GO:1905202 methylcrotonoyl-CoA carboxylase complex: Components, Assembly and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1905202 describes the methylcrotonoyl-CoA carboxylase complex, a mitochondrial enzyme complex that catalyzes the ATP-dependent carboxylation of 3-methylcrotonyl-CoA, a critical step in leucine catabolism.
• In mammals, the complex is a dodecamer composed of six alpha (MCCC1) and six beta (MCCC2) subunits; MCCC1 carries a covalently bound biotin essential for carboxylation, while MCCC2 provides carboxyltransferase activity.
• Deficiency of this complex causes 3-methylcrotonyl-CoA carboxylase deficiency, an inborn error of leucine metabolism identified through newborn screening, with elevated 3-hydroxyisovalerylcarnitine and 3-methylcrotonylglycine.
• Beyond metabolism, MCCC1 and MCCC2 have been implicated in innate immune signaling and cancer biology, including NF-κB activation and hepatocellular carcinoma stemness.
• The complex is conserved across plants and bacteria, where it supports seed development and host colonization, making it a model for metabolic enzyme evolution.
• CRISPR-based knockout, knock-in, and overexpression models are powerful tools to dissect the roles of MCCC1 and MCCC2 in metabolism, immunity, and cancer.
Description
The methylcrotonoyl-CoA carboxylase complex (GO:1905202) is a mitochondrial enzyme complex that catalyzes the ATP-dependent carboxylation of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA, an essential step in the leucine catabolic pathway. This complex is highly conserved from bacteria to humans and is composed of two distinct subunits, alpha (MCCC1) and beta (MCCC2), which assemble into a dodecameric structure. The complex is of significant interest to researchers because mutations in its subunits cause 3-methylcrotonyl-CoA carboxylase deficiency, a metabolic disorder with variable clinical presentation, and because emerging evidence links it to immune regulation and cancer progression. Understanding the structure, function, and regulation of this complex is therefore important for both basic metabolism and translational research.
methylcrotonoyl-CoA carboxylase complex At A Glance
| GO ID | GO:1905202 |
|---|---|
| GO term | methylcrotonoyl-CoA carboxylase complex |
| Ontology | cellular_component |
| Synonym | None |
| Major function | Catalyzes ATP-dependent carboxylation of 3-methylcrotonyl-CoA in leucine catabolism |
| Subunit composition | Dodecamer of 6 alpha (MCCC1) and 6 beta (MCCC2) subunits in mammals |
| Cofactor | Covalently bound biotin on MCCC1 |
| Localization | Mitochondrion |
| Enzyme class | Ligase (carboxylase) |
What Is GO:1905202?
GO:1905202 is a Gene Ontology cellular component term that defines a protein complex capable of methylcrotonoyl-CoA carboxylase activity. In mammals, it is a mitochondrial complex comprising a dodecamer of six alpha and six beta subunits. The alpha subunit (MCCC1) contains a covalently bound biotin that is essential for ATP-dependent carboxylation, while the beta subunit (MCCC2) possesses carboxyltransferase activity that is presumably essential for binding to 3-methylcrotonyl-CoA.
Why Is methylcrotonoyl-CoA carboxylase complex Important in Cell Biology?
The methylcrotonoyl-CoA carboxylase complex is critical for leucine catabolism, and its dysfunction leads to 3-methylcrotonyl-CoA carboxylase deficiency, a disorder identified in newborns through elevated acylcarnitine profiles. Beyond its metabolic role, the complex has been implicated in innate immune signaling, where MCCC1 potentiates NF-κB activation by targeting MAVS, and in cancer, where MCCC2 deacetylation by SIRT4 promotes acetyl-CoA synthesis and hepatocellular carcinoma stemness. These findings highlight the complex as a multifunctional player in health and disease.
• Essential for leucine catabolism; deficiency causes 3-methylcrotonyl-CoA carboxylase deficiency.
• MCCC1 potentiates RLR-induced NF-κB signaling by targeting MAVS complex.
• MCCC2 deacetylation by SIRT4 controls acetyl-CoA synthesis and promotes hepatocellular carcinoma stemness and invasiveness.
• The complex is conserved in plants and bacteria, influencing seed development and host colonization.
• Newborn screening programs detect MCCC deficiency, raising questions about routine screening necessity.
• MCCC1 and MCCC2 are potential targets for metabolic and cancer therapies.
• The complex is a model for studying mitochondrial enzyme assembly and biotin-dependent carboxylases.
• Deficiency leads to mitochondrial dysfunction and oxidative stress in patient fibroblasts.
• SLC25A21 promotes ferroptosis by inducing mitochondrial GPX4 deficiency, linking mitochondrial metabolism to cell death.
