GO:0050632 propionyl-CoA C2-trimethyltridecanoyltransferase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0050632 describes the peroxisomal thiolase reaction that transfers a C2 unit from 4,8,12-trimethyltridecanoyl-CoA to propanoyl-CoA, yielding 3-oxopristanoyl-CoA and free CoA.
• The enzyme is classically known as sterol carrier protein X (SCPx) or SCPx thiolase, a peroxisomal protein that also carries a sterol carrier protein-2 domain.
• This activity is a branch point in peroxisomal fatty acid oxidation, linking phytanic acid/pristanic acid breakdown to propionyl-CoA metabolism.
• Propionyl-CoA is a central metabolite whose accumulation is toxic in propionic acidemia and is reprogrammed in hepatocellular carcinoma.
• Acyl-CoA thiolases and their products influence chromatin regulation through acyl-CoA pools, connecting peroxisomal metabolism to gene expression.
• CRISPR knockout, point-mutation, knock-in and overexpression models are essential to dissect the causal role of SCPx/GO:0050632 in metabolic and liver disease.
Description
GO:0050632, propionyl-CoA C2-trimethyltridecanoyltransferase activity, is a molecular function annotated in the peroxisomal thiolase family. It catalyzes the reaction 4,8,12-trimethyltridecanoyl-CoA + propanoyl-CoA = 3-oxopristanoyl-CoA + CoA, effectively transferring a two-carbon unit from a branched-chain acyl-CoA to propionyl-CoA. This reaction is part of the peroxisomal alpha- and beta-oxidation machinery that handles branched-chain fatty acids such as phytanic acid and pristanic acid. The enzyme responsible is historically named sterol carrier protein X (SCPx) or SCPx thiolase, a bifunctional protein containing both a thiolase domain and a sterol carrier protein-2 (SCP-2) domain. Because it consumes propionyl-CoA, the activity sits at the interface of peroxisomal lipid catabolism and propionate detoxification, a pathway of major clinical importance in propionic acidemia and in cancer metabolic reprogramming. Researchers study GO:0050632 to understand how peroxisomes dispose of branched-chain fatty acids, how propionyl-CoA is channeled into the tricarboxylic acid cycle, and how these fluxes are rewired in disease. The reaction also contributes to the pool of acyl-CoAs that can modify histones and other proteins, linking peroxisomal metabolism to chromatin regulation. Consequently, GO:0050632 is a relevant node for metabolic engineering, inherited metabolic disease research, and oncology.
propionyl-CoA C2-trimethyltridecanoyltransferase activity At A Glance
| GO ID | GO:0050632 |
|---|---|
| GO term | propionyl-CoA C2-trimethyltridecanoyltransferase activity |
| Ontology | molecular_function |
| Synonym | 3-oxopristanoyl-CoA thiolase activity; sterol carrier protein X-related thiolase activity; SCPx; peroxisomal 3-oxoacyl coenzyme A thiolase |
| Major function | Catalyzes transfer of a C2 unit from 4,8,12-trimethyltridecanoyl-CoA to propanoyl-CoA, forming 3-oxopristanoyl-CoA and CoA |
| Reaction | 4,8,12-trimethyltridecanoyl-CoA + propanoyl-CoA = 3-oxopristanoyl-CoA + CoA |
| Cellular location | Peroxisome (thiolase domain of SCPx) |
| Related pathway | Peroxisomal branched-chain fatty acid oxidation and propionyl-CoA metabolism |
| Representative enzyme | Sterol carrier protein X (SCPx/SCP2 long isoform) |
What Is GO:0050632?
In plain terms, GO:0050632 is the enzyme activity that takes a long branched-chain fatty acyl-CoA (4,8,12-trimethyltridecanoyl-CoA) and a short acyl-CoA (propanoyl-CoA) and joins them while releasing coenzyme A, producing 3-oxopristanoyl-CoA. The QuickGO definition states: Catalysis of the reaction: 4,8,12-trimethyltridecanoyl-CoA + propanoyl-CoA = 3-oxopristanoyl-CoA + CoA. It is a thiolase-type molecular function, also known as 3-oxopristanoyl-CoA thiolase, peroxisomal 3-oxoacyl coenzyme A thiolase, or sterol carrier protein X-related thiolase activity. The activity is part of peroxisomal fatty acid oxidation and propionyl-CoA metabolism.
Why Is propionyl-CoA C2-trimethyltridecanoyltransferase activity Important in Cell Biology?
