine delivered by the carnitine/acylcarnitine translocase is reconverted. Both mitochondrion rows get the same action. Zebrafish Cpt2 protein was itself detected by Western blotting of mitochondrial fractions from 5 dpi larvae, so the organelle assignment is directly supported in this species. Supporting Evidence: PMID:39199302 A representative Western blot of CPT2 protein levels isolated from the mitochondrial fraction of 200 WT, CTRL-injected, TB-injected, and SB-injected zebrafish is shown file:DANRE/cpt2/cpt2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane {ECO:0000250}; Peripheral membrane protein {ECO:0000250}; Matrix side PMID:39199302 Carnitine palmitoyltransferase 2 (CPT2) is an inner mitochondrial membrane protein of the carnitine shuttle and is involved in the beta-oxidation of long chain fatty acids PMID:39199302 carnitine palmitoyltransferase 2 (CPT2) that converts the long-chain acylcarnitine to acyl-CoA for oxidation in the inner mitochondrial membrane |
| GO:0004095 carnitine O-palmitoyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Carnitine O-palmitoyltransferase activity: reversible transfer of the palmitoyl group between CoA and carnitine, which UniProt lists for this protein with a right-to-left physiological direction, i.e. palmitoylcarnitine + CoA -> palmitoyl-CoA + carnitine. Propagated from node PTN000501944, whose donors include the experimentally characterized human CPT2. Reason: This is the core molecular function. The reaction is listed for the zebrafish protein, the human ortholog carries EXP/IDA evidence for it, and the zebrafish knockdown paper describes Cpt2 as the enzyme that converts long-chain acylcarnitine to acyl-CoA at the inner membrane. All three rows for this term get the same action. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reaction=(R)-carnitine + hexadecanoyl-CoA = O-hexadecanoyl-(R)-carnitine + CoA file:DANRE/cpt2/cpt2-uniprot.txt PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:12663 PMID:39199302 carnitine palmitoyltransferase 2 (CPT2) that converts the long-chain acylcarnitine to acyl-CoA for oxidation in the inner mitochondrial membrane PMID:20538056 We show that CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters, whereas virtually no activity was found with short- and very long-chain acyl-CoAs or with branched-chain amino acid oxidation intermediates |
| GO:0006635 fatty acid beta-oxidation | IBA GO_REF:0000033 | ACCEPT | Summary: Fatty acid beta-oxidation: Cpt2 performs the matrix-side step of the carnitine shuttle that regenerates acyl-CoA, the substrate the beta-oxidation spiral acts on. Propagated from node PTN000501944 (human, rat and Drosophila donors). Reason: The gene product catalyses a step of the pathway rather than merely being required for it, and its loss in zebrafish produced abnormal lipid utilization and deposition, showing that fatty acid oxidation depends on it in this species. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reconverts acylcarnitines back into the respective acyl-CoA esters that can then undergo beta-oxidation, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion file:DANRE/cpt2/cpt2-uniprot.txt PATHWAY: Lipid metabolism; fatty acid beta-oxidation. PMID:39199302 CPT2 knockdown resulted in abnormal lipid utilization and deposition, reduction in body size, and abnormal brain development PMID:39199302 Carnitine palmitoyltransferase 2 (CPT2) is an inner mitochondrial membrane protein of the carnitine shuttle and is involved in the beta-oxidation of long chain fatty acids |
| GO:0004095 carnitine O-palmitoyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Carnitine O-palmitoyltransferase activity: reversible transfer of the palmitoyl group between CoA and carnitine, which UniProt lists for this protein with a right-to-left physiological direction, i.e. palmitoylcarnitine + CoA -> palmitoyl-CoA + carnitine. Mapped from RHEA:12661 and EC 2.3.1.21. Reason: This is the core molecular function. The reaction is listed for the zebrafish protein, the human ortholog carries EXP/IDA evidence for it, and the zebrafish knockdown paper describes Cpt2 as the enzyme that converts long-chain acylcarnitine to acyl-CoA at the inner membrane. All three rows for this term get the same action. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reaction=(R)-carnitine + hexadecanoyl-CoA = O-hexadecanoyl-(R)-carnitine + CoA file:DANRE/cpt2/cpt2-uniprot.txt PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:12663 PMID:39199302 carnitine palmitoyltransferase 2 (CPT2) that converts the long-chain acylcarnitine to acyl-CoA for oxidation in the inner mitochondrial membrane PMID:20538056 We show that CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters, whereas virtually no activity was found with short- and very long-chain acyl-CoAs or with branched-chain amino acid oxidation intermediates |