• CRISPR screens can identify modifiers of MCCC complex function in disease models.
What Happens During methylcrotonoyl-CoA carboxylase complex?
Substrate Binding and Carboxylation
In simple terms: The complex grabs 3-methylcrotonyl-CoA and adds a carboxyl group to it.
The methylcrotonoyl-CoA carboxylase complex catalyzes the ATP-dependent carboxylation of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA. The alpha subunit (MCCC1) contains a covalently bound biotin that is carboxylated in an ATP-dependent reaction, and the beta subunit (MCCC2) transfers the carboxyl group to 3-methylcrotonyl-CoA.
Leucine Catabolism
In simple terms: This step helps break down the amino acid leucine to produce energy.
This carboxylation is a critical step in the leucine catabolic pathway, converting 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA, which is further metabolized to acetyl-CoA and acetoacetate.
Mitochondrial Localization
In simple terms: The complex works inside mitochondria, the cell's power plants.
The complex is localized in the mitochondrion, where it participates in energy metabolism and is subject to regulation by mitochondrial sirtuins such as SIRT4.
Assembly of the Dodecamer
In simple terms: Six alpha and six beta subunits come together to form the active enzyme.
In mammals, the complex assembles as a dodecamer of six MCCC1 (alpha) and six MCCC2 (beta) subunits. MCCC1 provides the biotin carboxylase activity, while MCCC2 provides carboxyltransferase activity.
Key Genes Involved in GO:1905202 methylcrotonoyl-CoA carboxylase complex
The following genes and proteins are key components or regulators of the methylcrotonoyl-CoA carboxylase complex and its associated pathways.
| Gene | Major Role | Research Relevance |
|---|---|---|
| MCCC1 | Alpha subunit; biotin carboxylase; ATP-dependent carboxylation | Mutations cause MCCC deficiency; implicated in NF-κB signaling |
| MCCC2 | Beta subunit; carboxyltransferase; binds 3-methylcrotonyl-CoA | Deacetylation by SIRT4 promotes HCC stemness; mutations cause deficiency |
| SIRT4 | Mitochondrial sirtuin; deacetylates MCCC2 | Regulates acetyl-CoA synthesis and cancer progression |
| MAVS | Mitochondrial antiviral signaling protein | Targeted by MCCC1 to potentiate NF-κB signaling |
| SLC25A21 | Mitochondrial carrier; affects GPX4 and ferroptosis | Links mitochondrial metabolism to ferroptosis in colorectal cancer |
| GPX4 | Glutathione peroxidase 4; protects against ferroptosis | Deficiency induced by SLC25A21 promotes ferroptosis |
| NF-κB | Transcription factor; innate immune response | Activated downstream of MCCC1-MAVS interaction |
| Acetyl-CoA | Central metabolite; acetyl group donor | Synthesis controlled by SIRT4-MCCC2 axis |
| 3-methylcrotonyl-CoA | Substrate of MCCC complex | Accumulates in MCCC deficiency |
| 3-methylglutaconyl-CoA | Product of MCCC complex | Further metabolized in leucine catabolism |
| 3-hydroxyisovalerylcarnitine | Diagnostic marker in newborn screening | Elevated in MCCC deficiency |
| 3-methylcrotonylglycine | Urinary metabolite in MCCC deficiency | Used for diagnosis |
| MCCC1/MCCC2 dodecamer | Active enzyme complex | Target for structural and functional studies |
| Biotin | Cofactor covalently bound to MCCC1 | Essential for carboxylation activity |
| ATP | Energy source for carboxylation | Required for biotin activation |
| Leucine | Amino acid catabolized via MCCC | Source of 3-methylcrotonyl-CoA |
How Is methylcrotonoyl-CoA carboxylase complex Regulated?
The methylcrotonoyl-CoA carboxylase complex is regulated at multiple levels. SIRT4 deacetylates MCCC2, thereby controlling acetyl-CoA synthesis and promoting hepatocellular carcinoma stemness and invasiveness. In innate immunity, MCCC1 potentiates RLR-induced NF-κB signaling by targeting the MAVS complex, linking metabolic enzyme function to immune signaling. Additionally, mitochondrial dysfunction and oxidative stress are observed in MCCC-deficient fibroblasts, suggesting feedback regulation.
methylcrotonoyl-CoA carboxylase complex and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| MCCC1 | 3-methylcrotonyl-CoA carboxylase deficiency; NF-κB signaling | Knockout cell lines, patient fibroblasts |
| MCCC2 | MCCC deficiency; hepatocellular carcinoma stemness | Knockout and overexpression in HCC cells |
| SIRT4 | Cancer metabolism; acetyl-CoA regulation | Knockout and deacetylation mutants |
| SLC25A21 | Colorectal cancer; ferroptosis | Knockout and overexpression in CRC cells |
| GPX4 | Ferroptosis regulation | Knockout and point mutants |
3-Methylcrotonyl-CoA Carboxylase Deficiency
Mutations in MCCC1 or MCCC2 cause 3-methylcrotonyl-CoA carboxylase deficiency, an inborn error of leucine metabolism. Newborn screening detects elevated 3-hydroxyisovalerylcarnitine and 3-methylcrotonylglycine, but the clinical significance and necessity of routine screening remain debated. Patient fibroblasts show mitochondrial dysfunction and oxidative stress.
