GO:0032564 dATP binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0032564 (dATP binding) is a molecular function defined as binding to deoxyadenosine triphosphate (dATP), a deoxynucleoside triphosphate that serves as a substrate for DNA synthesis and a signaling molecule.
• dATP binding proteins include Apaf-1, which assembles the apoptosome and activates caspase-9 during apoptosis.
• Cryopyrin/NALP3 binds ATP/dATP and requires ATP binding to mediate inflammatory signaling.
• A conserved family of immune effectors cleaves cellular ATP/dATP upon viral infection, linking dATP binding to antiviral defense.
• Plant NLR resistosomes bind dATP/dADP as part of immune signaling, demonstrating evolutionary conservation of dATP-binding mechanisms.
• dATP binding can be studied using photoaffinity labeling, structural biology, and CRISPR-based gene editing to dissect function.
Description
dATP binding (GO:0032564) is a molecular function that describes the selective interaction of a protein or biomolecule with deoxyadenosine triphosphate (dATP), a deoxynucleoside triphosphate. dATP is best known as a substrate for DNA polymerases, but it also acts as a signaling molecule in apoptosis, inflammation, and immunity. Proteins that bind dATP often use it as a cofactor, allosteric regulator, or substrate to drive conformational changes and downstream signaling. Understanding dATP binding is therefore critical for dissecting mechanisms of cell death, innate immune sensing, and nucleotide metabolism. This article integrates authoritative QuickGO annotation and verified PubMed literature to provide a research-grade overview of GO:0032564, its associated genes, disease relevance, and experimental approaches.
dATP binding At A Glance
| GO ID | GO:0032564 |
|---|---|
| GO term | dATP binding |
| Ontology | molecular_function |
| Synonym | None |
| Definition | Binding to dATP, deoxyadenosine triphosphate. |
| Major function | Mediates interactions with dATP for signaling, apoptosis, immunity, and DNA metabolism. |
| Related molecules | dATP, Apaf-1, caspase-9, NALP3, plant NLRs, eIF4A. |
| Disease relevance | Apoptosis dysregulation, inflammatory disorders, cancer, viral infection. |
What Is GO:0032564?
According to the Gene Ontology, GO:0032564 (dATP binding) is defined as the binding to dATP, deoxyadenosine triphosphate. This molecular function encompasses non-covalent and covalent interactions with dATP, including its role as a substrate, cofactor, or allosteric regulator in enzymatic and signaling complexes. The term is distinct from ATP binding (GO:0005524) because it specifically recognizes the deoxyribonucleotide form, which lacks the 2'-hydroxyl group and is primarily associated with DNA metabolism and specialized signaling.
Why Is dATP binding Important in Cell Biology?
dATP binding is important because it underpins fundamental cellular decisions such as apoptosis, inflammation, and antiviral defense. For example, Apaf-1 binds dATP to assemble the apoptosome, a platform for caspase-9 activation, which is essential for developmental cell death and tumor suppression. Cryopyrin/NALP3 requires ATP/dATP binding to mediate inflammatory signaling, linking dATP binding to innate immunity. Moreover, a conserved family of immune effectors cleaves cellular ATP/dATP upon viral infection, highlighting dATP as a central node in host-pathogen interactions. Studying dATP binding provides insights into mechanisms of disease and potential therapeutic targets.
• dATP binding is required for apoptosome assembly and caspase-9 activation during apoptosis.
• Cryopyrin/NALP3 binds ATP/dATP and requires ATP binding for inflammatory signaling.
• A conserved family of immune effectors cleaves ATP/dATP upon viral infection, linking dATP to antiviral defense.
• Plant NLR resistosomes bind dATP/dADP, showing evolutionary conservation of dATP-binding in immunity.
• dATP-binding proteins can be studied by photoaffinity labeling with [alpha-32P]ATP/dATP.
• Dysregulation of dATP-dependent processes is implicated in cancer, autoinflammatory diseases, and neurodegeneration.
• dATP binding is distinct from ATP binding and is critical for DNA synthesis and repair.
• Targeting dATP-binding proteins offers therapeutic opportunities in oncology and immunology.
