CPT2

UniProt ID: P23786
Organism: Homo sapiens
Review Status: INITIALIZED
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Gene Description

Carnitine O-palmitoyltransferase 2 (CPT2, EC 2.3.1.21) is a mitochondrial enzyme of the carnitine/choline acetyltransferase family that is peripherally associated with the matrix side of the mitochondrial inner membrane. It catalyzes the final, matrix-side step of the carnitine shuttle, regenerating long-chain acyl-CoA from imported acylcarnitine (long-chain acylcarnitine + CoA to long-chain acyl-CoA + L-carnitine), the reverse-direction reaction to CPT1. This reconstitutes the acyl-CoA pool inside the matrix so that long-chain fatty acids can enter mitochondrial beta-oxidation; CPT2 is therefore essential for the mitochondrial uptake and oxidation of long-chain fatty acids. The enzyme is active with medium-chain (C8-C12) and long-chain (C14-C18) acyl-CoA esters. Loss of CPT2 function causes carnitine palmitoyltransferase II deficiency, an autosomal recessive disorder of long-chain fatty acid oxidation with lethal neonatal, severe infantile hepatocardiomuscular, and common adult myopathic (exercise/fever/fasting-triggered rhabdomyolysis) forms; thermolabile variants predispose to influenza-associated encephalopathy.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005739 mitochondrion
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (PAN-GO) inference that CPT2 is active in the mitochondrion. Correct but general; CPT2 is more precisely at the mitochondrial inner membrane (matrix side). Accept as a correct broad localization.
Reason: CPT2 is a well-established mitochondrial enzyme. The IBA reflects the conserved mitochondrial localization across the ortholog set and is consistent with all experimental data.
Supporting Evidence:
PMID:1988962
an inner mitochondrial membrane enzyme that plays a major role in
GO:0004095 carnitine O-palmitoyltransferase activity
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic inference of the core molecular function, carnitine O-palmitoyltransferase (EC 2.3.1.21). This is the defining activity of CPT2 and is directly supported by human enzyme assays.
Reason: Well-supported core function; the IBA is at the correct level of specificity and agrees with direct experimental evidence in human CPT2.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0006635 fatty acid beta-oxidation
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic inference that CPT2 is involved in fatty acid beta-oxidation. By regenerating matrix acyl-CoA, CPT2 is required for long-chain fatty acids to enter beta-oxidation. Core biological process.
Reason: The carnitine shuttle step catalyzed by CPT2 is an obligatory prerequisite for mitochondrial long-chain fatty acid beta-oxidation; this is confirmed both by disease phenotypes and enzyme studies.
Supporting Evidence:
PMID:25578732
Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA
GO:0004095 carnitine O-palmitoyltransferase activity
IEA
GO_REF:0000120
ACCEPT
Summary: Electronic (multi-method, includes Rhea RHEA:12661 / EC 2.3.1.21) assignment of carnitine O-palmitoyltransferase activity. Correct core molecular function.
Reason: Matches the experimentally verified catalytic activity of human CPT2 (RHEA:12661, EC 2.3.1.21).
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0005743 mitochondrial inner membrane
IEA
GO_REF:0000044
ACCEPT
Summary: Subcellular-location mapping (UniProt SL-0168) to mitochondrial inner membrane. Correct; CPT2 is a peripheral inner-membrane protein on the matrix side.
Reason: Agrees with the UniProt-curated subcellular location and with the topology features (intramembrane 179-208; matrix-facing catalytic domain).
Supporting Evidence:
file:human/CPT2/CPT2-uniprot.txt
Mitochondrion inner membrane; Peripheral membrane
GO:0008458 carnitine O-octanoyltransferase activity
IEA
GO_REF:0000116
ACCEPT
Summary: Rhea-based (RHEA:17177) electronic assignment of carnitine O-octanoyltransferase activity (C8 acyl-CoA). CPT2 is experimentally active toward medium-chain (C8-C12) acyl-CoAs, so this is a genuine, if secondary, activity of the same catalytic site.
Reason: Human CPT2 has measurable activity with octanoyl-CoA (medium chain); this reflects the broad chain-length specificity of the single carnitine acyltransferase active site rather than a distinct enzyme, but the activity is real and experimentally documented.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0015909 long-chain fatty acid transport
IEA
GO_REF:0000117
MODIFY
Summary: ARBA machine-learning assignment of long-chain fatty acid transport. CPT2 does not itself transport fatty acids or acylcarnitines across the membrane (that is done by CPT1 plus the carnitine/acylcarnitine translocase SLC25A20); CPT2 is the matrix-side enzyme that regenerates acyl-CoA. The functional essence (enabling mitochondrial long-chain FA import for oxidation) is sound but the transport term mis-describes the mechanism.
Reason: CPT2 is an acyltransferase, not a transporter. Its contribution to long-chain fatty acid uptake is indirect (completing the carnitine shuttle). The more accurate terms are the carnitine shuttle and fatty acid beta-oxidation processes it enables.
Supporting Evidence:
PMID:25578732
Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA
GO:0016746 acyltransferase activity
IEA
GO_REF:0000002
MODIFY
Summary: InterPro2GO (IPR000542, carnitine acyltransferase) mapping to the general parent term acyltransferase activity. Correct but far too general given that the specific carnitine O-palmitoyltransferase activity (GO:0004095) is directly established for CPT2.
Reason: An uninformative high-level term; the specific molecular function is known and experimentally supported.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0005515 protein binding
IPI
PMID:28514442
Architecture of the human interactome defines protein commun...
MARK AS OVER ANNOTATED
Summary: High-throughput affinity-capture (BioPlex) interactome screen. Bare protein binding is uninformative and does not describe a specific molecular function of CPT2. CPT2 appears only in the large-scale interaction dataset.
Reason: Per curation guidelines, bare GO:0005515 protein binding from high-throughput interactome data adds no functional information and should not be treated as a core or informative annotation. Retained (not removed) as it derives from experimental IPI evidence.
Supporting Evidence:
PMID:28514442
Architecture of the human interactome defines protein communities and disease networks.
GO:0005515 protein binding
IPI
PMID:32296183
A reference map of the human binary protein interactome.
MARK AS OVER ANNOTATED
Summary: Binary yeast two-hybrid interactome (HuRI); partners recorded in UniProt include CYSRT1 (A8MQ03) and OTX1 (P32242). Bare protein binding is uninformative about CPT2 molecular function.
Reason: Bare protein binding from a high-throughput binary interactome screen does not describe a specific, biologically meaningful molecular function of CPT2. Retained as experimental IPI evidence rather than removed.
Supporting Evidence:
PMID:32296183
A reference map of the human binary protein interactome.
GO:0005515 protein binding
IPI
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling...
MARK AS OVER ANNOTATED
Summary: Cell-specific proteome-scale interactome (BioPlex, HCT116/293T); interaction with MCUR1 (Q96AQ8) recorded. Bare protein binding is uninformative.
Reason: As with the other interactome-derived protein binding annotations, this adds no specific functional information for CPT2. Retained as experimental IPI evidence.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
GO:0005759 mitochondrial matrix
IEA
GO_REF:0000107
ACCEPT
Summary: Ortholog-transfer (Ensembl Compara, from mouse P52825) assignment placing the active enzyme on the matrix side. Consistent with the UniProt topology (matrix-facing catalytic domain, matrix side of the inner membrane).
Reason: CPT2's catalytic domain faces the mitochondrial matrix; is_active_in mitochondrial matrix accurately reflects where catalysis occurs, complementing the inner-membrane location.
Supporting Evidence:
file:human/CPT2/CPT2-uniprot.txt
Mitochondrion inner membrane; Peripheral membrane
GO:0006853 carnitine shuttle
IEA
GO_REF:0000107
ACCEPT
Summary: Ortholog-transfer assignment of the carnitine shuttle process. CPT2 catalyzes the final matrix-side step of the shuttle, regenerating acyl-CoA. Core biological process.
Reason: CPT2 is a defining member of the carnitine shuttle; this is the process most specifically describing its physiological role.
Supporting Evidence:
file:human/CPT2/CPT2-uniprot.txt
Reconverts
GO:0120162 positive regulation of cold-induced thermogenesis
IEA
GO_REF:0000107
KEEP AS NON CORE
Summary: Ortholog-transfer (from mouse) of a role in positive regulation of cold-induced thermogenesis. Based on adipose-specific Cpt2 knockout mice that become hypothermic after cold challenge and fail to upregulate thermogenic genes in brown adipose tissue. This is a genuine but tissue-specific (BAT), downstream organismal consequence of CPT2-dependent fatty acid oxidation, not the core enzymatic function.
Reason: The phenotype is real (mouse adipose Cpt2 loss impairs cold-induced thermogenesis) but it is a context-dependent physiological role in a specific tissue, downstream of the enzyme's fatty acid beta-oxidation function. Keep as non-core.
Supporting Evidence:
PMID:25578732
CPT2(A-/-) mice became hypothermic after an
PMID:25578732
adipose tissue fatty acid oxidation is not only required for acute cold adaptation, but also for the induction of thermogenic genes in BAT
GO:0006853 carnitine shuttle
TAS
Reactome:R-HSA-200425
ACCEPT
Summary: Reactome (Carnitine shuttle pathway) traceable-author-statement assignment. CPT2 catalyzes the matrix-side acylcarnitine-to-acyl-CoA step of this pathway. Core process, correctly attributed.
Reason: Directly and authoritatively describes CPT2's role in the carnitine shuttle.
Supporting Evidence:
file:human/CPT2/CPT2-uniprot.txt
Reconverts
GO:0006635 fatty acid beta-oxidation
IEA
GO_REF:0000041
ACCEPT
Summary: UniPathway (UPA00659, fatty acid beta-oxidation) mapping. CPT2 is required for long-chain fatty acids to enter beta-oxidation. Core process.
Reason: Consistent with the curated UniProt PATHWAY assignment (fatty acid beta-oxidation) and with all experimental data.
Supporting Evidence:
PMID:25578732
Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA
GO:0005739 mitochondrion
IDA
GO_REF:0000052
ACCEPT
Summary: Direct immunofluorescence (Human Protein Atlas) localization to the mitochondrion. Correct, though more precisely the inner membrane / matrix.
Reason: Direct experimental localization consistent with all other evidence. Broad but correct.
Supporting Evidence:
PMID:1988962
an inner mitochondrial membrane enzyme that plays a major role in
GO:0016406 carnitine O-acyltransferase activity
EXP
PMID:20538056
Carnitine palmitoyltransferase 2: New insights on the substr...
ACCEPT
Summary: Experimental (substrate profiling of human CPT2) support for carnitine O-acyltransferase activity, the parent term covering both the palmitoyl (C16) and octanoyl (C8) activities. Accurate.
Reason: Directly supported by enzyme assays showing CPT2 acts on medium- and long-chain acyl-CoAs. Correct, if somewhat general relative to the more specific GO:0004095.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0016406 carnitine O-acyltransferase activity
EXP
PMID:7711730
Carnitine palmitoyltransferase II deficiency: structure of t...
ACCEPT
Summary: Experimental support (transfection/COS-cell CPT II activity assays in the context of disease-mutation characterization) for carnitine O-acyltransferase activity of CPT2. Accurate parent-level MF.
Reason: The study measured CPT II catalytic activity in cells expressing wild-type and mutant CPT2, confirming carnitine acyltransferase activity for the gene product.
Supporting Evidence:
PMID:7711730
Transfection experiments in COS cells demonstrated that both mutations drastically depressed the catalytic activity of CPT II.
GO:0004095 carnitine O-palmitoyltransferase activity
EXP
PMID:24780397
Functional analysis of iPSC-derived myocytes from a patient ...
ACCEPT
Summary: Experimental support (CPT II-deficient patient iPSC-derived myocytes; accumulation of C16 palmitoylcarnitine reflecting loss of the palmitoyltransferase step) for carnitine O-palmitoyltransferase activity. Core molecular function.
Reason: The disease-model data (C16 acylcarnitine accumulation with impaired CPT2) confirm the carnitine O-palmitoyltransferase activity of human CPT2.
Supporting Evidence:
PMID:24780397
CPT II-deficient myocytes accumulated more palmitoylcarnitine (C16)
GO:0008458 carnitine O-octanoyltransferase activity
EXP
PMID:20538056
Carnitine palmitoyltransferase 2: New insights on the substr...
ACCEPT
Summary: Experimental support for octanoyl-CoA (C8, medium chain) activity of human CPT2 from the substrate-specificity study. Genuine secondary activity of the same catalytic site.
Reason: Human CPT2 has measurable medium-chain (C8) carnitine acyltransferase activity; experimentally documented.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0005739 mitochondrion
HTP
PMID:34800366
Quantitative high-confidence human mitochondrial proteome an...
ACCEPT
Summary: High-throughput proteomic identification of CPT2 in the high-confidence human mitochondrial proteome (MitoCoP). Confirms mitochondrial localization.
Reason: Consistent with all other localization evidence; a correct, if broad, mitochondrial assignment from a rigorous proteomic dataset.
Supporting Evidence:
PMID:34800366
mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP)
GO:0001676 long-chain fatty acid metabolic process
IDA
PMID:20538056
Carnitine palmitoyltransferase 2: New insights on the substr...
ACCEPT
Summary: Direct experimental support that CPT2 participates in long-chain fatty acid metabolism, from its activity toward long-chain (C14-C18) acyl-CoAs. Accurate process annotation.
Reason: CPT2's substrate profile and its obligatory role in mitochondrial long-chain fatty acid oxidation directly support this process.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0004095 carnitine O-palmitoyltransferase activity
IDA
PMID:20538056
Carnitine palmitoyltransferase 2: New insights on the substr...
ACCEPT
Summary: Direct enzyme assay (human CPT2 expressed in yeast) of carnitine O-palmitoyltransferase activity toward long-chain acyl-CoAs. This is the primary experimental basis for the core molecular function.
Reason: Strongest, most specific experimental support for the defining catalytic activity of CPT2.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0006635 fatty acid beta-oxidation
IDA
PMID:20538056
Carnitine palmitoyltransferase 2: New insights on the substr...
ACCEPT
Summary: Direct experimental support that CPT2 functions in fatty acid beta-oxidation, based on demonstration that CPT2 handles the medium/long-chain acyl-CoAs that feed beta-oxidation. Core process.
Reason: CPT2's role in regenerating matrix acyl-CoA is an obligatory step enabling beta-oxidation, directly supported by its substrate specificity and by disease phenotypes.
Supporting Evidence:
PMID:20538056
reflect the potentially toxic
GO:0009437 carnitine metabolic process
IDA
PMID:20538056
Carnitine palmitoyltransferase 2: New insights on the substr...
ACCEPT
Summary: Direct experimental support that CPT2 participates in carnitine metabolism, as it interconverts acylcarnitine and free carnitine during the shuttle. Accurate.
Reason: CPT2 consumes acylcarnitine and releases free L-carnitine, directly acting on carnitine-containing metabolites; supported by the substrate/product profiling.
Supporting Evidence:
PMID:20538056
CPT2 is able to reverse its physiological mechanism for
GO:0016746 acyltransferase activity
IDA
PMID:20538056
Carnitine palmitoyltransferase 2: New insights on the substr...
MODIFY
Summary: Direct experimental support at the general acyltransferase level. As with the InterPro IEA, this parent term is correct but far less informative than the specific carnitine O-palmitoyltransferase activity established in the same study.
Reason: Too general; the specific molecular function (carnitine O-palmitoyltransferase) is directly demonstrated in this very paper and should be used instead.
Supporting Evidence:
PMID:20538056
CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
GO:0120162 positive regulation of cold-induced thermogenesis
ISS
PMID:25578732
Adipose fatty acid oxidation is required for thermogenesis a...
KEEP AS NON CORE
Summary: Sequence/ortholog-based (ISS from mouse P52825) transfer of a role in positive regulation of cold-induced thermogenesis, grounded in adipose-specific Cpt2 knockout mice that become hypothermic and fail to induce BAT thermogenic genes. Genuine but tissue-specific downstream physiological role.
Reason: Real phenotype in mouse adipose tissue, but a context-dependent organismal consequence downstream of CPT2's fatty acid beta-oxidation function rather than its core molecular activity. Keep as non-core.
Supporting Evidence:
PMID:25578732
CPT2(A-/-) mice became hypothermic after an
PMID:25578732
adipose tissue fatty acid oxidation is not only required for acute cold adaptation, but also for the induction of thermogenic genes in BAT
GO:0005743 mitochondrial inner membrane
TAS
Reactome:R-HSA-1989773
ACCEPT
Summary: Reactome traceable-author-statement localization to the mitochondrial inner membrane. Correct; CPT2 is a peripheral inner-membrane protein on the matrix side.
Reason: Matches the curated UniProt subcellular location and topology.
Supporting Evidence:
file:human/CPT2/CPT2-uniprot.txt
Mitochondrion inner membrane; Peripheral membrane
GO:0005743 mitochondrial inner membrane
TAS
Reactome:R-HSA-200410
ACCEPT
Summary: Reactome (CPT2 converts acylcarnitine to acyl-CoA) traceable-author-statement localization to the mitochondrial inner membrane. Correct core localization.
Reason: Matches curated UniProt localization; this Reactome reaction is exactly the matrix-side step CPT2 catalyzes.
Supporting Evidence:
file:human/CPT2/CPT2-uniprot.txt
Mitochondrion inner membrane; Peripheral membrane
GO:0004095 carnitine O-palmitoyltransferase activity
NAS
PMID:1988962
cDNA cloning, sequence analysis, and chromosomal localizatio...
ACCEPT
Summary: Non-traceable author statement (original cloning paper describing CPT2 as palmitoyl-CoA:L-carnitine O-palmitoyltransferase, EC 2.3.1.21). Correct core molecular function, later confirmed experimentally.
Reason: The defining catalytic activity of CPT2, asserted in the founding cloning study and subsequently verified by direct assay.
Supporting Evidence:
PMID:1988962
an inner mitochondrial membrane enzyme that plays a major role in
GO:0005743 mitochondrial inner membrane
NAS
PMID:1988962
cDNA cloning, sequence analysis, and chromosomal localizatio...
ACCEPT
Summary: Non-traceable author statement from the cloning paper describing CPT2 as an inner mitochondrial membrane enzyme. Correct core localization.
Reason: Consistent with curated UniProt subcellular location and with experimental proteomic/imaging localization.
Supporting Evidence:
PMID:1988962
an inner mitochondrial membrane enzyme that plays a major role in

