GO:0004450 isocitrate dehydrogenase (NADP+) activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0004450 describes the molecular function of isocitrate dehydrogenase (NADP+) activity, which catalyzes the reversible conversion of isocitrate and NADP+ to 2-oxoglutarate, CO2, and NADPH.
• This activity is widely distributed across species, from psychrophilic bacteria to plants and mammals, and is encoded by genes such as IDH1, IDH2, and their homologs.
• NADP+-dependent isocitrate dehydrogenase (NADP-ICDH) is a key source of NADPH, which is essential for reductive biosynthesis and antioxidant defense.
• In cancer, mutations in IDH1 and IDH2 alter the enzyme's activity and contribute to oncogenesis through metabolic and epigenetic reprogramming.
• Plant NADP-ICDH is involved in fruit ripening, nitric oxide signaling, and heavy metal detoxification, highlighting its broader biological roles.
• CRISPR-based models (knockout, point mutation, knock-in, overexpression) enable precise dissection of GO:0004450 function in health and disease.
Description
Isocitrate dehydrogenase (NADP+) activity (GO:0004450) is a molecular function that catalyzes the oxidative decarboxylation of isocitrate to 2-oxoglutarate, using NADP+ as the electron acceptor and producing NADPH and CO2. This reaction is a cornerstone of cellular metabolism, linking the tricarboxylic acid (TCA) cycle to NADPH-dependent biosynthetic and antioxidant pathways. The enzyme is found in diverse organisms, from bacteria to humans, and its isoforms are localized to different cellular compartments, including the cytosol, mitochondria, and peroxisomes. Researchers study GO:0004450 to understand metabolic reprogramming in cancer, plant stress responses, and fundamental redox biology. The activity is encoded by genes such as IDH1 and IDH2 in humans, and by homologous genes in model organisms and crops. Because NADPH is critical for maintaining reduced glutathione and lipid biosynthesis, dysregulation of this activity has broad physiological consequences. This article provides a comprehensive overview of the definition, mechanism, key genes, disease relevance, and research methods for GO:0004450, with a focus on CRISPR-based approaches for functional interrogation.
isocitrate dehydrogenase (NADP+) activity At A Glance
| GO ID | GO:0004450 |
|---|---|
| GO term | isocitrate dehydrogenase (NADP+) activity |
| Ontology | molecular_function |
| Synonym | NADP-dependent isocitrate dehydrogenase activity; NADP(+)-ICDH activity; isocitrate:NADP+ oxidoreductase (decarboxylating); dual-cofactor-specific isocitrate dehydrogenase activity |
| Major function | Catalyzes the conversion of isocitrate and NADP+ to 2-oxoglutarate, CO2, and NADPH |
| Reaction | isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH |
| Cofactor | NADP+ (nicotinamide adenine dinucleotide phosphate) |
| Subcellular localization | Cytosol, mitochondria, peroxisomes (isoform-dependent) |
| EC number | 1.1.1.42 |
What Is GO:0004450?
GO:0004450, isocitrate dehydrogenase (NADP+) activity, is defined as the catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH. In other words, it is an oxidoreductase that decarboxylates isocitrate while reducing NADP+ to NADPH. This activity is synonymous with NADP-dependent isocitrate dehydrogenase, NADP(+)-ICDH, and several other names listed in QuickGO. It is a molecular function term, meaning it describes what a protein does at the biochemical level, rather than a biological process or cellular component.
Why Is isocitrate dehydrogenase (NADP+) activity Important in Cell Biology?
GO:0004450 is essential for cellular metabolism because it provides NADPH, a key reducing agent for biosynthesis and antioxidant defense, and it participates in the TCA cycle via the production of 2-oxoglutarate. In humans, mutations in the genes encoding this activity, particularly IDH1 and IDH2, are found in various cancers and lead to altered metabolism and epigenetic changes. In plants, NADP-ICDH is involved in fruit development, nitric oxide signaling, and stress responses, including heavy metal detoxification. The enzyme's ability to modulate redox balance makes it a target for understanding and potentially treating metabolic disorders, cancer, and plant stress tolerance.
