GO:0005524 ATP binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0005524 ATP binding describes the molecular function of selectively binding adenosine 5'-triphosphate (ATP), a universal coenzyme and enzyme regulator.
• ATP binding is not limited to classical ATP-binding folds such as the RRM; it can occur in diverse nucleic-acid-binding domains.
• ATP binding is often driven by electrostatic interactions, with arginine residues playing a major role in general protein-binding ability.
• ATP competes with other ligands, such as PIP2 for gelsolin, demonstrating that ATP binding can directly regulate protein function.
• Kinetic characterization of enzymes like acetyl-CoA synthetase shows that ATP binding is a key step in catalysis and can be targeted for inhibition.
• Dysregulation of ATP binding is implicated in diseases such as diabetes and cancer, making it a focus for therapeutic development.
Description
ATP binding (GO:0005524) is a fundamental molecular function that underpins countless cellular processes, from energy metabolism to signal transduction. ATP, adenosine 5'-triphosphate, is a universally important coenzyme and enzyme regulator, and its binding to proteins is essential for their activity, stability, and regulation. This function is not restricted to canonical ATP-binding motifs; recent studies have shown that ATP can bind to nucleic-acid-binding domains beyond the RRM fold, expanding the repertoire of ATP-binding proteins. Understanding ATP binding is therefore critical for deciphering how cells sense and respond to energy status and how mutations in ATP-binding sites contribute to disease. The interaction is often mediated by electrostatic forces, with arginine residues frequently playing a central role in the binding interface. Moreover, ATP binding can be competitive with other ligands, as seen in gelsolin where ATP competes with PIP2, highlighting its regulatory potential. Given its ubiquity, ATP binding is a major target for drug discovery and a key consideration in the design of CRISPR-based disease models.
ATP binding At A Glance
| GO ID | GO:0005524 |
|---|---|
| GO term | ATP binding |
| Ontology | molecular_function |
| Synonym | Mg-ATP binding, MgATP binding |
| Definition | Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. |
| Major function | Non-covalent interaction with ATP to regulate protein activity, catalysis, or complex assembly. |
| Related cofactor | Magnesium ions (Mg2+) often required for ATP binding. |
| Representative domains | P-loop NTPases, kinases, ATP-binding cassette transporters, and some nucleic-acid-binding domains. |
What Is GO:0005524?
GO:0005524 ATP binding is defined as the selective interaction with ATP, adenosine 5'-triphosphate, a molecule that serves as a universal coenzyme and enzyme regulator. This function is characterized by the ability of a protein or domain to non-covalently bind ATP, often through conserved motifs such as the P-loop, but also through less canonical interfaces. The binding event can induce conformational changes, modulate enzymatic activity, or facilitate substrate transfer, and it is frequently dependent on the presence of divalent cations like magnesium, as reflected in the synonyms Mg-ATP binding and MgATP binding.
Why Is ATP binding Important in Cell Biology?
ATP binding is central to cellular energy homeostasis and signal transduction, as it controls the activity of kinases, ATPases, and many regulatory proteins. Disruption of ATP binding can lead to metabolic disorders, cancer, and neurological diseases, making it a prime target for therapeutic intervention. Moreover, understanding ATP binding is essential for interpreting the effects of genetic variants and for designing CRISPR models that accurately mimic human disease.
• ATP binding regulates the activity of kinases and ATPases, which are involved in nearly all signaling pathways.
• It is essential for energy metabolism, as seen in acetyl-CoA synthetase where ATP binding is required for catalysis.
• ATP binding can compete with other ligands, such as PIP2, to modulate protein function in a dynamic manner.
• Mutations in ATP-binding sites are associated with diseases like diabetes and cancer.
• ATP binding is a key mechanism in bacterial enhancer-binding proteins, which couple ATP hydrolysis to transcriptional activation.
• It plays a role in nuclear receptor regulation, as ATP-stimulated translocation promoter enhances nuclear binding of glucocorticoid receptor.
• ATP binding is a target for drug design, including peptoid-based chelators that strongly bind ATP.
• Understanding ATP binding helps in interpreting the effects of genetic variants in clinical genomics.
• It is a critical parameter in enzyme kinetics and inhibitor screening.
• ATP binding motifs are used as markers in protein annotation and functional genomics.
Molecular Mechanism of ATP binding
Initial Recognition and Electrostatic Attraction
In simple terms: The protein first attracts ATP through electrical charges.
ATP binding often begins with electrostatic interactions between the negatively charged phosphate groups of ATP and positively charged residues on the protein surface. Arginine residues are particularly important for this general protein-binding ability, as they can form stable salt bridges with ATP's phosphates. This initial recognition is crucial for orienting ATP for subsequent steps.