Core Functions

Carnitine O-palmitoyltransferase (EC 2.3.1.21) activity on the matrix side of the mitochondrial inner membrane, catalyzing the final step of the carnitine shuttle to regenerate long-chain acyl-CoA from imported acylcarnitine (long-chain acylcarnitine + CoA to long-chain acyl-CoA + L-carnitine), thereby enabling mitochondrial long-chain fatty acid beta-oxidation.

Supporting Evidence:
  • PMID:20538056
    CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters

Participation in mitochondrial long-chain fatty acid beta-oxidation by regenerating the matrix acyl-CoA pool, an obligatory step that allows imported long-chain fatty acids to be oxidized to acetyl-CoA.

Supporting Evidence:
  • PMID:25578732
    Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniPathway vocabulary mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Gene Ontology annotation based on curation of immunofluorescence data
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Automatic Gene Ontology annotation based on Rhea mapping
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase.
  • Cloned human liver CPT and identified it as an inner mitochondrial membrane enzyme (EC 2.3.1.21) central to fatty acid oxidation, encoding a 658-residue precursor with a 25-residue leader peptide.
Carnitine palmitoyltransferase 2: New insights on the substrate specificity and implications for acylcarnitine profiling.
  • Human CPT2 substrate profiling shows activity with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters, minimal activity on short/very-long-chain or branched substrates, and reversible operation contributing to acylcarnitine profiles.
Functional analysis of iPSC-derived myocytes from a patient with carnitine palmitoyltransferase II deficiency.
  • CPT II-deficient patient iPSC-derived myocytes accumulate palmitoylcarnitine (C16), especially under heat stress, recapitulating impaired long-chain fatty acid oxidation.
Adipose fatty acid oxidation is required for thermogenesis and potentiates oxidative stress-induced inflammation.
  • Adipose-specific Cpt2 knockout mice become hypothermic after cold challenge and fail to upregulate brown adipose thermogenic genes, showing CPT2-dependent fatty acid oxidation is required for cold-induced thermogenesis.
Architecture of the human interactome defines protein communities and disease networks.
A reference map of the human binary protein interactome.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
  • CPT2 is a member of the high-confidence human mitochondrial proteome (MitoCoP), supporting its mitochondrial localization.
Carnitine palmitoyltransferase II deficiency: structure of the gene and characterization of two novel disease-causing mutations.
  • Disease-mutation study confirming CPT II catalytic activity via COS-cell transfection assays; mutations that reduce CPT II activity cause CPT II deficiency.
Reactome:R-HSA-1989773
Expression of CPT2
Reactome:R-HSA-200410
CPT2 converts acylcarnitine to acyl-CoA
Reactome:R-HSA-200425
Carnitine shuttle

Deep Research

Falcon

(CPT2-deep-research-falcon.md)
Comprehensive Research Report: CPT2 (Carnitine O-Palmitoyltransferase 2, Mitochondrial) Falcon Edison Scientific Literature 45 citations 1 artifacts 2026-07-07T03:26:53.643067

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive Research Report: CPT2 (Carnitine O-Palmitoyltransferase 2, Mitochondrial)

Gene: CPT2 | UniProt: P23786 | EC: 2.3.1.21 | Organism: Homo sapiens

1. Gene and Protein Identity

CPT2 (Carnitine O-palmitoyltransferase 2, mitochondrial; also known as CPT II) is encoded by the CPT2 gene (HGNC:2330) in humans. The protein belongs to the carnitine/choline acetyltransferase family and is synthesized as a 658-amino acid precursor containing an N-terminal mitochondrial targeting sequence that is cleaved during import into the mitochondrion (yao2023mitochondrialcarnitinepalmitoyltransferaseii pages 2-4, virmani2015thecarnitinepalmitoyl pages 4-5). Unlike the CPT1 family, which comprises three tissue-specific isoforms (CPT1A, CPT1B, CPT1C), CPT2 exists as a single, ubiquitously expressed isoform, with particularly high expression in energy-demanding tissues such as heart, liver, and skeletal muscle (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 1-3, duan2024theroleof pages 4-5, ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4). The mature protein has a molecular weight of approximately 71 kDa (schreurs2010regulatoryenzymesof pages 2-3).

2. Enzymatic Function and Reaction

2.1 Catalyzed Reaction

CPT2 catalyzes the final step of the mitochondrial carnitine shuttle system. The enzyme performs a transesterification reaction, converting acylcarnitines back into their corresponding acyl-CoA thioesters while releasing free L-carnitine (violante2010carnitinepalmitoyltransferase2 pages 1-2, duan2024theroleof pages 2-4):

Acylcarnitine + CoA β‡Œ Acyl-CoA + L-Carnitine

This reaction is reversible and energy-neutral (virmani2015thecarnitinepalmitoyl pages 3-4). In the physiological forward direction, CPT2 regenerates acyl-CoA within the mitochondrial matrix, enabling the acyl chain to enter the Ξ²-oxidation spiral for energy production (knottnerus2018disordersofmitochondrial pages 2-3, schlaepfer2020cpt1amediatedfatoxidation pages 32-32). Under certain conditions, such as accumulation of intramitochondrial acyl-CoA species in fatty acid oxidation disorders, CPT2 can operate in the reverse direction, converting acyl-CoAs to acylcarnitines for export from the mitochondria (violante2010carnitinepalmitoyltransferase2 pages 1-2, violante2010carnitinepalmitoyltransferase2 pages 4-4).

2.2 Substrate Specificity

Detailed substrate specificity studies using recombinant human CPT2 expressed in yeast have revealed important insights into the enzyme's preferences (violante2010carnitinepalmitoyltransferase2 pages 4-4, violante2010carnitinepalmitoyltransferase2 pages 3-4):

  • Preferred substrates: CPT2 is active with medium-chain (C8–C12) and long-chain (C14–C18) acyl-CoA esters, with C10–C14 chains representing the most efficiently processed substrates (violante2010carnitinepalmitoyltransferase2 pages 4-4, violante2010carnitinepalmitoyltransferase2 pages 1-2).
  • Long-chain substrates: The enzyme also efficiently handles common long-chain species such as C12-CoA and C16-CoA (palmitoyl-CoA) and shows activity toward certain unsaturated acyl-CoAs (cis-5 and cis-9 species) and mitochondrial Ξ²-oxidation intermediates including 3-hydroxy and 3-keto-palmitoyl-CoA (violante2010carnitinepalmitoyltransferase2 pages 3-4).
  • Poor substrates: CPT2 shows virtually no activity with short-chain or very-long-chain acyl-CoAs. Notably, trans-2-enoyl-CoA intermediates are very poor substrates, demonstrating only 1–1.5% of the activity observed with corresponding straight-chain acyl-CoAs, and these intermediates act as competitive inhibitors (violante2010carnitinepalmitoyltransferase2 pages 4-4, violante2010carnitinepalmitoyltransferase2 pages 3-4).
  • Non-substrates: Branched-chain amino acid oxidation intermediates are not processed by CPT2. Among peroxisomal substrates, only 4,8-dimethylnonanoyl-CoA shows reactivity, while pristanoyl-CoA is not accepted (violante2010carnitinepalmitoyltransferase2 pages 3-4, violante2010carnitinepalmitoyltransferase2 pages 4-4).