Molecular Mechanism of dATP binding
dATP as a Substrate and Signaling Molecule
In simple terms: dATP is not just a DNA building block; it also acts as a signal that tells cells to die or fight infections.
dATP is a deoxynucleoside triphosphate that serves as a substrate for DNA polymerases and as a signaling molecule in apoptosis and immunity. In apoptosis, dATP binds to Apaf-1, triggering its oligomerization and apoptosome formation. In innate immunity, dATP binds to NALP3 and other inflammasome components to mediate inflammatory signaling. A conserved family of immune effectors cleaves ATP/dATP upon viral infection, further demonstrating dATP's signaling roles.
Apaf-1 and Apoptosome Assembly
In simple terms: Apaf-1 is a protein that, when it binds dATP, forms a wheel-like structure that activates caspases to dismantle the cell.
Apaf-1 binds dATP and cytochrome c to assemble the apoptosome, a heptameric platform that recruits and activates procaspase-9. This process is essential for the intrinsic apoptotic pathway. Structural studies have revealed that dATP binding induces conformational changes in Apaf-1 that promote oligomerization. The apoptosome then activates caspase-9, which in turn activates downstream executioner caspases.
dATP Binding in Inflammasome Signaling
In simple terms: Some immune sensors bind dATP to switch on inflammation, which helps fight infections but can also cause disease.
Cryopyrin/NALP3 binds ATP/dATP and is an ATPase; ATP binding is required for its inflammatory signaling. This links dATP binding to the NLRP3 inflammasome, which mediates responses to pathogens and danger signals. Mutations in NLRP3 cause cryopyrin-associated periodic syndromes, highlighting the clinical importance of dATP binding.
Plant NLR Resistosomes and dATP Binding
In simple terms: Plants also use dATP-binding proteins to detect pathogens and trigger immunity.
Plant NLR resistosomes, such as the ZAR1 resistosome, bind dATP/dADP as part of their activation mechanism. Reconstitution and structural studies have shown that nucleotide binding is essential for resistosome assembly and immune signaling. This demonstrates that dATP binding is an evolutionarily conserved mechanism in immunity.
Photoaffinity Labeling of dATP-Binding Proteins
In simple terms: Scientists can tag dATP with a radioactive label to find proteins that bind it.
Photoaffinity labeling with [alpha-32P]ATP/dATP has been used to identify and characterize dATP-binding proteins, such as eukaryotic initiation factor 4A (eIF4A) and the cap-binding protein complex. This technique allows differential labeling of free eIF4A and eIF4A within the cap-binding complex, providing insights into dATP-binding specificity. Such methods are valuable for discovering novel dATP-binding proteins.
Key Genes Involved in GO:0032564 dATP binding
The following genes and proteins are directly implicated in dATP binding or dATP-dependent processes, based on verified literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| APAF1 | Binds dATP to assemble apoptosome and activate caspase-9 | Apoptosis research, cancer therapeutics |
| CASP9 | Effector caspase activated by apoptosome | Apoptosis, neurodegeneration |
| NLRP3 | Binds ATP/dATP to mediate inflammasome signaling | Inflammatory diseases, autoimmunity |
| ZAR1 | Plant NLR that binds dATP/dADP for resistosome assembly | Plant immunity, structural biology |
| EIF4A | ATP/dATP-binding helicase in translation initiation | Translation regulation, cancer |
| NLRP1 | Inflammasome sensor potentially binding dATP | Innate immunity, inflammation |
| NLRC4 | Inflammasome sensor potentially binding dATP | Antimicrobial defense |
| AIM2 | Inflammasome sensor potentially binding dATP | DNA sensing, immunity |
| PYCARD | Adaptor in inflammasomes, may interact with dATP-bound sensors | Inflammation, apoptosis |
| CASP1 | Inflammatory caspase activated by inflammasomes | Inflammation, pyroptosis |
| CASP4 | Inflammatory caspase in non-canonical inflammasomes | Antibacterial defense |
| CASP5 | Inflammatory caspase in non-canonical inflammasomes | Antibacterial defense |
| CYCS | Cytochrome c, co-activator of apoptosome with dATP | Apoptosis |
| BIRC2 | Inhibitor of apoptosis, may regulate dATP-dependent apoptosis | Cancer, apoptosis |
| BIRC3 | Inhibitor of apoptosis, may regulate dATP-dependent apoptosis | Cancer, apoptosis |
| XIAP | Inhibitor of apoptosis, regulates caspase-9 | Cancer, apoptosis |
| DIABLO | Antagonist of IAPs, promotes apoptosis | Cancer, apoptosis |
How Is dATP binding Regulated?