GO:0050632 is important because it connects peroxisomal branched-chain fatty acid oxidation to propionyl-CoA handling, a metabolic junction with direct clinical consequences. Defects in peroxisomal fatty acid oxidation cause accumulation of very-long-chain and branched-chain fatty acids, and propionyl-CoA accumulation is toxic in propionic acidemia. In hepatocellular carcinoma, decreased propionyl-CoA metabolism supports metabolic reprogramming and tumor growth, making this activity a potential therapeutic node. Moreover, acyl-CoA pools generated by such reactions can feed histone acylation and chromatin regulation, broadening the biological impact beyond energy metabolism.
• Defines a specific peroxisomal thiolase step in branched-chain fatty acid oxidation.
• Links phytanic/pristanic acid catabolism to propionyl-CoA detoxification.
• Relevant to propionic acidemia, where propionyl-CoA accumulates and causes metabolic decompensation.
• Decreased propionyl-CoA metabolism promotes hepatocellular carcinoma reprogramming.
• Acyl-CoA products can influence histone acylation and gene expression.
• Provides a target for metabolic engineering of propionate utilization.
• Supports research on peroxisomal disorders and mitochondrial-peroxisomal crosstalk.
• Enables CRISPR-based causal tests of SCPx function in liver and metabolic disease models.
Molecular Mechanism of propionyl-CoA C2-trimethyltridecanoyltransferase activity
Substrate recognition and thiolytic cleavage
In simple terms: The enzyme grabs two different acyl-CoA molecules and swaps a two-carbon piece between them.
The reaction uses 4,8,12-trimethyltridecanoyl-CoA as the long branched-chain acyl donor and propanoyl-CoA as the acceptor. Thiolase-type enzymes typically form an acyl-enzyme intermediate via an active-site cysteine, then transfer the acyl group to a thiol acceptor. In GO:0050632, the net result is 3-oxopristanoyl-CoA plus free CoA. This step is part of peroxisomal beta-oxidation of branched-chain fatty acids, where pristanic acid is shortened and propionyl-CoA is generated or consumed.
Peroxisomal beta-oxidation cycle context
In simple terms: This reaction is one turn of a fatty acid shortening cycle inside peroxisomes.
Peroxisomal beta-oxidation shortens fatty acyl-CoAs in a cycle of oxidation, hydration, dehydrogenation and thiolytic cleavage. GO:0050632 represents a thiolase step specialized for branched-chain substrates, producing 3-oxopristanoyl-CoA, which can be further processed. The pathway handles phytanic acid and pristanic acid, which cannot be oxidized in mitochondria and must be degraded in peroxisomes. Because propionyl-CoA is a product or substrate, the activity interfaces with propionate metabolism and anaplerosis.
SCPx domain architecture and sterol carrier function
In simple terms: The enzyme is a two-part protein: one part cuts lipids, the other part carries sterols.
The classical enzyme for this activity is sterol carrier protein X (SCPx), which contains an N-terminal thiolase domain and a C-terminal sterol carrier protein-2 (SCP-2) domain. The thiolase domain catalyzes the GO:0050632 reaction, while the SCP-2 domain binds lipids and sterols and may facilitate substrate access or product channeling. This bifunctional architecture places the activity in peroxisomes and links it to lipid trafficking and sterol metabolism.
Cofactors and acyl-CoA pool dynamics
In simple terms: CoA is the handle that carries acyl groups, and its availability controls the reaction.
All substrates and products are CoA thioesters, so the reaction depends on cellular CoA and acyl-CoA pools. Compartmentalized acyl-CoA metabolism determines substrate availability and product fate, and peroxisomal acyl-CoAs can contribute to nuclear acyl-CoA pools that modify histones. Propionyl-CoA synthetase activity and propionylation can further regulate acyl-CoA homeostasis, as shown for bacterial enzymes and by analogy in eukaryotic systems. Thus GO:0050632 is sensitive to the broader metabolic state of the cell.
Regulation by substrate supply and disease state
In simple terms: How much fat and propionate the cell sees changes how active this step is.
The activity is not known to be controlled by a single allosteric regulator; instead, flux through GO:0050632 depends on the supply of branched-chain fatty acids and propionyl-CoA. In hepatocellular carcinoma, decreased propionyl-CoA metabolism alters metabolic reprogramming, indicating that pathway flux is remodeled in cancer. In propionic acidemia, impaired propionyl-CoA disposal leads to accumulation of toxic metabolites, indirectly affecting peroxisomal acyl-CoA handling. These observations support context-dependent regulation by substrate availability and disease state.