These specificity characteristics have important implications for acylcarnitine profiling in the diagnosis of metabolic disorders (violante2010carnitinepalmitoyltransferase2 pages 4-4).

3. Subcellular Localization and Membrane Topology

CPT2 is localized to the inner mitochondrial membrane (IMM) with its catalytic domain oriented toward the mitochondrial matrix (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 1-3, duan2024theroleof pages 2-4, rufer2009structuralinsightinto pages 2-4). Crystal structures of rat CPT2, solved at 1.6–2.6 Γ… resolution by two independent groups, have confirmed that the protein is monomeric and peripherally associated with the inner membrane rather than being a transmembrane protein like CPT1 (rufer2009structuralinsightinto pages 5-7, rufer2009structuralinsightinto pages 4-5).

A distinctive structural feature unique to CPT2 among carnitine acyltransferases is a membrane-anchoring insertion comprising residues Asn179–Asn208, which forms a pair of anti-parallel helices that insert into the inner leaflet of the inner mitochondrial membrane (rufer2009structuralinsightinto pages 5-7). This insertion mediates membrane association but does not span the bilayer. CPT2 adopts a hairpin polytopic conformation with only a 27-residue loop predicted to be exposed to the intermembrane space (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 1-3). The protein is more lightly attached to the inner membrane compared to CPT1's firm anchoring to the outer membrane via two transmembrane domains (duan2024theroleof pages 4-5).

CPT2 is synthesized as a precursor protein with an N-terminal signal sequence that directs its import into the mitochondrion; this targeting peptide is cleaved during translocation (virmani2015thecarnitinepalmitoyl pages 4-5).

4. Structural Features and Catalytic Mechanism

4.1 Domain Architecture

The overall fold of CPT2 consists of N-terminal and C-terminal domains, each containing a six-stranded central antiparallel Ξ²-sheet surrounded by Ξ±-helicesβ€”a fold shared with other carnitine acyltransferases including CrAT and carnitine octanoyltransferase (rufer2009structuralinsightinto pages 5-7, duan2024theroleof pages 4-5).

4.2 Active Site

The active site of CPT2 is positioned at the interface between the N-terminal and C-terminal domains. It forms a Y-shaped tunnel with three binding sites for CoA, acyl, and carnitine moieties, with both the acyl and CoA tunnels opening to the protein surface (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4). Key catalytic and binding residues include:

  • His372: A conserved catalytic histidine essential for catalytic activity, forming hydrogen bonds with substrates (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4).
  • Ser590: Part of a conserved Ser-Thr-Ser motif that hydrogen bonds to carbonyl groups (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4).
  • Tyr486, Ser488, Thr499: Bind the carboxylic group of carnitine (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4).
  • Arg498: Forms strong interactions with Asp376 and Ser373 to position active-site residues for catalysis (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4).

A crystallized CPT2 structure (PDB: 2DEB) complexed with CoA and palmitate has provided further structural insights into substrate binding (volpicella2025carnitineoacetyltransferaseas pages 8-9).

5. Role in the Carnitine Shuttle and Fatty Acid Ξ²-Oxidation

5.1 The Carnitine Shuttle System

CPT2 functions as the terminal enzyme of the three-component carnitine shuttle, which transports long-chain fatty acids across the mitochondrial membranes for Ξ²-oxidation (duan2024theroleof pages 2-4, knottnerus2018disordersofmitochondrial pages 2-3):

  1. CPT1 (outer mitochondrial membrane): Converts cytosolic long-chain acyl-CoA to acylcarnitine, releasing CoA. This is the rate-limiting, malonyl-CoA-regulated step.
  2. CACT/SLC25A20 (inner mitochondrial membrane transporter): Translocates acylcarnitines across the inner membrane in exchange for free carnitine.
  3. CPT2 (inner mitochondrial membrane, matrix side): Reconverts acylcarnitines back to acyl-CoA by transferring the acyl group from carnitine to intramitochondrial CoA, releasing free carnitine for recycling.

The regenerated acyl-CoA then enters the Ξ²-oxidation spiral within the mitochondrial matrix, ultimately producing acetyl-CoA units that feed into the tricarboxylic acid (TCA) cycle for ATP production (virmani2015thecarnitinepalmitoyl pages 3-4, schlaepfer2020cpt1amediatedfatoxidation pages 32-32). The complete oxidation of a single palmitate molecule through this system yields approximately 106 ATP molecules, substantially exceeding the ~30 ATP produced from glucose metabolism (virmani2015thecarnitinepalmitoyl pages 3-4).

5.2 Regulation

A critical distinction between CPT2 and CPT1 is their regulation. CPT1 is the main regulatory point for fatty acid oxidation, being allosterically inhibited by malonyl-CoA (the first committed intermediate of fatty acid synthesis), thereby coordinating the inverse regulation of fatty acid synthesis and oxidation (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4, schreurs2010regulatoryenzymesof pages 2-3, duan2024theroleof pages 2-4). In contrast, wild-type CPT2 is not subject to allosteric inhibition by malonyl-CoA and is considered constitutively active rather than rate-limiting (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4, schreurs2010regulatoryenzymesof pages 2-3). However, CPT2 expression and activity levels can vary in response to physiological status (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4).

6. Evolutionary Context

Phylogenetic analysis reveals that CPT2 and CPT1, despite their functional partnership in the carnitine shuttle, are actually the most distantly related genes within the carnitine and choline acyltransferase family (hoek2018evolutionaryanalysisof pages 1-6). CPT2 is most closely related to yeast cytosolic carnitine transferases Sc-YAT1 and Sc-YAT2, whereas CPT1 shares closer ancestry with the intramitochondrial yeast enzyme Sc-CAT2 (hoek2018evolutionaryanalysisof pages 15-20, hoek2018evolutionaryanalysisof pages 1-6).

Remarkably, CPT2 and CPT1 underwent a subcellular localization switch during evolution relative to their ancestral yeast counterparts (hoek2018evolutionaryanalysisof pages 15-20, hoek2018evolutionaryanalysisof pages 6-10). Unlike CPT1, CPT2 did not undergo the isoform-expanding gene duplications seen in the CPT1 lineage, consistent with its constitutive, unregulated nature (hoek2018evolutionaryanalysisof pages 15-20). CPT2 shows relatively short evolutionary branch lengths, indicating stable protein sequences over evolutionary time (hoek2018evolutionaryanalysisof pages 10-15). The human CPT2 cDNA and protein sequences share approximately 85% and 82% similarity, respectively, with the rat orthologue (duan2024theroleof pages 4-5).

7. Disease Associations

7.1 CPT2 Deficiency

CPT2 deficiency (OMIM #255110, #600649, #608836) is an autosomal recessive inborn error of mitochondrial long-chain fatty acid oxidation. It represents the most common inherited disorder of fatty acid metabolism affecting skeletal muscle (castillo2023myopathiccarnitinepalmitoyltransferase pages 5-7). The estimated incidence from newborn screening programs in Australia, Germany, and the USA is approximately 1:750,000 to 1:2,000,000, with over 300 patients described in the literature (knottnerus2018disordersofmitochondrial pages 5-6).

Three clinical phenotypes are recognized, representing a spectrum of disease severity (elgharbawy2018inbornerrorsof pages 6-8, lu2024recurrentrhabdomyolysiscaused pages 4-4, thuillier2003correlationbetweengenotype pages 1-2):

  • Lethal neonatal form: The most severe presentation, manifesting within days of birth with liver failure, hypoketotic hypoglycemia, cardiomyopathy, seizures, dysmorphic features, cystic renal dysplasia, and neuronal migration defects. Universally fatal, typically within the first month of life (lu2024recurrentrhabdomyolysiscaused pages 4-4, thuillier2003correlationbetweengenotype pages 1-2).
  • Severe infantile hepatocardiomuscular form: Emerges within the first year of life with liver failure, cardiomyopathy, peripheral myopathy, seizures, and hypoglycemia, often triggered by fasting, stress, or infection. Life-threatening with poor prognosis (elgharbawy2018inbornerrorsof pages 6-8, lu2024recurrentrhabdomyolysiscaused pages 4-4).
  • Adult/myopathic form: The most common phenotype (~192 of 245 reported cases in one review), characterized by recurrent episodes of exercise-induced myalgia, rhabdomyolysis, and myoglobinuria. Attacks are triggered by prolonged exercise, fasting, cold exposure, febrile illness, or infection. Physical examination and muscle appearance are typically normal between episodes. This form predominantly affects males (>75%) and does not affect longevity (elgharbawy2018inbornerrorsof pages 6-8, castillo2023myopathiccarnitinepalmitoyltransferase pages 5-7, lu2024recurrentrhabdomyolysiscaused pages 2-3).

7.2 Mutational Landscape

Over 60 mutations in the CPT2 gene have been identified, with most being private mutations (lehmann2017musclecarnitinepalmitoyltransferase pages 1-3, knottnerus2018disordersofmitochondrial pages 6-7). The p.S113L (c.338C>T) mutation is the most prevalent, accounting for approximately 64% of variant alleles in the myopathic form and found in up to 90% of patients in either homozygous or compound heterozygous state (lehmann2017musclecarnitinepalmitoyltransferase pages 1-3, lu2024recurrentrhabdomyolysiscaused pages 3-4). Other notable mutations include p.P50H, p.F383Y, and p.V368I, the latter two accounting for 31.2% of alleles in the severe infantile form (lu2024recurrentrhabdomyolysiscaused pages 3-4, thuillier2003correlationbetweengenotype pages 1-2).

7.3 S113L Thermolability Mechanism

The common S113L variant demonstrates a distinctive thermolabile mechanism: at normal body temperature (37Β°C), the mutant enzyme displays normal catalytic activity and long-chain fatty acid oxidation flux appears normal in fibroblasts (lehmann2017musclecarnitinepalmitoyltransferase pages 1-3, knottnerus2018disordersofmitochondrial pages 6-7). However, at elevated temperatures (40–45Β°C), the S113L variant shows markedly accelerated enzyme inactivation and significantly reduced activity compared to wild-type (knottnerus2018disordersofmitochondrial pages 6-7, lehmann2017musclecarnitinepalmitoyltransferase pages 3-6). Molecular dynamics simulations revealed that the S113L mutation increases backbone flexibility at the mutation site (residues S110–L121), causing conformational changes in the binding pocket that alter substrate and inhibitor interactions (lehmann2017musclecarnitinepalmitoyltransferase pages 3-6). Additionally, the S113L mutant shows abnormal sensitivity to malonyl-CoA inhibition, meaning that even under fasting conditions when malonyl-CoA levels should decrease to permit fatty acid oxidation, the mutant enzyme remains significantly inhibited (lehmann2017musclecarnitinepalmitoyltransferase pages 3-6, lehmann2017musclecarnitinepalmitoyltransferase pages 6-8). Natural substrates such as palmitoyl-L-carnitine can partially stabilize the S113L variant (lehmann2017musclecarnitinepalmitoyltransferase pages 3-6).

7.4 CPT2 in Cancer

Recent research (2023–2024) has revealed context-dependent roles for CPT2 in cancer biology. CPT2 acts as a pro-carcinogenic factor in chronic lymphocytic leukemia (CLL), epithelial ovarian cancer, gastrointestinal cancer, and triple-negative breast cancer, promoting proliferation, migration, invasion, and chemoresistance (duan2024theroleof pages 11-12, duan2024theroleof pages 9-11). Conversely, CPT2 underexpression promotes cancer progression in hepatocellular carcinoma and colorectal cancer through mechanisms involving ROS signaling, glycolytic metabolism, and the Wnt/Ξ²-catenin pathway (duan2024theroleof pages 11-12).