| GO:0005739 mitochondrion | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Mitochondrion: correct but less specific than the mitochondrial inner membrane, where Cpt2 sits as a peripheral protein on the matrix side. The ARBA mapping restates the UniProt location at the organelle level. Reason: The enzyme is mitochondrial in every characterized ortholog and in the zebrafish knockdown study, but the informative location is the inner membrane facing the matrix, which is annotated separately and is where the acylcarnitine delivered by the carnitine/acylcarnitine translocase is reconverted. Both mitochondrion rows get the same action. Zebrafish Cpt2 protein was itself detected by Western blotting of mitochondrial fractions from 5 dpi larvae, so the organelle assignment is directly supported in this species. Supporting Evidence: PMID:39199302 A representative Western blot of CPT2 protein levels isolated from the mitochondrial fraction of 200 WT, CTRL-injected, TB-injected, and SB-injected zebrafish is shown file:DANRE/cpt2/cpt2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane {ECO:0000250}; Peripheral membrane protein {ECO:0000250}; Matrix side PMID:39199302 Carnitine palmitoyltransferase 2 (CPT2) is an inner mitochondrial membrane protein of the carnitine shuttle and is involved in the beta-oxidation of long chain fatty acids PMID:39199302 carnitine palmitoyltransferase 2 (CPT2) that converts the long-chain acylcarnitine to acyl-CoA for oxidation in the inner mitochondrial membrane |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Mitochondrial inner membrane: UniProt places the protein on the matrix side of the inner membrane as a peripheral membrane protein, and the zebrafish study describes the same topology. Reason: This is the informative location and the one the catalytic step requires: acylcarnitine arriving through the translocase is converted on the matrix face, so the enzyme must be there. Core location for this gene. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane {ECO:0000250}; Peripheral membrane protein {ECO:0000250}; Matrix side PMID:39199302 Carnitine palmitoyltransferase 2 (CPT2) is an inner mitochondrial membrane protein of the carnitine shuttle and is involved in the beta-oxidation of long chain fatty acids PMID:39199302 carnitine palmitoyltransferase 2 (CPT2) that converts the long-chain acylcarnitine to acyl-CoA for oxidation in the inner mitochondrial membrane |
| GO:0008458 carnitine O-octanoyltransferase activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: Carnitine O-octanoyltransferase activity: the medium-chain (C8) version of the same transesterification. Mapped from RHEA:17177. Reason: Real and directly measured for the human ortholog, which is active on C8-C12 as well as C14-C18 acyl-CoAs, and UniProt lists the octanoyl reaction for the zebrafish protein. But the physiological role of the carnitine shuttle is long-chain fatty acid import; medium-chain acyl-CoAs largely enter the matrix without the shuttle, so the medium-chain activity is a genuine but secondary capability rather than a core function. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reaction=octanoyl-CoA + (R)-carnitine = O-octanoyl-(R)-carnitine + CoA file:DANRE/cpt2/cpt2-uniprot.txt Active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters. PMID:20538056 We show that CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters, whereas virtually no activity was found with short- and very long-chain acyl-CoAs or with branched-chain amino acid oxidation intermediates |
| GO:0015909 long-chain fatty acid transport | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Long-chain fatty acid transport: an ARBA mapping reflecting the position of Cpt2 in the carnitine shuttle, the system that delivers long-chain fatty acyl groups into the matrix. Reason: Cpt2 does not translocate anything across the membrane - that is done by the carnitine/acylcarnitine translocase - but it catalyses the matrix-side transesterification that releases the acyl group from carnitine and makes the shuttle vectorial, so it does part of the work of the transport process. UniProt itself frames the reaction as an essential step for mitochondrial uptake of long-chain fatty acids. Retained, but as a non-core contribution beside the catalytic and beta-oxidation terms. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reconverts acylcarnitines back into the respective acyl-CoA esters that can then undergo beta-oxidation, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion PMID:39199302 carnitine palmitoyltransferase 2 (CPT2) that converts the long-chain acylcarnitine to acyl-CoA for oxidation in the inner mitochondrial membrane PMID:39199302 Carnitine palmitoyltransferase 2 (CPT2) is an inner mitochondrial membrane protein of the carnitine shuttle and is involved in the beta-oxidation of long chain fatty acids |
| GO:0016746 acyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: Acyltransferase activity from InterPro IPR000542 (carnitine/choline acetyltransferase family) is the correct chemistry at family level but says nothing about the acyl donor or acceptor. Reason: The specific reaction is documented for this protein in UniProt and measured for the ortholog, so the substrate-specific carnitine O-palmitoyltransferase term should carry the annotation; the generic term adds nothing beside it. Proposed replacements: carnitine O-palmitoyltransferase activity Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Belongs to the carnitine/choline acetyltransferase family. file:DANRE/cpt2/cpt2-uniprot.txt Reaction=(R)-carnitine + hexadecanoyl-CoA = O-hexadecanoyl-(R)-carnitine + CoA PMID:20538056 We show that CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters, whereas virtually no activity was found with short- and very long-chain acyl-CoAs or with branched-chain amino acid oxidation intermediates file:DANRE/cpt2/cpt2-deep-research-falcon.md summarizes structural binding architecture (distinct CoA, acyl, and carnitine binding sites) and key residues implicated in catalysis and substrate binding |