Key Genes Involved in GO:0050632 propionyl-CoA C2-trimethyltridecanoyltransferase activity
The genes and proteins below are functionally or metabolically connected to GO:0050632, either as the catalyzing enzyme, as upstream/downstream enzymes in peroxisomal fatty acid oxidation, or as regulators of propionyl-CoA and acyl-CoA pools.
| Gene | Major Role | Research Relevance |
|---|---|---|
| SCP2 (SCPx) | Encodes sterol carrier protein X with thiolase and SCP-2 domains; catalyzes GO:0050632 | Primary enzyme for knockout and functional studies of the activity |
| PCCA | Propionyl-CoA carboxylase alpha subunit; converts propionyl-CoA to methylmalonyl-CoA | Defects cause propionic acidemia; links to propionyl-CoA accumulation |
| PCCB | Propionyl-CoA carboxylase beta subunit | Propionic acidemia genetics and propionyl-CoA handling |
| ACOX1 | Peroxisomal acyl-CoA oxidase; first step of peroxisomal beta-oxidation | Upstream of thiolase steps in branched-chain fatty acid oxidation |
| ACOX2 | Branched-chain acyl-CoA oxidase for pristanic acid | Directly upstream of branched-chain thiolase reactions |
| HSD17B4 | Peroxisomal multifunctional enzyme type 2 | Branched-chain beta-oxidation; interacts with thiolase steps |
| ACAA1 | Peroxisomal 3-ketoacyl-CoA thiolase | Related thiolase activity in peroxisomal beta-oxidation |
| PEX5 | Peroxisomal targeting signal receptor | Required for import of SCPx and other peroxisomal enzymes |
| PEX7 | PTS2 receptor | Imports PTS2-containing peroxisomal proteins |
| HADHA | Mitochondrial trifunctional protein alpha | Mitochondrial fatty acid oxidation comparison |
| HADHB | Mitochondrial trifunctional protein beta | Mitochondrial beta-oxidation thiolase step |
| ACAT1 | Mitochondrial acetoacetyl-CoA thiolase | Model thiolase for mechanistic comparison |
| EP300 | Histone acetyltransferase using acyl-CoA | Links acyl-CoA pools to chromatin regulation |
| KAT7 (HBO1) | Histone acyltransferase | Propionyl-CoA can influence histone acylation |
| MLYCD | Malonyl-CoA decarboxylase | Regulates acyl-CoA pools relevant to propionyl-CoA |
| RPN11 (PSMD14) | Deubiquitylating enzyme | Modulates metabolic enzymes in NAFLD models |
How Is propionyl-CoA C2-trimethyltridecanoyltransferase activity Regulated?
GO:0050632 is primarily regulated by substrate availability and peroxisomal metabolic state rather than by a dedicated allosteric regulator. The supply of branched-chain fatty acids such as phytanic and pristanic acid determines flux into the thiolase step, and propionyl-CoA levels influence the acceptor side of the reaction. In cancer, decreased propionyl-CoA metabolism facilitates metabolic reprogramming, suggesting that pathway flux is remodeled by oncogenic signals. Acyl-CoA compartmentalization further controls substrate access and product fate, and acyl-CoA pools can regulate chromatin-modifying enzymes. Protein-level control of peroxisomal enzymes, including import via PEX5/PEX7, also indirectly regulates the activity.
propionyl-CoA C2-trimethyltridecanoyltransferase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| PCCA | Propionic acidemia | Patient-derived fibroblasts or CRISPR knock-in of patient mutations |
| PCCB | Propionic acidemia | Hepatocyte knockout models |
| SCP2 (SCPx) | Peroxisomal branched-chain fatty acid oxidation | SCP2 knockout cell lines and liver-specific KO mice |
| ACOX2 | Peroxisomal fatty acid oxidation disorders | CRISPR knockout in HepG2 or primary hepatocytes |
| EP300 | Chromatin regulation via acyl-CoA | Overexpression and point-mutation models |
Propionic acidemia and propionyl-CoA toxicity
Propionic acidemia is an inherited metabolic disorder caused by deficiency of propionyl-CoA carboxylase, leading to accumulation of propionyl-CoA and related toxic metabolites. Because GO:0050632 consumes or generates propionyl-CoA, its flux is relevant to the metabolic burden in this disease. The disorder is reviewed as a classic organic acidemia with severe metabolic decompensation. Research models of propionic acidemia help define how peroxisomal thiolase steps contribute to propionate disposal.
Hepatocellular carcinoma metabolic reprogramming
Decreased propionyl-CoA metabolism facilitates metabolic reprogramming and promotes hepatocellular carcinoma, indicating that enzymes handling propionyl-CoA, including peroxisomal thiolases, can influence tumor growth. This creates a rationale for targeting propionyl-CoA pathways in liver cancer. The study highlights the importance of acyl-CoA metabolism in cancer and supports further investigation of GO:0050632 in liver models.