At the post-translational level, recent work has identified that CPT2 lactylation by AARS2 under hypoxic conditions inhibits oxidative phosphorylation by restricting fatty acid oxidation, while SIRT3-mediated reversal of this modification reactivates OXPHOS (duan2024theroleof pages 15-17). HRD1 has been identified as an E3 ubiquitin ligase for CPT2 in triple-negative breast cancer, though protein-level regulation of CPT2 remains understudied (duan2024theroleof pages 15-17).

7.5 CPT2 in NAFLD and Hepatocarcinogenesis

CPT2 dysfunction has been linked to nonalcoholic fatty liver disease (NAFLD)/metabolic dysfunction-associated fatty liver disease (MAFLD), where loss of CPT-II activity on the inner mitochondrial membrane leads to impaired long-chain fatty acid Ξ²-oxidation, lipid accumulation, and potential progression toward hepatocarcinogenesis involving liver cancer stem cell activation and the Wnt/Ξ²-catenin pathway (yao2023mitochondrialcarnitinepalmitoyltransferaseii pages 2-4).

8. Summary

The following table provides a consolidated overview of CPT2's key molecular, biochemical, and clinical properties:

Category Key property Summary Evidence
Gene/protein identity Human target verification CPT2 encodes carnitine O-palmitoyltransferase 2, mitochondrial (CPT II), the inner-mitochondrial-membrane enzyme of the carnitine shuttle; it is distinct from CPT1 isoforms despite historical naming confusion in some resources. (duan2024theroleof pages 2-4, ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4, ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 1-3)
Protein family Family membership CPT2 belongs to the carnitine/choline acyltransferase family and is evolutionarily distinct from CPT1 proteins, despite their complementary function in the shuttle. (rufer2009structuralinsightinto pages 5-7, hoek2018evolutionaryanalysisof pages 15-20, hoek2018evolutionaryanalysisof pages 1-6)
Isoforms/expression Tissue distribution CPT2 is reported as a single, ubiquitously expressed isoform, with comparatively high functional importance in energy-demanding tissues such as heart, liver, and skeletal muscle. (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 1-3, duan2024theroleof pages 4-5, ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4)
Core biochemical function Enzymatic role CPT2 catalyzes the final step of the carnitine shuttle, regenerating mitochondrial acyl-CoA from acylcarnitine and releasing free L-carnitine, thereby enabling long-chain fatty acid Ξ²-oxidation. (violante2010carnitinepalmitoyltransferase2 pages 1-2, duan2024theroleof pages 2-4, knottnerus2018disordersofmitochondrial pages 2-3)
Reaction Catalyzed chemistry The reaction is reversible and can be written as acylcarnitine + CoA β‡Œ acyl-CoA + carnitine; under some experimental conditions CPT2 can also catalyze the reverse direction with acyl-CoA + carnitine. (violante2010carnitinepalmitoyltransferase2 pages 3-4, virmani2015thecarnitinepalmitoyl pages 3-4, duan2024theroleof pages 2-4)
Physiologic substrates Main substrate class CPT2 primarily handles medium- to long-chain fatty acyl groups, especially those entering mitochondria for oxidation after CPT1/CACT-mediated transport. (violante2010carnitinepalmitoyltransferase2 pages 1-2, schlaepfer2020cpt1amediatedfatoxidation pages 32-32)
Substrate specificity Chain-length preference Human CPT2 shows activity across about C8-C20, with C10-C14 reported as preferred and robust activity for common long-chain substrates such as C12 and C16 species. (violante2010carnitinepalmitoyltransferase2 pages 4-4, violante2010carnitinepalmitoyltransferase2 pages 3-4)
Specificity limits Poor/negative substrates CPT2 has very low activity toward short-chain and very-long-chain substrates, poor activity toward trans-2-enoyl-CoA intermediates, and does not significantly process branched-chain amino acid oxidation intermediates. (violante2010carnitinepalmitoyltransferase2 pages 1-2, violante2010carnitinepalmitoyltransferase2 pages 3-4, violante2010carnitinepalmitoyltransferase2 pages 4-4)
Pathway role Carnitine shuttle CPT2 works with CPT1 on the outer mitochondrial membrane and CACT/SLC25A20 on the inner membrane to move long-chain fatty acid equivalents into the matrix for oxidation. (knottnerus2018disordersofmitochondrial pages 2-3, virmani2015thecarnitinepalmitoyl pages 4-5, schlaepfer2020cpt1amediatedfatoxidation pages 32-32)
Cellular localization Organelle/subcompartment CPT2 is localized to the inner mitochondrial membrane and functions on the matrix side/intramitochondrial space, consistent with regeneration of Ξ²-oxidation-competent acyl-CoA inside mitochondria. (duan2024theroleof pages 2-4, rufer2009structuralinsightinto pages 2-4, virmani2015thecarnitinepalmitoyl pages 3-4)
Membrane topology Membrane association Structural studies indicate CPT2 is monomeric and associated with the inner membrane through a membrane-anchoring insertion that inserts into the inner leaflet rather than spanning the membrane like CPT1. (rufer2009structuralinsightinto pages 4-5, rufer2009structuralinsightinto pages 5-7)
Precursor processing Mitochondrial targeting CPT2 is synthesized as a precursor protein with an N-terminal targeting sequence that is cleaved during mitochondrial import/localization. (virmani2015thecarnitinepalmitoyl pages 4-5, duan2024theroleof pages 4-5)
Structural organization Domain architecture CPT2 has N-terminal and C-terminal domains, each built around a six-stranded antiparallel Ξ²-sheet surrounded by Ξ±-helices, with the active site located at the domain interface. (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4, rufer2009structuralinsightinto pages 5-7)
Active-site architecture Ligand-binding tunnel The enzyme contains a Y-shaped tunnel accommodating CoA, acyl, and carnitine moieties; this architecture helps explain chain-length selectivity and acyltransferase chemistry. (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4, rufer2009structuralinsightinto pages 5-7)
Catalytic residues Key residues/mechanism Important structural/catalytic residues include His372, Ser590, and carnitine-binding residues such as Tyr486, Ser488, Thr499, with Arg498 helping position active-site elements. (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4)
Regulation vs CPT1 Malonyl-CoA sensitivity Unlike CPT1, CPT2 is generally described as not allosterically inhibited by malonyl-CoA and is not the main rate-limiting regulatory step of fatty acid entry into mitochondria. (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4, schreurs2010regulatoryenzymesof pages 2-3, duan2024theroleof pages 2-4)
Evolution Relationship to CPT1 CPT2 and CPT1 are functionally linked but evolutionarily distant within the acyltransferase family; CPT2 appears to have undergone a distinct evolutionary trajectory without the isoform-expanding duplications seen for CPT1. (hoek2018evolutionaryanalysisof pages 15-20, hoek2018evolutionaryanalysisof pages 1-6, hoek2018evolutionaryanalysisof pages 10-15)
Human disease Deficiency syndrome CPT2 deficiency is a rare autosomal recessive long-chain fatty acid oxidation disorder with three major forms: neonatal lethal, severe infantile hepatocardiomuscular, and adult/myopathic. (elgharbawy2018inbornerrorsof pages 6-8, lu2024recurrentrhabdomyolysiscaused pages 4-4, thuillier2003correlationbetweengenotype pages 1-2)
Clinical manifestations Major phenotypes Severe forms feature hypoketotic hypoglycemia, liver dysfunction/failure, cardiomyopathy, renal/cerebral anomalies, whereas the common myopathic form causes exercise-induced myalgia, rhabdomyolysis, and myoglobinuria with normal intervals between attacks. (elgharbawy2018inbornerrorsof pages 6-8, castillo2023myopathiccarnitinepalmitoyltransferase pages 5-7, knottnerus2018disordersofmitochondrial pages 5-6)
Disease epidemiology Recent summary statistics Literature summaries report >300 described patients and newborn-screening-based incidence estimates around 1:750,000 to 1:2,000,000, although ascertainment is incomplete. (lu2024recurrentrhabdomyolysiscaused pages 2-3, knottnerus2018disordersofmitochondrial pages 5-6)
Mutational landscape Common variants More than 60 CPT2 mutations have been reported; p.S113L is the most common mutation in the myopathic form, accounting for roughly 64% of variant alleles in one 2024 literature summary and up to 90% in older cohorts/reviews. (lu2024recurrentrhabdomyolysiscaused pages 3-4, lehmann2017musclecarnitinepalmitoyltransferase pages 1-3, knottnerus2018disordersofmitochondrial pages 6-7)
Variant mechanism S113L effect The common S113L variant is often thermolabile rather than catalytically dead at baseline, showing reduced stability and increased inhibition susceptibility under metabolic stress, helping explain attacks during fever, exercise, fasting, or cold exposure. (lehmann2017musclecarnitinepalmitoyltransferase pages 1-3, lehmann2017musclecarnitinepalmitoyltransferase pages 3-6, lehmann2017musclecarnitinepalmitoyltransferase pages 6-8)
Recent research directions 2023-2024 developments Recent work links CPT2 dysfunction or altered expression to NAFLD/MAFLD and hepatocarcinogenesis, and cancer literature describes context-dependent roles for CPT2, acting as either tumor-promoting or tumor-suppressive depending on tissue context. (yao2023mitochondrialcarnitinepalmitoyltransferaseii pages 2-4, duan2024theroleof pages 11-12, duan2024theroleof pages 15-17)

Table: This table summarizes the main molecular, biochemical, structural, and clinical properties of human CPT2. It is useful as a compact reference for functional annotation and for distinguishing CPT2’s core mitochondrial fatty-acid-oxidation role from disease and emerging cancer-related findings.

In summary, CPT2 is the inner mitochondrial membrane enzyme that catalyzes the final step of the carnitine shuttle, reconverting acylcarnitines to acyl-CoA within the mitochondrial matrix to enable long-chain fatty acid Ξ²-oxidation. It is a single-isoform, ubiquitously expressed enzyme with substrate preference for medium- to long-chain (C8–C18) acyl species. Unlike CPT1, CPT2 is constitutively active and not allosterically regulated by malonyl-CoA under normal physiological conditions. Deficiency of CPT2 causes a spectrum of disease from fatal neonatal multiorgan failure to the most common inherited muscular lipid metabolism disorder, with the thermolabile S113L variant underlying the majority of myopathic cases. Emerging research highlights additional roles for CPT2 in cancer metabolism and liver disease pathogenesis.

References

  1. (yao2023mitochondrialcarnitinepalmitoyltransferaseii pages 2-4): Min Yao, Ping Zhou, Yan-Yan Qin, Li Wang, and Dengbing Yao. Mitochondrial carnitine palmitoyltransferase-ii dysfunction: a possible novel mechanism for nonalcoholic fatty liver disease in hepatocarcinogenesis. World Journal of Gastroenterology, 29:1765-1778, Mar 2023. URL: https://doi.org/10.3748/wjg.v29.i12.1765, doi:10.3748/wjg.v29.i12.1765. This article has 14 citations.

  2. (virmani2015thecarnitinepalmitoyl pages 4-5): Ashraf Virmani, Luigi Pinto, Otto Bauermann, Saf Zerelli, Andreas Diedenhofen, Zbigniew K. Binienda, Syed F. Ali, and Feike R. van der Leij. The carnitine palmitoyl transferase (cpt) system and possible relevance for neuropsychiatric and neurological conditions. Molecular Neurobiology, 52:826-836, Jun 2015. URL: https://doi.org/10.1007/s12035-015-9238-7, doi:10.1007/s12035-015-9238-7. This article has 81 citations and is from a peer-reviewed journal.

  3. (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 1-3): Simona M. Ceccarelli, Odile Chomienne, Marcel Gubler, and Arduino Arduini. Carnitine palmitoyltransferase (cpt) modulators: a medicinal chemistry perspective on 35 years of research. Journal of medicinal chemistry, 54 9:3109-52, Apr 2011. URL: https://doi.org/10.1021/jm100809g, doi:10.1021/jm100809g. This article has 129 citations and is from a highest quality peer-reviewed journal.

  4. (duan2024theroleof pages 4-5): Yanxia Duan, Jiaxin Liu, Ailin Li, Chang Liu, Guang Shu, and Gang Yin. The role of the cpt family in cancer: searching for new therapeutic strategies. Biology, 13:892, Nov 2024. URL: https://doi.org/10.3390/biology13110892, doi:10.3390/biology13110892. This article has 16 citations.