Cancer
MCCC2 deacetylation by SIRT4 promotes acetyl-CoA synthesis and enhances stemness and invasiveness of hepatocellular carcinoma. SLC25A21, a mitochondrial carrier, promotes ferroptosis by inducing GPX4 deficiency in colorectal cancer, linking mitochondrial metabolism to cell death pathways.
Innate Immunity
MCCC1 potentiates RLR-induced NF-κB signaling by targeting the MAVS complex, suggesting a role for the complex in antiviral innate immunity beyond metabolism.
From methylcrotonoyl-CoA carboxylase complex-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does MCCC1 loss affect leucine catabolism? | MCCC1 knockout cell lines |
| How does MCCC2 deacetylation affect cancer stemness? | MCCC2 point mutations (acetylation-deficient) in HCC cells |
| Can MCCC1 potentiate NF-κB signaling? | MCCC1 overexpression and knockout in immune cells |
| What is the role of SLC25A21 in ferroptosis? | SLC25A21 knockout and overexpression in CRC cells |
| Does MCCC deficiency cause oxidative stress? | Patient-derived fibroblasts and CRISPR-corrected isogenic lines |
| How is the dodecamer assembled? | Tagged knock-in of MCCC1 and MCCC2 for structural studies |
How to Study the methylcrotonoyl-CoA carboxylase complex Process
| Method | What It Measures | Typical Application |
|---|---|---|
| RNA-seq | Gene expression changes | Transcriptome of MCCC-deficient cells |
| Proteomics | Protein abundance and modifications | MCCC2 acetylation status |
| Metabolomics | Metabolite levels | Diagnosis of MCCC deficiency |
| Enzyme activity assay | Carboxylase activity | Functional characterization of MCCC variants |
| Co-immunoprecipitation | Protein-protein interactions | MCCC1-MAVS interaction |
| Fluorescence microscopy | Subcellular localization | Mitochondrial targeting of MCCC |
| CRISPR screening | Gene essentiality and modifiers | Identify regulators of MCCC function |
| Newborn screening (tandem MS) | Acylcarnitine profiles | Detection of MCCC deficiency |
Genomic and Transcriptomic Analysis
RNA-seq of MCCC-deficient fibroblasts reveals underlying mitochondrial dysfunction and oxidative stress pathways. Transcriptome profiling can identify downstream targets of MCCC1 and MCCC2 in cancer and immunity.
Proteomics and Metabolomics
Mass spectrometry-based proteomics can quantify MCCC1 and MCCC2 acetylation status, as shown for SIRT4-mediated deacetylation of MCCC2. Metabolomics detects 3-methylcrotonyl-CoA, 3-hydroxyisovalerylcarnitine, and 3-methylcrotonylglycine in patient samples.
Enzyme Activity Assays
Recombinant human MCCC complex can be expressed, purified, and characterized for carboxylase activity using ATP-dependent assays. Such assays are essential for validating the functional impact of mutations.
Imaging and Localization
Fluorescence microscopy of tagged MCCC1 and MCCC2 can confirm mitochondrial localization and assembly of the dodecamer. Co-immunoprecipitation can detect interactions with MAVS and other partners.
How CRISPR Can Be Used to Study GO:1905202 methylcrotonoyl-CoA carboxylase complex
Knockout
CRISPR knockout of MCCC1 or MCCC2 in cell lines can model MCCC deficiency, leading to impaired leucine catabolism and accumulation of metabolites. Knockout of SIRT4 or SLC25A21 can reveal their roles in cancer metabolism and ferroptosis.
Point Mutation
Introducing patient-specific point mutations in MCCC1 or MCCC2 via CRISPR can validate their pathogenicity and dissect catalytic residues. For example, acetylation-deficient mutants of MCCC2 can test the impact of SIRT4-mediated deacetylation on cancer stemness.
Knock-in
Tagged knock-in of MCCC1 or MCCC2 with fluorescent or affinity tags enables visualization and purification of the complex for structural and interaction studies. Knock-in of disease-associated variants can create isogenic models for drug testing.