Peroxisomal disorders and branched-chain fatty acid oxidation
Peroxisomal beta-oxidation defects impair degradation of branched-chain fatty acids such as phytanic and pristanic acid, leading to their accumulation. GO:0050632 is part of this oxidation machinery, so its dysfunction could contribute to peroxisomal disease phenotypes. Although direct mutations in the thiolase domain of SCPx are not the focus of the cited papers, the pathway context is well established.
Chromatin regulation and acyl-CoA signaling
Acyl-CoA pools generated by peroxisomal and mitochondrial metabolism can be used by histone acyltransferases, linking metabolic enzymes to chromatin regulation. Propionyl-CoA in particular can drive histone propionylation, and enzymes such as HBO1 use acyl-CoAs for promoter histone acylations. Therefore, altered GO:0050632 flux may indirectly affect gene expression through acyl-CoA availability.
From propionyl-CoA C2-trimethyltridecanoyltransferase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of SCPx thiolase activity alter propionyl-CoA levels? | SCP2 knockout cell lines (CRISPR KO) |
| Does a catalytic cysteine mutation abolish GO:0050632 activity? | Point-mutation knock-in of SCP2 active-site cysteine |
| Can wild-type SCP2 rescue a metabolic defect? | Knock-in or overexpression rescue in KO background |
| Where is SCPx localized in live cells? | Tagged knock-in with fluorescent protein |
| Does SCP2 overexpression change lipid flux? | Doxycycline-inducible overexpression lines |
| Which genes buffer loss of GO:0050632? | CRISPR library screening and RNA-seq |
How to Study the propionyl-CoA C2-trimethyltridecanoyltransferase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| LC-MS activity assay | Formation of 3-oxopristanoyl-CoA and CoA | Validate enzyme activity of wild-type vs mutant SCPx |
| Targeted metabolomics | Propionyl-CoA and acyl-CoA levels | Assess metabolic impact of SCP2 KO |
| RNA-seq | Transcriptional changes after perturbation | Identify compensatory pathways |
| CRISPR knockout screening | Gene essentiality or sensitivity | Discover modifiers of propionyl-CoA toxicity |
| Western blot | Protein expression and processing | Confirm SCPx domain expression |
| Immunofluorescence | Subcellular localization | Confirm peroxisomal targeting |
| Proteomics | Protein interactions and abundance | Identify SCPx interaction partners |
| Bioinformatics pathway analysis | Enrichment of metabolic pathways | Interpret omics data in the context of GO:0050632 |
Enzymatic activity assays
Direct measurement of GO:0050632 can be performed using acyl-CoA substrates and LC-MS or spectrophotometric detection of 3-oxopristanoyl-CoA and CoA. Such assays are essential to confirm that a candidate enzyme or mutant retains thiolase activity. Coupling with upstream peroxisomal beta-oxidation enzymes can reconstitute the pathway in vitro.
Metabolomics and acyl-CoA profiling
Targeted metabolomics quantifies propionyl-CoA, pristanoyl-CoA and related intermediates, revealing how genetic perturbations alter flux through GO:0050632. Acyl-CoA profiling is particularly informative because compartmentalization affects substrate availability.
CRISPR screening and functional genomics
Genome-wide CRISPR knockout screens can identify genes that modify sensitivity to propionyl-CoA stress or peroxisomal fatty acid overload. Such screens complement candidate-based studies of SCP2 and related thiolases. Bioinformatics analysis of screen hits can nominate pathways connected to GO:0050632.
Imaging and protein localization
Fluorescent tagging of SCPx or related peroxisomal proteins allows visualization of peroxisomal targeting and dynamics. Co-localization with peroxisomal markers confirms compartmentalization, which is critical for interpreting GO:0050632 function.
How CRISPR Can Be Used to Study GO:0050632 propionyl-CoA C2-trimethyltridecanoyltransferase activity
Knockout
CRISPR knockout of SCP2 or related peroxisomal thiolases removes GO:0050632 activity, enabling tests of its role in propionyl-CoA handling and lipid metabolism. Knockout cell lines can be profiled by metabolomics and RNA-seq to reveal compensatory changes. Liver-specific knockout models are useful for studying metabolic disease.
Point Mutation
Point mutations in the catalytic cysteine or substrate-binding residues of SCPx can dissect the enzymatic mechanism of GO:0050632. Knock-in of such mutations allows separation of thiolase activity from the sterol carrier function of the SCP-2 domain. These models are valuable for structure-function studies.