  5. (ceccarelli2011carnitinepalmitoyltransferase(cpt) pages 3-4): Simona M. Ceccarelli, Odile Chomienne, Marcel Gubler, and Arduino Arduini. Carnitine palmitoyltransferase (cpt) modulators: a medicinal chemistry perspective on 35 years of research. Journal of medicinal chemistry, 54 9:3109-52, Apr 2011. URL: https://doi.org/10.1021/jm100809g, doi:10.1021/jm100809g. This article has 129 citations and is from a highest quality peer-reviewed journal.

  6. (schreurs2010regulatoryenzymesof pages 2-3): M. Schreurs, F. Kuipers, and F. R. Van Der Leij. Regulatory enzymes of mitochondrial β‐oxidation as targets for treatment of the metabolic syndrome. Obesity Reviews, 11:380-388, May 2010. URL: https://doi.org/10.1111/j.1467-789x.2009.00642.x, doi:10.1111/j.1467-789x.2009.00642.x. This article has 371 citations and is from a peer-reviewed journal.

  7. (violante2010carnitinepalmitoyltransferase2 pages 1-2): Sara Violante, Lodewijk IJlst, Henk van Lenthe, Isabel Tavares de Almeida, Ronald J. Wanders, and FΓ‘tima V. Ventura. Carnitine palmitoyltransferase 2: new insights on the substrate specificity and implications for acylcarnitine profiling. Biochimica et biophysica acta, 1802 9:728-32, Sep 2010. URL: https://doi.org/10.1016/j.bbadis.2010.06.002, doi:10.1016/j.bbadis.2010.06.002. This article has 64 citations.

  8. (duan2024theroleof pages 2-4): Yanxia Duan, Jiaxin Liu, Ailin Li, Chang Liu, Guang Shu, and Gang Yin. The role of the cpt family in cancer: searching for new therapeutic strategies. Biology, 13:892, Nov 2024. URL: https://doi.org/10.3390/biology13110892, doi:10.3390/biology13110892. This article has 16 citations.

  9. (virmani2015thecarnitinepalmitoyl pages 3-4): Ashraf Virmani, Luigi Pinto, Otto Bauermann, Saf Zerelli, Andreas Diedenhofen, Zbigniew K. Binienda, Syed F. Ali, and Feike R. van der Leij. The carnitine palmitoyl transferase (cpt) system and possible relevance for neuropsychiatric and neurological conditions. Molecular Neurobiology, 52:826-836, Jun 2015. URL: https://doi.org/10.1007/s12035-015-9238-7, doi:10.1007/s12035-015-9238-7. This article has 81 citations and is from a peer-reviewed journal.

  10. (knottnerus2018disordersofmitochondrial pages 2-3): Suzan J. G. Knottnerus, Jeannette C. Bleeker, Rob C. I. WΓΌst, Sacha Ferdinandusse, Lodewijk IJlst, Frits A. Wijburg, Ronald J. A. Wanders, Gepke Visser, and Riekelt H. Houtkooper. Disorders of mitochondrial long-chain fatty acid oxidation and the carnitine shuttle. Reviews in Endocrine & Metabolic Disorders, 19:93-106, Mar 2018. URL: https://doi.org/10.1007/s11154-018-9448-1, doi:10.1007/s11154-018-9448-1. This article has 385 citations and is from a peer-reviewed journal.

  11. (schlaepfer2020cpt1amediatedfatoxidation pages 32-32): Isabel R Schlaepfer and Molishree Joshi. Cpt1a-mediated fat oxidation, mechanisms and therapeutic potential. Endocrinology, Jan 2020. URL: https://doi.org/10.1210/endocr/bqz046, doi:10.1210/endocr/bqz046. This article has 807 citations and is from a domain leading peer-reviewed journal.

  12. (violante2010carnitinepalmitoyltransferase2 pages 4-4): Sara Violante, Lodewijk IJlst, Henk van Lenthe, Isabel Tavares de Almeida, Ronald J. Wanders, and FΓ‘tima V. Ventura. Carnitine palmitoyltransferase 2: new insights on the substrate specificity and implications for acylcarnitine profiling. Biochimica et biophysica acta, 1802 9:728-32, Sep 2010. URL: https://doi.org/10.1016/j.bbadis.2010.06.002, doi:10.1016/j.bbadis.2010.06.002. This article has 64 citations.

  13. (violante2010carnitinepalmitoyltransferase2 pages 3-4): Sara Violante, Lodewijk IJlst, Henk van Lenthe, Isabel Tavares de Almeida, Ronald J. Wanders, and FΓ‘tima V. Ventura. Carnitine palmitoyltransferase 2: new insights on the substrate specificity and implications for acylcarnitine profiling. Biochimica et biophysica acta, 1802 9:728-32, Sep 2010. URL: https://doi.org/10.1016/j.bbadis.2010.06.002, doi:10.1016/j.bbadis.2010.06.002. This article has 64 citations.

  14. (rufer2009structuralinsightinto pages 2-4): Arne C. Rufer, Ralf Thoma, and Michael Hennig. Structural insight into function and regulation of carnitine palmitoyltransferase. Cellular and Molecular Life Sciences, 66:2489-2501, May 2009. URL: https://doi.org/10.1007/s00018-009-0035-1, doi:10.1007/s00018-009-0035-1. This article has 113 citations and is from a domain leading peer-reviewed journal.

  15. (rufer2009structuralinsightinto pages 5-7): Arne C. Rufer, Ralf Thoma, and Michael Hennig. Structural insight into function and regulation of carnitine palmitoyltransferase. Cellular and Molecular Life Sciences, 66:2489-2501, May 2009. URL: https://doi.org/10.1007/s00018-009-0035-1, doi:10.1007/s00018-009-0035-1. This article has 113 citations and is from a domain leading peer-reviewed journal.

  16. (rufer2009structuralinsightinto pages 4-5): Arne C. Rufer, Ralf Thoma, and Michael Hennig. Structural insight into function and regulation of carnitine palmitoyltransferase. Cellular and Molecular Life Sciences, 66:2489-2501, May 2009. URL: https://doi.org/10.1007/s00018-009-0035-1, doi:10.1007/s00018-009-0035-1. This article has 113 citations and is from a domain leading peer-reviewed journal.

  17. (volpicella2025carnitineoacetyltransferaseas pages 8-9): Mariateresa Volpicella, Maria Noemi Sgobba, Luna Laera, Anna Lucia Francavilla, Danila Imperia De Luca, Lorenzo Guerra, Ciro Leonardo Pierri, and Anna De Grassi. Carnitine o-acetyltransferase as a central player in lipid and branched-chain amino acid metabolism, epigenetics, cell plasticity, and organelle function. Biomolecules, 15:216, Feb 2025. URL: https://doi.org/10.3390/biom15020216, doi:10.3390/biom15020216. This article has 22 citations.

  18. (hoek2018evolutionaryanalysisof pages 1-6): Marjanne D. van der Hoek, Ole Madsen, Jaap Keijer, and Feike R. van der Leij. Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of cpt2 versus cpt1 and related variants. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1863(8):909-918, Aug 2018. URL: https://doi.org/10.1016/j.bbalip.2018.05.001, doi:10.1016/j.bbalip.2018.05.001. This article has 10 citations and is from a peer-reviewed journal.

  19. (hoek2018evolutionaryanalysisof pages 15-20): Marjanne D. van der Hoek, Ole Madsen, Jaap Keijer, and Feike R. van der Leij. Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of cpt2 versus cpt1 and related variants. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1863(8):909-918, Aug 2018. URL: https://doi.org/10.1016/j.bbalip.2018.05.001, doi:10.1016/j.bbalip.2018.05.001. This article has 10 citations and is from a peer-reviewed journal.

  20. (hoek2018evolutionaryanalysisof pages 6-10): Marjanne D. van der Hoek, Ole Madsen, Jaap Keijer, and Feike R. van der Leij. Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of cpt2 versus cpt1 and related variants. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1863(8):909-918, Aug 2018. URL: https://doi.org/10.1016/j.bbalip.2018.05.001, doi:10.1016/j.bbalip.2018.05.001. This article has 10 citations and is from a peer-reviewed journal.

  21. (hoek2018evolutionaryanalysisof pages 10-15): Marjanne D. van der Hoek, Ole Madsen, Jaap Keijer, and Feike R. van der Leij. Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of cpt2 versus cpt1 and related variants. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 1863(8):909-918, Aug 2018. URL: https://doi.org/10.1016/j.bbalip.2018.05.001, doi:10.1016/j.bbalip.2018.05.001. This article has 10 citations and is from a peer-reviewed journal.

  22. (castillo2023myopathiccarnitinepalmitoyltransferase pages 5-7): Efrain Castillo, Debbie Medina, and Nick Schoenmann. Myopathic carnitine palmitoyltransferase ii (cpt ii) deficiency: a rare cause of acute kidney injury and cardiomyopathy. Cureus, Oct 2023. URL: https://doi.org/10.7759/cureus.46595, doi:10.7759/cureus.46595. This article has 6 citations.

  23. (knottnerus2018disordersofmitochondrial pages 5-6): Suzan J. G. Knottnerus, Jeannette C. Bleeker, Rob C. I. WΓΌst, Sacha Ferdinandusse, Lodewijk IJlst, Frits A. Wijburg, Ronald J. A. Wanders, Gepke Visser, and Riekelt H. Houtkooper. Disorders of mitochondrial long-chain fatty acid oxidation and the carnitine shuttle. Reviews in Endocrine & Metabolic Disorders, 19:93-106, Mar 2018. URL: https://doi.org/10.1007/s11154-018-9448-1, doi:10.1007/s11154-018-9448-1. This article has 385 citations and is from a peer-reviewed journal.

  24. (elgharbawy2018inbornerrorsof pages 6-8): Areeg El-Gharbawy and Jerry Vockley. Inborn errors of metabolism with myopathy. Apr 2018. URL: https://doi.org/10.1016/j.pcl.2017.11.006, doi:10.1016/j.pcl.2017.11.006. This article has 130 citations and is from a peer-reviewed journal.

  25. (lu2024recurrentrhabdomyolysiscaused pages 4-4): Chih-Hsuan Lu, Chia-Feng Yang, Yun-Ru Chen, Yann-Jang Chen, Yung-Hsiu Lu, and Dau-Ming Niu. Recurrent rhabdomyolysis caused by palmitoyltransferase ii (cpt-2) deficiency but complete normal acylcarnitine profile: a patient presentation and review of the literature. Molecular Genetics and Metabolism Reports, 41:101151, Dec 2024. URL: https://doi.org/10.1016/j.ymgmr.2024.101151, doi:10.1016/j.ymgmr.2024.101151. This article has 4 citations.

  26. (thuillier2003correlationbetweengenotype pages 1-2): Laure Thuillier, Hidayeth Rostane, Veronique Droin, France Demaugre, Michèle Brivet, Noman Kadhom, Carina Prip-Buus, Stéphanie Gobin, Jean-Marie Saudubray, and Jean-Paul Bonnefont. Correlation between genotype, metabolic data, and clinical presentation in carnitine palmitoyltransferase 2 (cpt2) deficiency. Human Mutation, 21:493-501, May 2003. URL: https://doi.org/10.1002/humu.10201, doi:10.1002/humu.10201. This article has 136 citations and is from a domain leading peer-reviewed journal.

  27. (lu2024recurrentrhabdomyolysiscaused pages 2-3): Chih-Hsuan Lu, Chia-Feng Yang, Yun-Ru Chen, Yann-Jang Chen, Yung-Hsiu Lu, and Dau-Ming Niu. Recurrent rhabdomyolysis caused by palmitoyltransferase ii (cpt-2) deficiency but complete normal acylcarnitine profile: a patient presentation and review of the literature. Molecular Genetics and Metabolism Reports, 41:101151, Dec 2024. URL: https://doi.org/10.1016/j.ymgmr.2024.101151, doi:10.1016/j.ymgmr.2024.101151. This article has 4 citations.

  28. (lehmann2017musclecarnitinepalmitoyltransferase pages 1-3): Diana Lehmann, Leila Scholle, Dina Robaa, and Stephan Zierz. Muscle carnitine palmitoyltransferase ii deficiency: a review of enzymatic controversy and clinical features. International Journal of Molecular Sciences, Jan 2017. URL: https://doi.org/10.3390/ijms18010082, doi:10.3390/ijms18010082. This article has 45 citations.