Conformational Change and Induced Fit
In simple terms: The protein changes shape to grip ATP tightly.
Upon initial contact, many ATP-binding proteins undergo conformational changes that bury ATP within a binding pocket. This induced fit increases affinity and specificity. For example, in bacterial enhancer-binding proteins, ATP binding induces structural rearrangements that are necessary for their function. Such changes can also expose or hide interaction surfaces, regulating downstream signaling.
Coordination with Magnesium Ions
In simple terms: Magnesium helps ATP bind more tightly.
ATP binding is frequently dependent on divalent cations, especially Mg2+, which coordinates the phosphate groups and stabilizes the bound state. The synonyms Mg-ATP binding and MgATP binding reflect this common requirement. Magnesium neutralizes the negative charge of ATP, facilitating its interaction with the protein and often participating directly in catalysis.
Competition and Regulation by Other Ligands
In simple terms: Other molecules can compete with ATP for the same spot.
ATP binding can be modulated by competing ligands. For instance, in gelsolin, ATP competes with PIP2 for binding, allowing the cell to switch between different regulatory states. This competition provides a mechanism for integrating metabolic signals with other pathways, such as lipid signaling.
Functional Consequences: Catalysis and Regulation
In simple terms: Once ATP is bound, the protein can do its job.
The ultimate outcome of ATP binding varies: it can lead to ATP hydrolysis and energy release, as in acetyl-CoA synthetase, or it can act as a regulatory switch, as in the ATP-stimulated translocation promoter that enhances nuclear binding of glucocorticoid receptor. In some cases, ATP binding alone is sufficient to alter protein-protein interactions, as seen with peptoid chelators that strongly bind ATP.
Key Genes Involved in GO:0005524 ATP binding
The following genes encode proteins that bind ATP and are representative of the diverse functions associated with GO:0005524.
| Gene | Major Role | Research Relevance |
|---|---|---|
| ACSS2 | Acetyl-CoA synthetase, binds ATP for acetate activation | Metabolic studies, cancer metabolism |
| GSN | Gelsolin, ATP competes with PIP2 for binding | Cytoskeleton regulation, apoptosis |
| KCNJ11 | Potassium channel subunit, ATP binding regulates insulin secretion | Diabetes, channelopathies |
| ABCC8 | Sulfonylurea receptor, ATP-sensitive potassium channel | Diabetes, drug response |
| HSP90AA1 | Chaperone, ATP binding drives client protein folding | Cancer, protein homeostasis |
| CDK1 | Cyclin-dependent kinase, ATP binding for phosphorylation | Cell cycle, cancer |
| EGFR | Receptor tyrosine kinase, ATP binding for kinase activity | Cancer, targeted therapy |
| BCR | Breakpoint cluster region, ATP binding in kinase domain | Leukemia, fusion proteins |
| ABL1 | Tyrosine kinase, ATP binding for oncogenic signaling | Leukemia, drug resistance |
| P2RX7 | ATP-gated ion channel | Inflammation, pain |
| NLRP3 | Inflammasome sensor, ATP binding for activation | Inflammation, autoimmunity |
| GR | Glucocorticoid receptor, ATP-stimulated nuclear binding | Stress response, inflammation |
| BEBP | Bacterial enhancer-binding protein, ATP hydrolysis for transcription | Gene regulation, microbiology |
| RRM | RNA recognition motif, can bind ATP beyond canonical folds | RNA biology, protein evolution |
| PEPT | Peptoid-based ATP chelators | Chemical biology, drug design |
| ATPase | Generic ATPase, binds and hydrolyzes ATP | Energy metabolism, transport |
| Kinase | Protein kinase, ATP binding for phosphorylation | Signal transduction, drug targets |
How Is ATP binding Regulated?
ATP binding is regulated at multiple levels. Intracellular ATP concentrations fluctuate with metabolic state, directly influencing the occupancy of ATP-binding sites. Competition with other ligands, such as PIP2 for gelsolin, provides a switch mechanism. Additionally, post-translational modifications and interacting proteins can alter the affinity for ATP. For example, the ATP-stimulated translocation promoter enhances nuclear binding of the glucocorticoid receptor complex in an ATP-dependent manner. In bacteria, enhancer-binding proteins couple ATP binding and hydrolysis to transcriptional activation, a process that is tightly regulated by signal transduction pathways.