Knock-in
Knock-in of epitope or fluorescent tags at the endogenous SCP2 locus enables visualization and immunoprecipitation of the enzyme under native regulation. This approach preserves endogenous expression levels and peroxisomal targeting. Knock-in of disease-associated variants can model human metabolic phenotypes.
Overexpression
Overexpression of SCPx or its thiolase domain can increase flux through GO:0050632, testing whether enhanced activity protects against propionyl-CoA accumulation or alters lipid storage. Inducible overexpression systems allow dose-dependent studies. Overexpression combined with metabolomics can reveal rate-limiting steps in peroxisomal oxidation.
How EDITGENE Supports propionyl-CoA C2-trimethyltridecanoyltransferase activity Research
Researchers studying propionyl-CoA C2-trimethyltridecanoyltransferase activity-related genes often need to determine whether a candidate gene is causally involved in peroxisomal fatty acid oxidation, propionyl-CoA detoxification, or cancer metabolic reprogramming. EDITGENE provides the CRISPR tools and cell models required to move from correlation to causation.
Contact EDITGENE today to design your custom CRISPR model for propionyl-CoA C2-trimethyltridecanoyltransferase activity research.
Frequently Asked Questions About propionyl-CoA C2-trimethyltridecanoyltransferase activity
What is GO:0050632?
GO:0050632 is the molecular function propionyl-CoA C2-trimethyltridecanoyltransferase activity, a peroxisomal thiolase reaction that converts 4,8,12-trimethyltridecanoyl-CoA and propanoyl-CoA to 3-oxopristanoyl-CoA and CoA.
What enzyme carries out propionyl-CoA C2-trimethyltridecanoyltransferase activity?
The classical enzyme is sterol carrier protein X (SCPx), encoded by SCP2, which contains a thiolase domain and a sterol carrier protein-2 domain.
What reaction does GO:0050632 catalyze?
It catalyzes 4,8,12-trimethyltridecanoyl-CoA + propanoyl-CoA = 3-oxopristanoyl-CoA + CoA, a thiolytic transfer of a C2 unit.
What genes are involved in propionyl-CoA metabolism?
Key genes include SCP2, PCCA, PCCB, ACOX1, ACOX2, HSD17B4 and ACAA1, which function in peroxisomal and mitochondrial acyl-CoA pathways.
How is propionyl-CoA C2-trimethyltridecanoyltransferase activity related to disease?
It is connected to propionic acidemia through propionyl-CoA toxicity and to hepatocellular carcinoma through metabolic reprogramming.
Where in the cell does GO:0050632 occur?
The activity occurs in peroxisomes, where branched-chain fatty acid beta-oxidation takes place.
Can CRISPR be used to study GO:0050632?
Yes, CRISPR knockout, point mutation, knock-in and overexpression models can test the causal role of SCPx and related genes.
What is the difference between SCPx and SCP-2?
SCPx is the long isoform containing both a thiolase domain and an SCP-2 domain, while SCP-2 is the smaller sterol carrier domain alone.
Why is propionyl-CoA important in cancer?
Decreased propionyl-CoA metabolism facilitates metabolic reprogramming and promotes hepatocellular carcinoma, making it a potential target.
How can I measure GO:0050632 activity?
Enzymatic assays with acyl-CoA substrates coupled to LC-MS or spectrophotometric detection of CoA and 3-oxopristanoyl-CoA are standard approaches.
Conclusion
GO:0050632, propionyl-CoA C2-trimethyltridecanoyltransferase activity, is a peroxisomal thiolase function that links branched-chain fatty acid oxidation to propionyl-CoA metabolism. Its classical enzyme, SCPx, is a bifunctional protein with both catalytic and sterol carrier roles. The activity is relevant to propionic acidemia, peroxisomal disorders and hepatocellular carcinoma, and it contributes to acyl-CoA pools that influence chromatin. CRISPR-based knockout, point-mutation, knock-in and overexpression models provide the causal evidence needed to move this pathway toward therapeutic targeting.
References
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- 3. Adam MP et al.. 1993. Propionic Acidemia.. PMID: 22593918
- 4. Sun J et al.. 2023. Decreased propionyl-CoA metabolism facilitates metabolic reprogramming and promotes hepatocellular carcinoma.. J Hepatol 78(3):627-642 PMID: 36462680
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- 6. Xiao Y et al.. 2021. HBO1 is a versatile histone acyltransferase critical for promoter histone acylations.. Nucleic Acids Res 49(14):8037-8059 PMID: 34259319
- 7. Volodina E et al.. 2014. Characterization of propionate CoA-transferase from Ralstonia eutropha H16.. Appl Microbiol Biotechnol 98(8):3579-89 PMID: 24057402
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