  29. (knottnerus2018disordersofmitochondrial pages 6-7): Suzan J. G. Knottnerus, Jeannette C. Bleeker, Rob C. I. WΓΌst, Sacha Ferdinandusse, Lodewijk IJlst, Frits A. Wijburg, Ronald J. A. Wanders, Gepke Visser, and Riekelt H. Houtkooper. Disorders of mitochondrial long-chain fatty acid oxidation and the carnitine shuttle. Reviews in Endocrine & Metabolic Disorders, 19:93-106, Mar 2018. URL: https://doi.org/10.1007/s11154-018-9448-1, doi:10.1007/s11154-018-9448-1. This article has 385 citations and is from a peer-reviewed journal.

  30. (lu2024recurrentrhabdomyolysiscaused pages 3-4): Chih-Hsuan Lu, Chia-Feng Yang, Yun-Ru Chen, Yann-Jang Chen, Yung-Hsiu Lu, and Dau-Ming Niu. Recurrent rhabdomyolysis caused by palmitoyltransferase ii (cpt-2) deficiency but complete normal acylcarnitine profile: a patient presentation and review of the literature. Molecular Genetics and Metabolism Reports, 41:101151, Dec 2024. URL: https://doi.org/10.1016/j.ymgmr.2024.101151, doi:10.1016/j.ymgmr.2024.101151. This article has 4 citations.

  31. (lehmann2017musclecarnitinepalmitoyltransferase pages 3-6): Diana Lehmann, Leila Scholle, Dina Robaa, and Stephan Zierz. Muscle carnitine palmitoyltransferase ii deficiency: a review of enzymatic controversy and clinical features. International Journal of Molecular Sciences, Jan 2017. URL: https://doi.org/10.3390/ijms18010082, doi:10.3390/ijms18010082. This article has 45 citations.

  32. (lehmann2017musclecarnitinepalmitoyltransferase pages 6-8): Diana Lehmann, Leila Scholle, Dina Robaa, and Stephan Zierz. Muscle carnitine palmitoyltransferase ii deficiency: a review of enzymatic controversy and clinical features. International Journal of Molecular Sciences, Jan 2017. URL: https://doi.org/10.3390/ijms18010082, doi:10.3390/ijms18010082. This article has 45 citations.

  33. (duan2024theroleof pages 11-12): Yanxia Duan, Jiaxin Liu, Ailin Li, Chang Liu, Guang Shu, and Gang Yin. The role of the cpt family in cancer: searching for new therapeutic strategies. Biology, 13:892, Nov 2024. URL: https://doi.org/10.3390/biology13110892, doi:10.3390/biology13110892. This article has 16 citations.

  34. (duan2024theroleof pages 9-11): Yanxia Duan, Jiaxin Liu, Ailin Li, Chang Liu, Guang Shu, and Gang Yin. The role of the cpt family in cancer: searching for new therapeutic strategies. Biology, 13:892, Nov 2024. URL: https://doi.org/10.3390/biology13110892, doi:10.3390/biology13110892. This article has 16 citations.

  35. (duan2024theroleof pages 15-17): Yanxia Duan, Jiaxin Liu, Ailin Li, Chang Liu, Guang Shu, and Gang Yin. The role of the cpt family in cancer: searching for new therapeutic strategies. Biology, 13:892, Nov 2024. URL: https://doi.org/10.3390/biology13110892, doi:10.3390/biology13110892. This article has 16 citations.

Artifacts

Citations

  1. schreurs2010regulatoryenzymesof pages 2-3
  2. virmani2015thecarnitinepalmitoyl pages 3-4
  3. rufer2009structuralinsightinto pages 5-7
  4. duan2024theroleof pages 4-5
  5. virmani2015thecarnitinepalmitoyl pages 4-5
  6. volpicella2025carnitineoacetyltransferaseas pages 8-9
  7. hoek2018evolutionaryanalysisof pages 1-6
  8. hoek2018evolutionaryanalysisof pages 15-20
  9. hoek2018evolutionaryanalysisof pages 10-15
  10. castillo2023myopathiccarnitinepalmitoyltransferase pages 5-7
  11. knottnerus2018disordersofmitochondrial pages 5-6
  12. lehmann2017musclecarnitinepalmitoyltransferase pages 3-6
  13. duan2024theroleof pages 11-12
  14. duan2024theroleof pages 15-17
  15. yao2023mitochondrialcarnitinepalmitoyltransferaseii pages 2-4
  16. duan2024theroleof pages 2-4
  17. knottnerus2018disordersofmitochondrial pages 2-3
  18. rufer2009structuralinsightinto pages 2-4
  19. rufer2009structuralinsightinto pages 4-5
  20. hoek2018evolutionaryanalysisof pages 6-10
  21. elgharbawy2018inbornerrorsof pages 6-8
  22. lu2024recurrentrhabdomyolysiscaused pages 4-4
  23. thuillier2003correlationbetweengenotype pages 1-2
  24. lu2024recurrentrhabdomyolysiscaused pages 2-3
  25. lehmann2017musclecarnitinepalmitoyltransferase pages 1-3
  26. knottnerus2018disordersofmitochondrial pages 6-7
  27. lu2024recurrentrhabdomyolysiscaused pages 3-4
  28. lehmann2017musclecarnitinepalmitoyltransferase pages 6-8
  29. duan2024theroleof pages 9-11
  30. https://doi.org/10.3748/wjg.v29.i12.1765,
  31. https://doi.org/10.1007/s12035-015-9238-7,
  32. https://doi.org/10.1021/jm100809g,
  33. https://doi.org/10.3390/biology13110892,
  34. https://doi.org/10.1111/j.1467-789x.2009.00642.x,
  35. https://doi.org/10.1016/j.bbadis.2010.06.002,
  36. https://doi.org/10.1007/s11154-018-9448-1,
  37. https://doi.org/10.1210/endocr/bqz046,
  38. https://doi.org/10.1007/s00018-009-0035-1,
  39. https://doi.org/10.3390/biom15020216,
  40. https://doi.org/10.1016/j.bbalip.2018.05.001,
  41. https://doi.org/10.7759/cureus.46595,
  42. https://doi.org/10.1016/j.pcl.2017.11.006,
  43. https://doi.org/10.1016/j.ymgmr.2024.101151,
  44. https://doi.org/10.1002/humu.10201,
  45. https://doi.org/10.3390/ijms18010082,

πŸ“š Additional Documentation

Notes

(CPT2-notes.md)

CPT2 (Carnitine O-palmitoyltransferase 2, mitochondrial) β€” review notes

UniProt: P23786 (CPT2_HUMAN), 658 aa, HGNC:2330, chromosome 1p32.
EC 2.3.1.21. Belongs to the carnitine/choline acetyltransferase family.

Core biology (verified)

CPT2 is the matrix-facing enzyme of the mitochondrial inner membrane that
completes the carnitine shuttle. After CPT1 (outer membrane) converts long-chain
acyl-CoA + carnitine to acylcarnitine, and the carnitine/acylcarnitine
translocase (SLC25A20) moves acylcarnitine across the inner membrane, CPT2
regenerates long-chain acyl-CoA in the matrix
: long-chain acylcarnitine + CoA β†’
long-chain acyl-CoA + L-carnitine. This is the final step of the shuttle and is
required so that beta-oxidation can proceed in the matrix.

  • UniProt FUNCTION: "Involved in the intramitochondrial synthesis of
    acylcarnitines from accumulated acyl-CoA metabolites ... 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. Active
    with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters."
    [ECO:0000269|PubMed:20538056, PubMed:24780397]
  • SUBCELLULAR LOCATION: "Mitochondrion inner membrane; Peripheral membrane
    protein; Matrix side." Topology features: matrix 26-178, intramembrane 179-208
    ("Mitochondrial inner membrane"), matrix 209-658. So the bulk (incl. catalytic
    domain) is matrix-facing but the protein is anchored/peripheral at the inner
    membrane. This makes both mitochondrial inner membrane (located_in) and
    mitochondrial matrix (is_active_in) reasonable.
  • Catalytic activity: RHEA:12661 (hexadecanoyl-CoA + carnitine β‡Œ palmitoylcarnitine
  • CoA), EC 2.3.1.21. Physiological direction annotated right-to-left (regenerating
    acyl-CoA). Multiple additional Rhea reactions for C8-C20 acyl-CoAs.

Substrate specificity (PMID:20538056, Violante et al. 2010)

Human CPT2 expressed in S. cerevisiae; substrate profiling by ESI-MS/MS.
- "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."
- Supports MF: carnitine O-palmitoyltransferase activity (GO:0004095, C16),
carnitine O-octanoyltransferase activity (GO:0008458, C8), and the parent
carnitine O-acyltransferase activity (GO:0016406).
- "trans-2-C16:1-CoA may act as a competitive inhibitor of CPT2 (K(i) of 18.8
microM)" β†’ ACTIVITY REGULATION.
- Km 7.1 uM for hexadecanoyl-CoA.
- This is the IDA/EXP basis for GO:0004095, GO:0008458, GO:0016406, GO:0016746
(acyltransferase), GO:0001676 (long-chain fatty acid metabolic process),
GO:0006635 (fatty acid beta-oxidation), GO:0009437 (carnitine metabolic process).
All from the same paper (Reactome/UniProt attributions).

Disease (context, not a GO BP by itself)

CPT2 deficiency (MONDO:0015515): autosomal recessive inborn error of mitochondrial
long-chain FAO. Three forms: lethal neonatal (CPT2DLN), severe infantile
hepatocardiomuscular (CPT2DI), and the common adult myopathic form (CPT2D,
MIM:255110) β€” the most common inherited disorder of muscle FA metabolism,
presenting as exercise/fever/fasting-triggered myalgia, rhabdomyolysis,
myoglobinuria. Thermolabile variants (F352C, V368I) predispose to
influenza-associated encephalopathy (IIAE4). Confirms core role in long-chain FAO
/ carnitine shuttle. (UniProt DISEASE; dismech KB
Carnitine_Palmitoyltransferase_II_Deficiency.yaml; PMID:24780397, PMID:7711730.)

Thermogenesis (GO:0120162)

PMID:25578732 (Lee et al.): adipose-specific Cpt2 knockout MOUSE (Cpt2^A-/-).
"CPT2(A-/-) mice became hypothermic after an acute cold challenge, and CPT2(A-/-)
brown adipose tissue (BAT) failed to upregulate thermogenic genes..." Shows adipose
FAO (via CPT2) is required for cold-induced thermogenesis. The human
GO:0120162 "positive regulation of cold-induced thermogenesis" is an ISS/IEA
transfer from mouse ortholog P52825. This is a genuine but tissue-specific
(BAT), context-dependent physiological role β€” KEEP_AS_NON_CORE. The core function
is the enzymatic step of the carnitine shuttle; thermogenesis is a downstream
organismal consequence in a specific tissue.

Protein-binding IPIs (bare protein binding)

  • PMID:28514442 (BioPlex/Huttlin interactome), PMID:32296183 (HuRI binary
    interactome; partners CYSRT1/A8MQ03, OTX1/P32242), PMID:33961781 (BioPlex
    cell-specific). MCUR1 (Q96AQ8) interaction also listed. These are high-throughput
    interactome screens; CPT2 appears only in supplementary partner tables, not main
    text. Bare protein binding (GO:0005515) is uninformative and none define a
    specific molecular function. Per policy: MARK_AS_OVER_ANNOTATED (not REMOVE for
    experimental IPI). UniProt INTERACTION section lists CYSRT1, MCUR1, OTX1.

Annotation plan summary

Core functions:
- MF GO:0004095 carnitine O-palmitoyltransferase activity (well supported IDA/EXP).
- BP GO:0006853 carnitine shuttle (directly_involved_in) β€” the process CPT2 completes.
- BP GO:0006635 fatty acid beta-oxidation (directly_involved_in) β€” enabled by CPT2's step.
- CC GO:0005743 mitochondrial inner membrane (location; matrix side).

Actions:
- ACCEPT: MF carnitine O-palmitoyltransferase (IBA, IEA, EXP, IDA, NAS);
carnitine O-octanoyltransferase (IEA, EXP); carnitine O-acyltransferase (EXP x2);
fatty acid beta-oxidation (IBA, IEA, IDA); carnitine shuttle (IEA, TAS);
carnitine metabolic process (IDA); long-chain fatty acid metabolic process (IDA);
mitochondrion (IBA, IDA, HTP); mitochondrial inner membrane (IEA, TAS x2, NAS);
mitochondrial matrix (IEA).
- MODIFY: GO:0016746 acyltransferase activity (IEA, IDA) β€” too general; replace with
GO:0004095. GO:0015909 long-chain fatty acid transport (ARBA IEA) β€” CPT2 does not
transport FAs across membrane (that's the translocase SLC25A20); its role is
enzymatic regeneration of acyl-CoA enabling import. Replace with carnitine shuttle
/ fatty acid beta-oxidation.
- KEEP_AS_NON_CORE: GO:0120162 positive regulation of cold-induced thermogenesis
(ISS, IEA) β€” real but tissue-specific downstream role.
- MARK_AS_OVER_ANNOTATED: three GO:0005515 protein binding IPIs (bare protein binding).