| GO:0006635 fatty acid beta-oxidation | IEA GO_REF:0000041 | ACCEPT | Summary: Fatty acid beta-oxidation: Cpt2 performs the matrix-side step of the carnitine shuttle that regenerates acyl-CoA, the substrate the beta-oxidation spiral acts on. Mapped from UniPathway UPA00659, matching the UniProt PATHWAY line. Reason: The gene product catalyses a step of the pathway rather than merely being required for it, and its loss in zebrafish produced abnormal lipid utilization and deposition, showing that fatty acid oxidation depends on it in this species. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reconverts acylcarnitines back into the respective acyl-CoA esters that can then undergo beta-oxidation, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion file:DANRE/cpt2/cpt2-uniprot.txt PATHWAY: Lipid metabolism; fatty acid beta-oxidation. PMID:39199302 CPT2 knockdown resulted in abnormal lipid utilization and deposition, reduction in body size, and abnormal brain development PMID:39199302 Carnitine palmitoyltransferase 2 (CPT2) is an inner mitochondrial membrane protein of the carnitine shuttle and is involved in the beta-oxidation of long chain fatty acids |
| GO:0004095 carnitine O-palmitoyltransferase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Carnitine O-palmitoyltransferase activity: reversible transfer of the palmitoyl group between CoA and carnitine, which UniProt lists for this protein with a right-to-left physiological direction, i.e. palmitoylcarnitine + CoA -> palmitoyl-CoA + carnitine. Transferred from human CPT2 (UniProtKB:P23786), which has EXP and IDA evidence for this activity. Reason: This is the core molecular function. The reaction is listed for the zebrafish protein, the human ortholog carries EXP/IDA evidence for it, and the zebrafish knockdown paper describes Cpt2 as the enzyme that converts long-chain acylcarnitine to acyl-CoA at the inner membrane. All three rows for this term get the same action. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reaction=(R)-carnitine + hexadecanoyl-CoA = O-hexadecanoyl-(R)-carnitine + CoA file:DANRE/cpt2/cpt2-uniprot.txt PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:12663 PMID:39199302 carnitine palmitoyltransferase 2 (CPT2) that converts the long-chain acylcarnitine to acyl-CoA for oxidation in the inner mitochondrial membrane PMID:20538056 We show that CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters, whereas virtually no activity was found with short- and very long-chain acyl-CoAs or with branched-chain amino acid oxidation intermediates |
| GO:0008458 carnitine O-octanoyltransferase activity | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Carnitine O-octanoyltransferase activity: the medium-chain (C8) version of the same transesterification. Transferred from human CPT2 (UniProtKB:P23786), which carries EXP evidence for it. Reason: Real and directly measured for the human ortholog, which is active on C8-C12 as well as C14-C18 acyl-CoAs, and UniProt lists the octanoyl reaction for the zebrafish protein. But the physiological role of the carnitine shuttle is long-chain fatty acid import; medium-chain acyl-CoAs largely enter the matrix without the shuttle, so the medium-chain activity is a genuine but secondary capability rather than a core function. Supporting Evidence: file:DANRE/cpt2/cpt2-uniprot.txt Reaction=octanoyl-CoA + (R)-carnitine = O-octanoyl-(R)-carnitine + CoA file:DANRE/cpt2/cpt2-uniprot.txt Active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters. PMID:20538056 We show that CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters, whereas virtually no activity was found with short- and very long-chain acyl-CoAs or with branched-chain amino acid oxidation intermediates |
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Download this section (compressed HTML)Q: Do zebrafish cpt2 mutants accumulate long-chain acylcarnitines and show the acylcarnitine profile used diagnostically in human CPT2 deficiency, and does the profile distinguish medium- from long-chain substrate use in vivo?
Q: Are the neural and behavioral phenotypes of cpt2 knockdown zebrafish a direct consequence of reduced fatty acid oxidation in neurons, or secondary to systemic energy deficit? This determines whether any neurodevelopmental process annotation could ever be justified for this gene.
Experiment: Generate a stable cpt2 loss-of-function zebrafish line and measure acylcarnitine and free carnitine profiles by tandem mass spectrometry across chain lengths, testing whether long-chain species accumulate as in human CPT2 deficiency.
Experiment: Assay recombinant zebrafish Cpt2 against a C2-C26 acyl-CoA panel with carnitine, to test whether the medium- plus long-chain specificity measured for the human enzyme is conserved and whether the octanoyltransferase annotation is warranted for the fish protein.
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