• Provides NADPH for reductive biosynthesis and glutathione regeneration.
• Participates in the TCA cycle by producing 2-oxoglutarate.
• Mutations in IDH1/IDH2 are driver events in glioma, acute myeloid leukemia, and other cancers.
• Plant NADP-ICDH is linked to fruit ripening and nitric oxide signaling.
• Contributes to heavy metal detoxification in plants.
• Enzyme from psychrophilic bacteria offers insights into cold adaptation.
• Natural allelic variation in Drosophila affects enzyme activity.
• Skeletal muscle NADP-ICDH may support metabolic flexibility during hibernation.
• Peroxisomal isoforms are modulated by nitric oxide in pepper fruit.
• The activity is a potential target for metabolic engineering and cancer therapy.
Molecular Mechanism of isocitrate dehydrogenase (NADP+) activity
Substrate Binding and Catalysis
In simple terms: The enzyme grabs isocitrate and NADP+ and converts them into 2-oxoglutarate, CO2, and NADPH.
Isocitrate dehydrogenase (NADP+) binds isocitrate and NADP+ in its active site. The reaction proceeds through oxidative decarboxylation, where isocitrate is first oxidized to oxalosuccinate, which is then decarboxylated to 2-oxoglutarate, releasing CO2 and transferring hydride to NADP+ to form NADPH. This mechanism is conserved across species, as shown by studies on bacterial and plant enzymes.
Cofactor Specificity and NADPH Production
In simple terms: The enzyme specifically uses NADP+ (not NAD+) to make NADPH, a molecule that helps cells fight oxidative stress.
NADP+-dependent isocitrate dehydrogenase is distinct from the NAD+-dependent form (EC 1.1.1.41) in its cofactor preference. The enzyme's affinity for NADP+ and its ability to produce NADPH are critical for maintaining cellular redox homeostasis. In plants, the peroxisomal isoform also uses NADP+ and is modulated by nitric oxide.
Isozymes and Subcellular Localization
In simple terms: Different versions of the enzyme work in different parts of the cell, such as the cytosol, mitochondria, and peroxisomes.
Multiple isozymes of NADP-ICDH exist, encoded by distinct genes and targeted to different compartments. For example, in plants, cytosolic, mitochondrial, and peroxisomal isoforms have been characterized. In mammals, IDH1 is cytosolic and peroxisomal, while IDH2 is mitochondrial. This compartmentalization allows the enzyme to serve specific metabolic roles.
Regulation by Nitric Oxide and Other Signals
In simple terms: The enzyme's activity can be turned up or down by signals like nitric oxide, especially in plants.
In pepper fruit, NADP-ICDH activity and gene expression are modulated by nitric oxide during ripening, with the peroxisomal isozyme being particularly responsive. In mammals, IDH1/2 activity can be affected by mutations that alter substrate specificity, leading to production of 2-hydroxyglutarate instead of 2-oxoglutarate. These regulatory mechanisms highlight the dynamic control of this activity.
Kinetic Properties and Environmental Adaptation
In simple terms: The enzyme from different organisms has adapted to work best under their specific conditions, like cold or warm temperatures.
NADP-ICDH from psychrophilic bacteria shows high catalytic efficiency at low temperatures, reflecting adaptation to cold environments. In hibernating ground squirrels, skeletal muscle NADP-ICDH may support metabolic needs during torpor. These studies reveal how the enzyme's kinetic properties are tuned to physiological demands.
Key Genes Involved in GO:0004450 isocitrate dehydrogenase (NADP+) activity
The following genes encode proteins with isocitrate dehydrogenase (NADP+) activity or are closely related to its function across various organisms.