Overexpression
CRISPR activation or lentiviral overexpression of MCCC1 can potentiate NF-κB signaling and immune responses. Overexpression of SLC25A21 can induce ferroptosis in colorectal cancer cells.
How EDITGENE Supports methylcrotonoyl-CoA carboxylase complex Research
Researchers studying methylcrotonoyl-CoA carboxylase complex-related genes often need to determine whether a candidate gene is causally involved in metabolism, immunity, or cancer. EDITGENE provides comprehensive CRISPR-based services to generate precise cellular models for such investigations.
Contact EDITGENE today to design your custom CRISPR model for methylcrotonoyl-CoA carboxylase complex research.
Frequently Asked Questions About methylcrotonoyl-CoA carboxylase complex
What is the methylcrotonoyl-CoA carboxylase complex?
It is a mitochondrial enzyme complex (GO:1905202) that catalyzes the ATP-dependent carboxylation of 3-methylcrotonyl-CoA in leucine catabolism.
What genes are involved in the methylcrotonoyl-CoA carboxylase complex?
The main genes are MCCC1 (alpha subunit) and MCCC2 (beta subunit), which assemble into a dodecamer.
What is the function of MCCC1?
MCCC1 contains a covalently bound biotin and provides biotin carboxylase activity for ATP-dependent carboxylation.
What is the function of MCCC2?
MCCC2 possesses carboxyltransferase activity and binds 3-methylcrotonyl-CoA.
What diseases are associated with MCCC deficiency?
Mutations cause 3-methylcrotonyl-CoA carboxylase deficiency, detected by newborn screening with elevated 3-hydroxyisovalerylcarnitine.
How is MCCC complex regulated?
SIRT4 deacetylates MCCC2 to control acetyl-CoA synthesis, and MCCC1 potentiates NF-κB signaling via MAVS.
Is the MCCC complex involved in cancer?
Yes, MCCC2 deacetylation promotes hepatocellular carcinoma stemness, and SLC25A21 affects ferroptosis in colorectal cancer.
What methods are used to study the MCCC complex?
Enzyme activity assays, RNA-seq, proteomics, metabolomics, and CRISPR screens are commonly used.
Can CRISPR be used to model MCCC deficiency?
Yes, CRISPR knockout of MCCC1 or MCCC2 in cell lines models the deficiency and its metabolic consequences.
Where is the MCCC complex located?
It is localized in the mitochondrion.
Conclusion
The methylcrotonoyl-CoA carboxylase complex (GO:1905202) is a mitochondrial dodecamer essential for leucine catabolism, with emerging roles in immunity and cancer. Its subunits, MCCC1 and MCCC2, are implicated in metabolic disorders and malignancy, making them attractive targets for research. CRISPR-based models from EDITGENE can accelerate the functional dissection of this complex in health and disease.
References
- 1. Cao Z et al.. 2016. Methylcrotonoyl-CoA carboxylase 1 potentiates RLR-induced NF-κB signaling by targeting MAVS complex.. Sci Rep 6:33557 PMID: 27629939
- 2. Sun T et al.. 2025. SIRT4 Controls Acetyl-CoA Synthesis to Promote Stemness and Invasiveness of Hepatocellular Carcinoma through Deacetylating MCCC2.. Int J Biol Sci 21(7):2973-2990 PMID: 40384857
- 3. Ding G et al.. 2012. Genetic dissection of methylcrotonyl CoA carboxylase indicates a complex role for mitochondrial leucine catabolism during seed development and germination.. Plant J 70(4):562-77 PMID: 22211474
- 4. Tomassetti M et al.. 2018. 3-methylcrotonyl Coenzyme A (CoA) carboxylase complex is involved in the Xanthomonas citri subsp. citri lifestyle during citrus infection.. PLoS One 13(6):e0198414 PMID: 29879157
- 5. Liu W et al.. 2026. SLC25A21 promotes ferroptosis by inducing mitochondrial GPX4 deficiency in colorectal cancer.. Cell Mol Life Sci 83(1) PMID: 42012504
- 6. Zandberg L et al.. 2016. A 3-methylcrotonyl-CoA carboxylase deficient human skin fibroblast transcriptome reveals underlying mitochondrial dysfunction and oxidative stress.. Int J Biochem Cell Biol 78:116-129 PMID: 27417235
- 7. Wang H et al.. 2019. 3-Methylcrotonyl-CoA carboxylase deficiency newborn screening in a population of 536,008: is routine screening necessary?. J Pediatr Endocrinol Metab 32(12):1321-1326 PMID: 31730530
- 8. Chu CH et al.. 2007. Expression, purification, characterization of human 3-methylcrotonyl-CoA carboxylase (MCCC).. Protein Expr Purif 53(2):421-7 PMID: 17360195