ATP binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| KCNJ11 | Neonatal diabetes, hyperinsulinism | Knock-in mouse with patient mutation |
| ABCC8 | Diabetes, congenital hyperinsulinism | CRISPR point mutation in iPSCs |
| ACSS2 | Cancer metabolism | Knockout cell lines, xenografts |
| P2RX7 | Inflammation, pain | Knockout mice, overexpression in macrophages |
| NLRP3 | Autoinflammatory diseases | Knock-in for gain-of-function mutations |
ATP Binding in Metabolic Disorders
Mutations in the ATP-binding subunits of ATP-sensitive potassium channels, such as KCNJ11 and ABCC8, cause neonatal diabetes and hyperinsulinism. The binding of ATP to these channels regulates insulin secretion, and impaired ATP binding leads to inappropriate channel activity. Repaglinide, a drug used to treat diabetes, binds to the pancreatic KATP channel and modulates its activity, highlighting the therapeutic relevance of ATP binding.
ATP Binding in Cancer
Many oncogenic kinases, such as EGFR and ABL1, rely on ATP binding for their activity. Mutations that alter ATP binding affinity can lead to drug resistance or constitutive activation. Targeting the ATP-binding site with small molecule inhibitors is a mainstay of cancer therapy. Additionally, metabolic enzymes like ACSS2 use ATP binding to support cancer cell metabolism, making them potential targets.
ATP Binding in Neurological and Inflammatory Diseases
ATP-gated ion channels like P2RX7 are involved in neuroinflammation and pain. ATP binding to these channels triggers calcium influx and cytokine release. In the context of inflammation, ATP binding to NLRP3 inflammasome components activates the inflammasome, contributing to autoimmune and inflammatory diseases. Modulating ATP binding may offer therapeutic avenues.
From ATP binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does a specific ATP-binding site mutation affect kinase activity? | Point mutation knock-in cell line |
| What is the effect of ATP-binding protein knockout on cell proliferation? | CRISPR knockout in cancer cell lines |
| How does ATP binding regulate protein localization? | Tagged knock-in with fluorescent reporter |
| Can overexpression of an ATP-binding protein drive transformation? | Overexpression in primary cells |
| What are the off-target effects of ATP-competitive inhibitors? | CRISPR library screening for resistance |
| How do ATP-binding site variants affect drug response? | Patient-derived organoids with knock-in mutations |
How to Study the ATP binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Isothermal titration calorimetry | Binding affinity and thermodynamics | Characterizing ATP binding to purified proteins |
| Fluorescence polarization | Binding affinity in solution | High-throughput screening for ATP-binding inhibitors |
| X-ray crystallography | Three-dimensional structure of ATP-protein complex | Structure-based drug design |
| CRISPR knockout screening | Gene essentiality and pathway involvement | Identifying ATP-binding proteins required for cell fitness |
| CRISPR knock-in | Effect of specific mutations on ATP binding | Modeling patient-derived mutations |
| RNA-seq | Transcriptional changes upon ATP-binding perturbation | Pathway analysis after knockout |
| Proteomics | Protein interaction networks and post-translational modifications | Identifying ATP-binding protein complexes |
| Molecular dynamics simulation | Dynamic behavior of ATP-binding site | Predicting mutation effects |
Biochemical Assays for ATP Binding
Direct measurement of ATP binding can be achieved using radiolabeled ATP, fluorescence polarization, or isothermal titration calorimetry. These methods provide affinity constants and stoichiometry. For enzymes like acetyl-CoA synthetase, kinetic characterization in the presence of ATP reveals binding constants and catalytic parameters.
Structural Biology Approaches
X-ray crystallography and cryo-EM can visualize ATP bound to proteins, revealing the molecular details of the binding pocket and conformational changes. For example, the structure of repaglinide bound to the pancreatic KATP channel elucidated how ATP binding is modulated by drugs. NMR can also detect dynamic aspects of ATP binding.
Computational and Bioinformatics Methods
Molecular dynamics simulations and docking studies can predict ATP-binding sites and estimate binding energies. These approaches are particularly useful for proteins where experimental structures are unavailable. Additionally, sequence analysis can identify conserved ATP-binding motifs across genomes.
CRISPR-Based Functional Genomics
CRISPR knockout and knock-in screens can systematically test the role of ATP-binding proteins in cellular processes. For instance, a library of guide RNAs targeting all kinases can identify which ATP-binding proteins are essential for cell growth or drug resistance. This approach links ATP binding to phenotype on a genome-wide scale.
How CRISPR Can Be Used to Study GO:0005524 ATP binding
Knockout
CRISPR knockout of genes encoding ATP-binding proteins can reveal their essentiality and downstream effects. For example, knocking out ACSS2 in cancer cell lines reduces acetate utilization and slows tumor growth. Knockout models are also used to study ATP-sensitive potassium channels in insulin secretion.
Point Mutation
Introducing specific point mutations in ATP-binding sites via CRISPR can mimic human disease variants. For instance, mutations in KCNJ11 that impair ATP binding cause neonatal diabetes, and knock-in models carrying these mutations help study disease mechanisms and test drugs.