πŸ“„ View Raw YAML

id: P23786
gene_symbol: CPT2
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  Carnitine O-palmitoyltransferase 2 (CPT2, EC 2.3.1.21) is a mitochondrial
  enzyme of the carnitine/choline acetyltransferase family that is peripherally
  associated with the matrix side of the mitochondrial inner membrane. It
  catalyzes the final, matrix-side step of the carnitine shuttle, regenerating
  long-chain acyl-CoA from imported acylcarnitine (long-chain acylcarnitine +
  CoA to long-chain acyl-CoA + L-carnitine), the reverse-direction reaction to
  CPT1. This reconstitutes the acyl-CoA pool inside the matrix so that long-chain
  fatty acids can enter mitochondrial beta-oxidation; CPT2 is therefore essential
  for the mitochondrial uptake and oxidation of long-chain fatty acids. The
  enzyme is active with medium-chain (C8-C12) and long-chain (C14-C18) acyl-CoA
  esters. Loss of CPT2 function causes carnitine palmitoyltransferase II
  deficiency, an autosomal recessive disorder of long-chain fatty acid oxidation
  with lethal neonatal, severe infantile hepatocardiomuscular, and common adult
  myopathic (exercise/fever/fasting-triggered rhabdomyolysis) forms; thermolabile
  variants predispose to influenza-associated encephalopathy.
existing_annotations:
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic (PAN-GO) inference that CPT2 is active in the mitochondrion.
      Correct but general; CPT2 is more precisely at the mitochondrial inner
      membrane (matrix side). Accept as a correct broad localization.
    action: ACCEPT
    reason: >-
      CPT2 is a well-established mitochondrial enzyme. The IBA reflects the
      conserved mitochondrial localization across the ortholog set and is
      consistent with all experimental data.
    supported_by:
    - reference_id: PMID:1988962
      supporting_text: an inner mitochondrial membrane enzyme that plays a major role in
- term:
    id: GO:0004095
    label: carnitine O-palmitoyltransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic inference of the core molecular function, carnitine
      O-palmitoyltransferase (EC 2.3.1.21). This is the defining activity of CPT2
      and is directly supported by human enzyme assays.
    action: ACCEPT
    reason: >-
      Well-supported core function; the IBA is at the correct level of
      specificity and agrees with direct experimental evidence in human CPT2.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic inference that CPT2 is involved in fatty acid beta-oxidation.
      By regenerating matrix acyl-CoA, CPT2 is required for long-chain fatty acids
      to enter beta-oxidation. Core biological process.
    action: ACCEPT
    reason: >-
      The carnitine shuttle step catalyzed by CPT2 is an obligatory prerequisite
      for mitochondrial long-chain fatty acid beta-oxidation; this is confirmed
      both by disease phenotypes and enzyme studies.
    supported_by:
    - reference_id: PMID:25578732
      supporting_text: Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA
- term:
    id: GO:0004095
    label: carnitine O-palmitoyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic (multi-method, includes Rhea RHEA:12661 / EC 2.3.1.21)
      assignment of carnitine O-palmitoyltransferase activity. Correct core
      molecular function.
    action: ACCEPT
    reason: >-
      Matches the experimentally verified catalytic activity of human CPT2
      (RHEA:12661, EC 2.3.1.21).
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Subcellular-location mapping (UniProt SL-0168) to mitochondrial inner
      membrane. Correct; CPT2 is a peripheral inner-membrane protein on the matrix
      side.
    action: ACCEPT
    reason: >-
      Agrees with the UniProt-curated subcellular location and with the topology
      features (intramembrane 179-208; matrix-facing catalytic domain).
    supported_by:
    - reference_id: file:human/CPT2/CPT2-uniprot.txt
      supporting_text: Mitochondrion inner membrane; Peripheral membrane
- term:
    id: GO:0008458
    label: carnitine O-octanoyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: >-
      Rhea-based (RHEA:17177) electronic assignment of carnitine
      O-octanoyltransferase activity (C8 acyl-CoA). CPT2 is experimentally active
      toward medium-chain (C8-C12) acyl-CoAs, so this is a genuine, if secondary,
      activity of the same catalytic site.
    action: ACCEPT
    reason: >-
      Human CPT2 has measurable activity with octanoyl-CoA (medium chain); this
      reflects the broad chain-length specificity of the single carnitine
      acyltransferase active site rather than a distinct enzyme, but the activity
      is real and experimentally documented.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0015909
    label: long-chain fatty acid transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      ARBA machine-learning assignment of long-chain fatty acid transport. CPT2
      does not itself transport fatty acids or acylcarnitines across the membrane
      (that is done by CPT1 plus the carnitine/acylcarnitine translocase
      SLC25A20); CPT2 is the matrix-side enzyme that regenerates acyl-CoA. The
      functional essence (enabling mitochondrial long-chain FA import for
      oxidation) is sound but the transport term mis-describes the mechanism.
    action: MODIFY
    reason: >-
      CPT2 is an acyltransferase, not a transporter. Its contribution to
      long-chain fatty acid uptake is indirect (completing the carnitine shuttle).
      The more accurate terms are the carnitine shuttle and fatty acid
      beta-oxidation processes it enables.
    proposed_replacement_terms:
    - id: GO:0006853
      label: carnitine shuttle
    - id: GO:0006635
      label: fatty acid beta-oxidation
    supported_by:
    - reference_id: PMID:25578732
      supporting_text: Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA
- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro2GO (IPR000542, carnitine acyltransferase) mapping to the general
      parent term acyltransferase activity. Correct but far too general given that
      the specific carnitine O-palmitoyltransferase activity (GO:0004095) is
      directly established for CPT2.
    action: MODIFY
    reason: >-
      An uninformative high-level term; the specific molecular function is known
      and experimentally supported.
    proposed_replacement_terms:
    - id: GO:0004095
      label: carnitine O-palmitoyltransferase activity
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  qualifier: enables
  review:
    summary: >-
      High-throughput affinity-capture (BioPlex) interactome screen. Bare protein
      binding is uninformative and does not describe a specific molecular function
      of CPT2. CPT2 appears only in the large-scale interaction dataset.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Per curation guidelines, bare GO:0005515 protein binding from high-throughput
      interactome data adds no functional information and should not be treated as
      a core or informative annotation. Retained (not removed) as it derives from
      experimental IPI evidence.
    supported_by:
    - reference_id: PMID:28514442
      supporting_text: Architecture of the human interactome defines protein communities and disease networks.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: >-
      Binary yeast two-hybrid interactome (HuRI); partners recorded in UniProt
      include CYSRT1 (A8MQ03) and OTX1 (P32242). Bare protein binding is
      uninformative about CPT2 molecular function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Bare protein binding from a high-throughput binary interactome screen does
      not describe a specific, biologically meaningful molecular function of CPT2.
      Retained as experimental IPI evidence rather than removed.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: A reference map of the human binary protein interactome.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  qualifier: enables
  review:
    summary: >-
      Cell-specific proteome-scale interactome (BioPlex, HCT116/293T); interaction
      with MCUR1 (Q96AQ8) recorded. Bare protein binding is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      As with the other interactome-derived protein binding annotations, this adds
      no specific functional information for CPT2. Retained as experimental IPI
      evidence.
    supported_by:
    - reference_id: PMID:33961781
      supporting_text: Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: is_active_in
  review:
    summary: >-
      Ortholog-transfer (Ensembl Compara, from mouse P52825) assignment placing
      the active enzyme on the matrix side. Consistent with the UniProt topology
      (matrix-facing catalytic domain, matrix side of the inner membrane).
    action: ACCEPT
    reason: >-
      CPT2's catalytic domain faces the mitochondrial matrix; is_active_in
      mitochondrial matrix accurately reflects where catalysis occurs,
      complementing the inner-membrane location.
    supported_by:
    - reference_id: file:human/CPT2/CPT2-uniprot.txt
      supporting_text: Mitochondrion inner membrane; Peripheral membrane
- term:
    id: GO:0006853
    label: carnitine shuttle
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer assignment of the carnitine shuttle process. CPT2
      catalyzes the final matrix-side step of the shuttle, regenerating acyl-CoA.
      Core biological process.
    action: ACCEPT
    reason: >-
      CPT2 is a defining member of the carnitine shuttle; this is the process most
      specifically describing its physiological role.
    supported_by:
    - reference_id: file:human/CPT2/CPT2-uniprot.txt
      supporting_text: Reconverts
- term:
    id: GO:0120162
    label: positive regulation of cold-induced thermogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ortholog-transfer (from mouse) of a role in positive regulation of
      cold-induced thermogenesis. Based on adipose-specific Cpt2 knockout mice that
      become hypothermic after cold challenge and fail to upregulate thermogenic
      genes in brown adipose tissue. This is a genuine but tissue-specific (BAT),
      downstream organismal consequence of CPT2-dependent fatty acid oxidation, not
      the core enzymatic function.
    action: KEEP_AS_NON_CORE
    reason: >-
      The phenotype is real (mouse adipose Cpt2 loss impairs cold-induced
      thermogenesis) but it is a context-dependent physiological role in a specific
      tissue, downstream of the enzyme's fatty acid beta-oxidation function. Keep as
      non-core.
    supported_by:
    - reference_id: PMID:25578732
      supporting_text: CPT2(A-/-) mice became hypothermic after an
    - reference_id: PMID:25578732
      supporting_text: adipose tissue fatty acid oxidation is not only required for acute cold adaptation, but also for the induction of thermogenic genes in BAT
- term:
    id: GO:0006853
    label: carnitine shuttle
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-200425
  qualifier: involved_in
  review:
    summary: >-
      Reactome (Carnitine shuttle pathway) traceable-author-statement assignment.
      CPT2 catalyzes the matrix-side acylcarnitine-to-acyl-CoA step of this pathway.
      Core process, correctly attributed.
    action: ACCEPT
    reason: Directly and authoritatively describes CPT2's role in the carnitine shuttle.
    supported_by:
    - reference_id: file:human/CPT2/CPT2-uniprot.txt
      supporting_text: Reconverts
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  qualifier: involved_in
  review:
    summary: >-
      UniPathway (UPA00659, fatty acid beta-oxidation) mapping. CPT2 is required for
      long-chain fatty acids to enter beta-oxidation. Core process.
    action: ACCEPT
    reason: >-
      Consistent with the curated UniProt PATHWAY assignment (fatty acid
      beta-oxidation) and with all experimental data.
    supported_by:
    - reference_id: PMID:25578732
      supporting_text: Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      Direct immunofluorescence (Human Protein Atlas) localization to the
      mitochondrion. Correct, though more precisely the inner membrane / matrix.
    action: ACCEPT
    reason: >-
      Direct experimental localization consistent with all other evidence. Broad but
      correct.
    supported_by:
    - reference_id: PMID:1988962
      supporting_text: an inner mitochondrial membrane enzyme that plays a major role in
- term:
    id: GO:0016406
    label: carnitine O-acyltransferase activity
  evidence_type: EXP
  original_reference_id: PMID:20538056
  qualifier: enables
  review:
    summary: >-
      Experimental (substrate profiling of human CPT2) support for carnitine
      O-acyltransferase activity, the parent term covering both the palmitoyl (C16)
      and octanoyl (C8) activities. Accurate.
    action: ACCEPT
    reason: >-
      Directly supported by enzyme assays showing CPT2 acts on medium- and long-chain
      acyl-CoAs. Correct, if somewhat general relative to the more specific GO:0004095.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0016406
    label: carnitine O-acyltransferase activity
  evidence_type: EXP
  original_reference_id: PMID:7711730
  qualifier: enables
  review:
    summary: >-
      Experimental support (transfection/COS-cell CPT II activity assays in the
      context of disease-mutation characterization) for carnitine O-acyltransferase
      activity of CPT2. Accurate parent-level MF.
    action: ACCEPT
    reason: >-
      The study measured CPT II catalytic activity in cells expressing wild-type and
      mutant CPT2, confirming carnitine acyltransferase activity for the gene product.
    supported_by:
    - reference_id: PMID:7711730
      supporting_text: Transfection experiments in COS cells demonstrated that both mutations drastically depressed the catalytic activity of CPT II.
- term:
    id: GO:0004095
    label: carnitine O-palmitoyltransferase activity
  evidence_type: EXP