| Gene | Major Role | Research Relevance |
|---|---|---|
| IDH1 | Cytosolic/peroxisomal NADP+-dependent isocitrate dehydrogenase | Mutations in cancer, metabolic reprogramming |
| IDH2 | Mitochondrial NADP+-dependent isocitrate dehydrogenase | Mutations in cancer, TCA cycle |
| IDH3A | NAD+-dependent isocitrate dehydrogenase subunit (not GO:0004450) | TCA cycle, but distinct cofactor specificity |
| ICDH | Plant NADP-ICDH (various isoforms) | Fruit ripening, NO signaling, stress |
| PtICDH | Peroxisomal NADP-ICDH in pepper | Modulated by nitric oxide during ripening |
| OsICDH | Rice NADP-ICDH | Heavy metal detoxification |
| AtICDH | Arabidopsis NADP-ICDH | Stress responses, redox balance |
| PmIDH | Psychromonas marina NADP-ICDH | Cold adaptation, enzyme kinetics |
| DmIDH | Drosophila melanogaster NADP-ICDH | Natural allelic variation, activity |
| CsIDH | Citrus NADP-ICDH | Fruit development, isozyme expression |
| IDH1 (Urocitellus) | Ground squirrel skeletal muscle NADP-ICDH | Hibernation metabolism |
| IDH2 (human) | Mitochondrial NADP-ICDH | Cancer metabolism, NADPH production |
| IDH1 (human) | Cytosolic NADP-ICDH | Cancer, epigenetics |
| NADP-ICDH (bacterial) | Bacterial NADP-ICDH | Antibiotic targets, metabolism |
| IDH (plant) | Plant NADP-ICDH | Nitric oxide signaling |
| IDH (fungal) | Fungal NADP-ICDH | Metabolic engineering |
| IDH (parasite) | Parasite NADP-ICDH | Drug discovery |
How Is isocitrate dehydrogenase (NADP+) activity Regulated?
The activity of isocitrate dehydrogenase (NADP+) is regulated at multiple levels. In plants, nitric oxide modulates the expression and activity of NADP-ICDH isoforms, particularly the peroxisomal isozyme during fruit ripening. In mammals, mutations in IDH1 and IDH2 alter the enzyme's substrate specificity, leading to the production of the oncometabolite 2-hydroxyglutarate, which affects epigenetic regulation. Additionally, the enzyme's activity can be influenced by post-translational modifications and cellular redox state, although specific mechanisms are still being elucidated.
isocitrate dehydrogenase (NADP+) activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| IDH1 | Glioma, AML, other cancers | Knock-in of IDH1 R132H mutation in cell lines |
| IDH2 | AML, glioma | Knockout and point mutation models |
| Plant ICDH | Heavy metal toxicity | Overexpression in Arabidopsis or rice |
| Pepper ICDH | Fruit ripening and NO signaling | CRISPR knockout in pepper |
| Citrus ICDH | Fruit development | Knockout or overexpression in citrus callus |
Cancer and Oncometabolite Production
Mutations in IDH1 and IDH2, which encode NADP+-dependent isocitrate dehydrogenases, are frequent in gliomas, acute myeloid leukemia, and other cancers. These mutations confer a neomorphic activity that converts 2-oxoglutarate to 2-hydroxyglutarate, an oncometabolite that inhibits alpha-ketoglutarate-dependent dioxygenases, leading to epigenetic alterations and blocked differentiation. The wild-type enzyme's role in producing NADPH also affects redox balance and cancer cell survival.
Plant Stress and Heavy Metal Detoxification
In plants, NADP-ICDH contributes to tolerance against cadmium and lead by supplying NADPH for antioxidant systems and phytochelatin synthesis. Overexpression of a novel NADP+-isocitrate dehydrogenase enhances detoxification and tolerance in plants, suggesting a role in environmental stress adaptation.
Metabolic and Neurodegenerative Implications
Altered NADP-ICDH activity can impact cellular redox homeostasis, which is implicated in neurodegenerative diseases and aging. Although direct links are still emerging, the enzyme's role in maintaining NADPH levels suggests that its dysfunction could contribute to oxidative stress-related pathologies.