Knock-in
Knock-in of tagged ATP-binding proteins allows real-time tracking of localization and interactions. For example, a GFP-tagged ATP-binding protein can be used to monitor its dynamics upon ATP binding. Knock-in of reporter genes under the control of ATP-responsive promoters can also be used to study signaling.
Overexpression
Overexpression of ATP-binding proteins can drive cellular transformation or metabolic reprogramming. For example, overexpression of ACSS2 in cancer cells enhances acetate-dependent lipid synthesis. Overexpression models are useful for gain-of-function studies and drug screening.
How EDITGENE Supports ATP binding Research
Researchers studying ATP binding-related genes often need to determine whether a candidate gene is causally involved in a specific phenotype, and CRISPR-based models are the gold standard for such functional validation. EDITGENE provides end-to-end services to generate precisely engineered cell models, enabling rigorous investigation of ATP binding mechanisms in health and disease.
Contact EDITGENE today to design your custom CRISPR model for ATP binding research.
Frequently Asked Questions About ATP binding
What is ATP binding?
ATP binding is the molecular function of selectively interacting with adenosine 5'-triphosphate (ATP), a universal coenzyme and enzyme regulator, as defined by GO:0005524.
What genes are involved in ATP binding?
Many genes encode ATP-binding proteins, including ACSS2, GSN, KCNJ11, ABCC8, HSP90AA1, CDK1, EGFR, ABL1, and P2RX7, among others [1,3,4,8].
What is the GO term for ATP binding?
The Gene Ontology term for ATP binding is GO:0005524, under the molecular_function ontology.
How does ATP binding regulate protein function?
ATP binding can induce conformational changes, compete with other ligands, and provide energy for catalysis, thereby regulating protein activity and signaling [2,3,7].
What diseases are associated with ATP binding defects?
Defects in ATP binding are linked to neonatal diabetes, cancer, inflammatory diseases, and neurological disorders [4,8].
What methods are used to study ATP binding?
Common methods include isothermal titration calorimetry, fluorescence polarization, X-ray crystallography, and CRISPR-based screens [4,8].
Can CRISPR be used to study ATP binding?
Yes, CRISPR knockout, knock-in, and point mutation models are widely used to dissect the role of ATP-binding proteins in cells and disease.
What are the synonyms for ATP binding?
Synonyms include Mg-ATP binding and MgATP binding, reflecting the common requirement for magnesium ions.
How is ATP binding regulated?
ATP binding is regulated by intracellular ATP levels, competing ligands, post-translational modifications, and interacting proteins [3,6].
Why is ATP binding important for drug discovery?
Many drugs target ATP-binding sites, especially in kinases and ATP-sensitive channels, making ATP binding a key focus for therapeutic development.
Conclusion
ATP binding (GO:0005524) is a ubiquitous and essential molecular function that impacts nearly every aspect of cellular physiology. From energy metabolism to signal transduction, the ability to bind ATP allows proteins to sense and respond to the cell's energy state. Dysregulation of ATP binding is implicated in a wide range of diseases, and understanding its mechanisms is crucial for developing targeted therapies. With advanced CRISPR tools and bioinformatics, researchers can now precisely model ATP-binding mutations and screen for novel modulators, paving the way for new treatments.
References
- 1. He Y et al.. 2020. ATP binds nucleic-acid-binding domains beyond RRM fold.. Biochem Biophys Res Commun 522(4):826-831 PMID: 31791586
- 2. Hu G et al.. 2022. Mechanistic Insight on General Protein-Binding Ability of ATP and the Impacts of Arginine Residues.. J Phys Chem B 126(25):4647-4658 PMID: 35713479
- 3. Szatmári D et al.. 2018. ATP competes with PIP2 for binding to gelsolin.. PLoS One 13(8):e0201826 PMID: 30086165
- 4. Gallego-Jara J et al.. 2019. Characterization of acetyl-CoA synthetase kinetics and ATP-binding.. Biochim Biophys Acta Gen Subj 1863(6):1040-1049 PMID: 30928490
- 5. Vorobyov N et al.. 2025. Water-Soluble Peptoids with Two Different Binding Sites for Strong ATP Chelation.. Chemistry 31(51):e202500693 PMID: 40755065
- 6. Isohashi F et al.. 1993. ATP-stimulated translocation promoter that enhances the nuclear binding of activated glucocorticoid receptor complex. Biochemical properties and its function (mini-review).. Receptor 3(2):113-24 PMID: 8251951
- 7. Bose D et al.. 2008. Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins.. Biochem Soc Trans 36(Pt 1):83-8 PMID: 18208391
- 8. Ding D et al.. 2019. The Structural Basis for the Binding of Repaglinide to the Pancreatic K(ATP) Channel.. Cell Rep 27(6):1848-1857.e4 PMID: 31067468