  original_reference_id: PMID:24780397
  qualifier: enables
  review:
    summary: >-
      Experimental support (CPT II-deficient patient iPSC-derived myocytes;
      accumulation of C16 palmitoylcarnitine reflecting loss of the palmitoyltransferase
      step) for carnitine O-palmitoyltransferase activity. Core molecular function.
    action: ACCEPT
    reason: >-
      The disease-model data (C16 acylcarnitine accumulation with impaired CPT2)
      confirm the carnitine O-palmitoyltransferase activity of human CPT2.
    supported_by:
    - reference_id: PMID:24780397
      supporting_text: CPT II-deficient myocytes accumulated more palmitoylcarnitine (C16)
- term:
    id: GO:0008458
    label: carnitine O-octanoyltransferase activity
  evidence_type: EXP
  original_reference_id: PMID:20538056
  qualifier: enables
  review:
    summary: >-
      Experimental support for octanoyl-CoA (C8, medium chain) activity of human CPT2
      from the substrate-specificity study. Genuine secondary activity of the same
      catalytic site.
    action: ACCEPT
    reason: >-
      Human CPT2 has measurable medium-chain (C8) carnitine acyltransferase activity;
      experimentally documented.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput proteomic identification of CPT2 in the high-confidence human
      mitochondrial proteome (MitoCoP). Confirms mitochondrial localization.
    action: ACCEPT
    reason: >-
      Consistent with all other localization evidence; a correct, if broad,
      mitochondrial assignment from a rigorous proteomic dataset.
    supported_by:
    - reference_id: PMID:34800366
      supporting_text: mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP)
- term:
    id: GO:0001676
    label: long-chain fatty acid metabolic process
  evidence_type: IDA
  original_reference_id: PMID:20538056
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental support that CPT2 participates in long-chain fatty acid
      metabolism, from its activity toward long-chain (C14-C18) acyl-CoAs. Accurate
      process annotation.
    action: ACCEPT
    reason: >-
      CPT2's substrate profile and its obligatory role in mitochondrial long-chain
      fatty acid oxidation directly support this process.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0004095
    label: carnitine O-palmitoyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:20538056
  qualifier: enables
  review:
    summary: >-
      Direct enzyme assay (human CPT2 expressed in yeast) of carnitine
      O-palmitoyltransferase activity toward long-chain acyl-CoAs. This is the primary
      experimental basis for the core molecular function.
    action: ACCEPT
    reason: >-
      Strongest, most specific experimental support for the defining catalytic
      activity of CPT2.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IDA
  original_reference_id: PMID:20538056
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental support that CPT2 functions in fatty acid beta-oxidation,
      based on demonstration that CPT2 handles the medium/long-chain acyl-CoAs that
      feed beta-oxidation. Core process.
    action: ACCEPT
    reason: >-
      CPT2's role in regenerating matrix acyl-CoA is an obligatory step enabling
      beta-oxidation, directly supported by its substrate specificity and by disease
      phenotypes.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: reflect the potentially toxic
- term:
    id: GO:0009437
    label: carnitine metabolic process
  evidence_type: IDA
  original_reference_id: PMID:20538056
  qualifier: involved_in
  review:
    summary: >-
      Direct experimental support that CPT2 participates in carnitine metabolism, as
      it interconverts acylcarnitine and free carnitine during the shuttle. Accurate.
    action: ACCEPT
    reason: >-
      CPT2 consumes acylcarnitine and releases free L-carnitine, directly acting on
      carnitine-containing metabolites; supported by the substrate/product profiling.
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is able to reverse its physiological mechanism for
- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:20538056
  qualifier: enables
  review:
    summary: >-
      Direct experimental support at the general acyltransferase level. As with the
      InterPro IEA, this parent term is correct but far less informative than the
      specific carnitine O-palmitoyltransferase activity established in the same study.
    action: MODIFY
    reason: >-
      Too general; the specific molecular function (carnitine O-palmitoyltransferase)
      is directly demonstrated in this very paper and should be used instead.
    proposed_replacement_terms:
    - id: GO:0004095
      label: carnitine O-palmitoyltransferase activity
    supported_by:
    - reference_id: PMID:20538056
      supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- term:
    id: GO:0120162
    label: positive regulation of cold-induced thermogenesis
  evidence_type: ISS
  original_reference_id: PMID:25578732
  qualifier: involved_in
  review:
    summary: >-
      Sequence/ortholog-based (ISS from mouse P52825) transfer of a role in positive
      regulation of cold-induced thermogenesis, grounded in adipose-specific Cpt2
      knockout mice that become hypothermic and fail to induce BAT thermogenic genes.
      Genuine but tissue-specific downstream physiological role.
    action: KEEP_AS_NON_CORE
    reason: >-
      Real phenotype in mouse adipose tissue, but a context-dependent organismal
      consequence downstream of CPT2's fatty acid beta-oxidation function rather than
      its core molecular activity. Keep as non-core.
    supported_by:
    - reference_id: PMID:25578732
      supporting_text: CPT2(A-/-) mice became hypothermic after an
    - reference_id: PMID:25578732
      supporting_text: adipose tissue fatty acid oxidation is not only required for acute cold adaptation, but also for the induction of thermogenic genes in BAT
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1989773
  qualifier: located_in
  review:
    summary: >-
      Reactome traceable-author-statement localization to the mitochondrial inner
      membrane. Correct; CPT2 is a peripheral inner-membrane protein on the matrix side.
    action: ACCEPT
    reason: Matches the curated UniProt subcellular location and topology.
    supported_by:
    - reference_id: file:human/CPT2/CPT2-uniprot.txt
      supporting_text: Mitochondrion inner membrane; Peripheral membrane
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-200410
  qualifier: located_in
  review:
    summary: >-
      Reactome (CPT2 converts acylcarnitine to acyl-CoA) traceable-author-statement
      localization to the mitochondrial inner membrane. Correct core localization.
    action: ACCEPT
    reason: >-
      Matches curated UniProt localization; this Reactome reaction is exactly the
      matrix-side step CPT2 catalyzes.
    supported_by:
    - reference_id: file:human/CPT2/CPT2-uniprot.txt
      supporting_text: Mitochondrion inner membrane; Peripheral membrane
- term:
    id: GO:0004095
    label: carnitine O-palmitoyltransferase activity
  evidence_type: NAS
  original_reference_id: PMID:1988962
  qualifier: enables
  review:
    summary: >-
      Non-traceable author statement (original cloning paper describing CPT2 as
      palmitoyl-CoA:L-carnitine O-palmitoyltransferase, EC 2.3.1.21). Correct core
      molecular function, later confirmed experimentally.
    action: ACCEPT
    reason: >-
      The defining catalytic activity of CPT2, asserted in the founding cloning study
      and subsequently verified by direct assay.
    supported_by:
    - reference_id: PMID:1988962
      supporting_text: an inner mitochondrial membrane enzyme that plays a major role in
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: NAS
  original_reference_id: PMID:1988962
  qualifier: located_in
  review:
    summary: >-
      Non-traceable author statement from the cloning paper describing CPT2 as an
      inner mitochondrial membrane enzyme. Correct core localization.
    action: ACCEPT
    reason: >-
      Consistent with curated UniProt subcellular location and with experimental
      proteomic/imaging localization.
    supported_by:
    - reference_id: PMID:1988962
      supporting_text: an inner mitochondrial membrane enzyme that plays a major role in
core_functions:
- description: >-
    Carnitine O-palmitoyltransferase (EC 2.3.1.21) activity on the matrix side of
    the mitochondrial inner membrane, catalyzing the final step of the carnitine
    shuttle to regenerate long-chain acyl-CoA from imported acylcarnitine
    (long-chain acylcarnitine + CoA to long-chain acyl-CoA + L-carnitine), thereby
    enabling mitochondrial long-chain fatty acid beta-oxidation.
  molecular_function:
    id: GO:0004095
    label: carnitine O-palmitoyltransferase activity
  directly_involved_in:
  - id: GO:0006853
    label: carnitine shuttle
  locations:
  - id: GO:0005743
    label: mitochondrial inner membrane
  supported_by:
  - reference_id: PMID:20538056
    supporting_text: CPT2 is active with medium (C8-C12) and long-chain (C14-C18) acyl-CoA esters
- description: >-
    Participation in mitochondrial long-chain fatty acid beta-oxidation by
    regenerating the matrix acyl-CoA pool, an obligatory step that allows imported
    long-chain fatty acids to be oxidized to acetyl-CoA.
  molecular_function:
    id: GO:0004095
    label: carnitine O-palmitoyltransferase activity
  directly_involved_in:
  - id: GO:0006635
    label: fatty acid beta-oxidation
  locations:
  - id: GO:0005743
    label: mitochondrial inner membrane
  supported_by:
  - reference_id: PMID:25578732
    supporting_text: Once inside the mitochondrial matrix, CPT2 generates acyl-CoAs from acyl-carnitines to initiate the beta-oxidation of long chain fatty acids to acetyl-CoA
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea mapping
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:1988962
  title: cDNA cloning, sequence analysis, and chromosomal localization of the gene
    for human carnitine palmitoyltransferase.
  findings:
  - statement: >-
      Cloned human liver CPT and identified it as an inner mitochondrial membrane
      enzyme (EC 2.3.1.21) central to fatty acid oxidation, encoding a 658-residue
      precursor with a 25-residue leader peptide.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Founding cloning/characterization paper for human CPT2; directly supports the
      inner-membrane localization and palmitoyltransferase activity.
- id: PMID:20538056
  title: 'Carnitine palmitoyltransferase 2: New insights on the substrate specificity
    and implications for acylcarnitine profiling.'
  findings:
  - statement: >-
      Human CPT2 substrate profiling shows activity with medium (C8-C12) and
      long-chain (C14-C18) acyl-CoA esters, minimal activity on short/very-long-chain
      or branched substrates, and reversible operation contributing to acylcarnitine
      profiles.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Primary experimental basis for the carnitine O-palmitoyltransferase /
      O-octanoyltransferase / O-acyltransferase molecular functions and substrate range.
- id: PMID:24780397
  title: Functional analysis of iPSC-derived myocytes from a patient with carnitine
    palmitoyltransferase II deficiency.
  findings:
  - statement: >-
      CPT II-deficient patient iPSC-derived myocytes accumulate palmitoylcarnitine
      (C16), especially under heat stress, recapitulating impaired long-chain fatty
      acid oxidation.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Disease-model evidence supporting the carnitine O-palmitoyltransferase activity
      and long-chain FAO role of CPT2.
- id: PMID:25578732
  title: Adipose fatty acid oxidation is required for thermogenesis and potentiates
    oxidative stress-induced inflammation.
  findings:
  - statement: >-
      Adipose-specific Cpt2 knockout mice become hypothermic after cold challenge and
      fail to upregulate brown adipose thermogenic genes, showing CPT2-dependent fatty
      acid oxidation is required for cold-induced thermogenesis.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Mouse study; basis for the ISS/IEA positive-regulation-of-cold-induced-thermogenesis
      annotation, which is a tissue-specific downstream role (kept as non-core).
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and disease
    networks.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      High-throughput BioPlex interactome; source of a bare protein binding IPI that
      is uninformative for CPT2 function.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      HuRI binary interactome; source of bare protein binding IPIs (CYSRT1, OTX1) with
      no specific functional interpretation.
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      BioPlex cell-specific interactome; source of a bare protein binding IPI (MCUR1).
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings:
  - statement: >-
      CPT2 is a member of the high-confidence human mitochondrial proteome (MitoCoP),
      supporting its mitochondrial localization.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Rigorous mitochondrial proteome dataset supporting the HTP mitochondrion
      localization.
- id: PMID:7711730
  title: 'Carnitine palmitoyltransferase II deficiency: structure of the gene and
    characterization of two novel disease-causing mutations.'
  findings:
  - statement: >-
      Disease-mutation study confirming CPT II catalytic activity via COS-cell
      transfection assays; mutations that reduce CPT II activity cause CPT II deficiency.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Supports carnitine O-acyltransferase activity of CPT2 and the disease link.
- id: Reactome:R-HSA-1989773
  title: Expression of CPT2
  findings: []
- id: Reactome:R-HSA-200410
  title: CPT2 converts acylcarnitine to acyl-CoA
  findings: []
- id: Reactome:R-HSA-200425
  title: Carnitine shuttle
  findings: []