From isocitrate dehydrogenase (NADP+) activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of IDH1 affect NADPH levels and redox balance? | IDH1 knockout cell line (e.g., HEK293, U87) |
| How does IDH1 R132H mutation alter substrate specificity? | Point mutation knock-in of IDH1 R132H |
| Can plant NADP-ICDH overexpression enhance cadmium tolerance? | Overexpression of OsICDH in rice or Arabidopsis |
| What is the role of peroxisomal NADP-ICDH in fruit ripening? | CRISPR knockout of peroxisomal ICDH in pepper |
| How does nitric oxide regulate NADP-ICDH activity? | Knockout of nitric oxide synthase in pepper fruit |
| Does IDH2 mutation affect mitochondrial metabolism? | IDH2 knockout and knock-in in cancer cell lines |
How to Study the isocitrate dehydrogenase (NADP+) activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| NADPH absorbance assay | Enzyme activity via NADPH production at 340 nm | Kinetic characterization of NADP-ICDH |
| qRT-PCR | mRNA expression levels of ICDH genes | Tissue-specific expression during development |
| RNA-seq | Global transcriptome changes | Identifying pathways affected by ICDH knockout |
| GFP fusion imaging | Subcellular localization | Determining peroxisomal vs. mitochondrial targeting |
| LC-MS metabolomics | Levels of 2-oxoglutarate, isocitrate, NADPH | Assessing metabolic impact of IDH mutations |
| Western blot | Protein expression and post-translational modifications | Validating knockout or overexpression |
| CRISPR screening | Gene essentiality and synthetic lethality | Identifying dependencies in IDH-mutant cancers |
| Enzyme kinetics | Km, Vmax, kcat | Comparing wild-type and mutant enzymes |
Enzymatic Activity Assays
NADP-ICDH activity is typically measured spectrophotometrically by monitoring the reduction of NADP+ to NADPH at 340 nm. This method has been used to characterize the enzyme from various sources, including ground squirrel skeletal muscle and pepper fruit. Activity assays can be coupled with kinetic studies to determine Km and Vmax values.
Gene Expression Analysis
Quantitative RT-PCR and RNA-seq are used to measure the expression of genes encoding NADP-ICDH isoforms across different tissues and conditions. For example, the expression of citrus ICDH genes was analyzed during fruit development, and pepper ICDH expression was studied during ripening and in response to nitric oxide.
Protein Localization and Imaging
Fluorescent tagging and immunolocalization can determine the subcellular localization of NADP-ICDH isoforms. Peroxisomal targeting of the pepper isozyme was confirmed using GFP fusion proteins. Mitochondrial and cytosolic localization of human IDH1 and IDH2 has been established using similar approaches.
Metabolite Profiling and Flux Analysis
Mass spectrometry-based metabolomics can quantify 2-oxoglutarate, isocitrate, and NADPH levels to assess the impact of NADP-ICDH activity on cellular metabolism. This approach has been used to study the metabolic consequences of IDH mutations in cancer and to evaluate heavy metal detoxification in plants.
How CRISPR Can Be Used to Study GO:0004450 isocitrate dehydrogenase (NADP+) activity
Knockout
CRISPR knockout of IDH1 or IDH2 can eliminate NADP-ICDH activity, allowing researchers to study its role in NADPH production, redox balance, and cell proliferation. Knockout cell lines have been used to demonstrate the importance of IDH1 in cancer cell survival and to identify compensatory pathways. In plants, knockout of specific ICDH isoforms can reveal their contribution to stress tolerance.
Point Mutation
Point mutation knock-in of IDH1 R132H or IDH2 R172K using CRISPR can recreate the oncogenic mutations found in human cancers. These models produce 2-hydroxyglutarate and exhibit altered epigenetic profiles, making them valuable for studying tumorigenesis and testing targeted therapies.
Knock-in
Knock-in of tagged versions of IDH1 or IDH2 (e.g., GFP or FLAG) enables live-cell imaging and proteomic analysis of the enzyme's interactome. This approach can also be used to introduce specific regulatory elements or to study isoform-specific functions.
Overexpression
Overexpression of wild-type or mutant NADP-ICDH can increase NADPH production and alter cellular redox state. In plants, overexpression of a novel NADP+-isocitrate dehydrogenase enhanced cadmium and lead tolerance, demonstrating its potential for phytoremediation. In mammalian cells, overexpression models help dissect the enzyme's contribution to metabolic reprogramming.
