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.
| 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.
Proposed replacements:
carnitine shuttle
fatty acid beta-oxidation
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.
Proposed replacements:
carnitine O-palmitoyltransferase activity
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.
Proposed replacements:
carnitine O-palmitoyltransferase activity
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
|
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.
Gene: CPT2 | UniProt: P23786 | EC: 2.3.1.21 | Organism: Homo sapiens
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).
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 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).
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):
These specificity characteristics have important implications for acylcarnitine profiling in the diagnosis of metabolic disorders (violante2010carnitinepalmitoyltransferase2 pages 4-4).
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 1.6β2.6 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 Asn179βAsn208, 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).
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±-helicesβa fold shared with other carnitine acyltransferases including CrAT and carnitine octanoyltransferase (rufer2009structuralinsightinto pages 5-7, duan2024theroleof pages 4-5).
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:
A crystallized CPT2 structure (PDB: 2DEB) complexed with CoA and palmitate has provided further structural insights into substrate binding (volpicella2025carnitineoacetyltransferaseas pages 8-9).
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):
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).
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).
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).
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):
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).
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 (40β45Β°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 S110βL121), 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).
Recent research (2023β2024) 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).
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).
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 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 CPT2βs 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 (C8βC18) 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.
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(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
UniProt: P23786 (CPT2_HUMAN), 658 aa, HGNC:2330, chromosome 1p32.
EC 2.3.1.21. Belongs to the carnitine/choline acetyltransferase family.
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.
mitochondrial inner membrane (located_in) andmitochondrial matrix (is_active_in) reasonable.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).
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.)
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 (GO:0005515) is uninformative and none define aCore 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).
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: []