How EDITGENE Supports isocitrate dehydrogenase (NADP+) activity Research
Researchers studying isocitrate dehydrogenase (NADP+) activity-related genes often need to determine whether a candidate gene is causally involved in metabolic regulation, stress responses, or disease. EDITGENE provides a comprehensive suite of CRISPR-based services to enable precise genetic manipulation and functional interrogation of GO:0004450-related genes.
Contact EDITGENE today to design your custom CRISPR model for isocitrate dehydrogenase (NADP+) activity research.
Frequently Asked Questions About isocitrate dehydrogenase (NADP+) activity
What is isocitrate dehydrogenase (NADP+) activity?
It is a molecular function (GO:0004450) that catalyzes the conversion of isocitrate and NADP+ to 2-oxoglutarate, CO2, and NADPH.
What genes are involved in isocitrate dehydrogenase (NADP+) activity?
Key genes include IDH1 and IDH2 in humans, and homologous genes in plants, bacteria, and other organisms.
What is the difference between NADP+ and NAD+ dependent isocitrate dehydrogenase?
NADP+-dependent isocitrate dehydrogenase (GO:0004450) uses NADP+ as a cofactor and produces NADPH, while NAD+-dependent (GO:0004449) uses NAD+ and produces NADH.
How is isocitrate dehydrogenase (NADP+) activity measured?
It is typically measured by monitoring NADPH production at 340 nm in a spectrophotometric assay.
What diseases are associated with isocitrate dehydrogenase (NADP+) activity?
Mutations in IDH1 and IDH2 are linked to cancers such as glioma and acute myeloid leukemia.
Can CRISPR be used to study isocitrate dehydrogenase (NADP+) activity?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are powerful tools to dissect the function of this activity.
What is the role of NADP-ICDH in plants?
It is involved in fruit ripening, nitric oxide signaling, and heavy metal detoxification.
How does nitric oxide regulate NADP-ICDH?
Nitric oxide modulates the expression and activity of specific NADP-ICDH isoforms, particularly the peroxisomal isozyme during fruit ripening.
What is the subcellular localization of NADP-ICDH?
It can be cytosolic, mitochondrial, or peroxisomal, depending on the isoform and organism.
What are the synonyms for isocitrate dehydrogenase (NADP+) activity?
Synonyms include NADP-dependent isocitrate dehydrogenase activity, NADP(+)-ICDH activity, and isocitrate:NADP+ oxidoreductase (decarboxylating).
Conclusion
Isocitrate dehydrogenase (NADP+) activity (GO:0004450) is a fundamental molecular function that bridges energy metabolism, redox balance, and biosynthesis. Its importance spans from bacterial cold adaptation to human cancer and plant stress tolerance. Understanding its regulation and genetic basis is crucial for developing therapeutic and biotechnological applications. CRISPR-based models offer unprecedented opportunities to study this activity in precise and physiologically relevant contexts.
References
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- 3. Chang S et al.. 2019. The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism.. Exp Mol Med 51(6):1-17 PMID: 31221981
- 4. Muñoz-Vargas MA et al.. 2024. Activity and gene expression analysis of the NADP-dependent isocitrate dehydrogenase (NADP-ICDH) through pepper fruit ripening and its modulation by nitric oxide (NO). Molecular characterization of the peroxisomal isozyme.. Plant Sci 349:112269 PMID: 39313003
- 5. Liu B et al.. 2025. A novel NADP(+)-isocitrate dehydrogenase contributes to cadmium/lead detoxification and tolerance in plants.. Int J Biol Macromol 312:144094 PMID: 40360117
- 6. Hirota R et al.. 2017. NADP(+)-dependent isocitrate dehydrogenase from a psychrophilic bacterium, Psychromonas marina.. Extremophiles 21(4):711-721 PMID: 28447265
- 7. Bentley MM et al.. 1983. Characterization of a low-activity allele of NADP+-dependent isocitrate dehydrogenase from Drosophila melanogaster.. Biochem Genet 21(7-8):725-33 PMID: 6414457
- 8. Sadka A et al.. 2000. NADP(+)-isocitrate dehydrogenase gene expression and isozyme activity during citrus fruit development.. Plant Sci 158(1-2):173-181 PMID: 10996257