dATP binding and its downstream effects are regulated at multiple levels. In apoptosis, the availability of dATP and cytochrome c controls apoptosome assembly, while inhibitor of apoptosis proteins (IAPs) such as XIAP can block caspase-9 activity. In inflammasome signaling, ATP/dATP binding to NLRP3 is required for inflammatory signaling, and its activity is further regulated by phosphorylation and ubiquitination. In plants, NLR resistosome assembly is tightly controlled to prevent autoimmunity. Additionally, cellular dATP levels are regulated by nucleotide metabolism enzymes, which can influence dATP-binding events.
dATP binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| APAF1 | Cancer, apoptosis evasion | APAF1 knockout cancer cell lines |
| NLRP3 | Cryopyrin-associated periodic syndromes | NLRP3 point-mutation knock-in mice |
| CASP9 | Neurodegeneration, cancer | CASP9 knockout neuronal cells |
| ZAR1 | Plant immunity | ZAR1 knockout Arabidopsis |
| EIF4A | Cancer, translation dysregulation | EIF4A overexpression cell lines |
dATP Binding in Cancer
Dysregulation of apoptosis contributes to cancer. Apaf-1, which binds dATP to form the apoptosome, is often downregulated in tumors, leading to evasion of apoptosis. Caspase-9, activated by the apoptosome, is also implicated in cancer progression. Targeting dATP-binding proteins may restore apoptotic sensitivity in cancer cells.
dATP Binding in Inflammatory Diseases
NLRP3 binds ATP/dATP and mediates inflammatory signaling; gain-of-function mutations cause cryopyrin-associated periodic syndromes. This links dATP binding to autoinflammatory diseases and highlights the therapeutic potential of targeting NLRP3.
dATP Binding in Viral Infection
A conserved family of immune effectors cleaves cellular ATP/dATP upon viral infection, suggesting that dATP binding is part of antiviral defense. Viruses may manipulate dATP metabolism to evade immunity.
dATP Binding in Neurodegeneration
Apoptosis mediated by dATP-dependent apoptosome assembly is implicated in neuronal loss in neurodegenerative diseases. Modulating dATP binding could be neuroprotective.
From dATP binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does APAF1 dATP binding drive apoptosome assembly? | APAF1 point-mutation knock-in (dATP-binding deficient) |
| What is the role of NLRP3 dATP binding in inflammation? | NLRP3 knockout and point-mutation knock-in macrophages |
| How does dATP binding affect caspase-9 activation? | CASP9 knockout cells reconstituted with wild-type or mutant caspase-9 |
| Is ZAR1 dATP binding required for plant immunity? | ZAR1 knockout and tagged knock-in Arabidopsis |
| Can dATP-binding proteins be identified systematically? | Photoaffinity labeling with [alpha-32P]ATP/dATP |
| Does dATP binding regulate translation initiation? | EIF4A overexpression and knockout cells |
How to Study the dATP binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Photoaffinity labeling | Direct binding of dATP to proteins | Identifying dATP-binding proteins |
| Cryo-EM | 3D structure of protein-dATP complexes | Apoptosome and resistosome assembly |
| ATPase assay | Nucleotide hydrolysis | NLRP3 function |
| CRISPR knockout screen | Gene essentiality in dATP-dependent pathways | Apoptosis and inflammation |
| Western blot | Protein expression and cleavage | Caspase activation |
| Flow cytometry | Cell death and inflammasome activation | Apoptosis and pyroptosis |
| Isothermal titration calorimetry | Binding affinity for dATP | Protein-nucleotide interactions |
| Surface plasmon resonance | Real-time binding kinetics | dATP-protein interaction studies |
Photoaffinity Labeling
Photoaffinity labeling with [alpha-32P]ATP/dATP allows detection and characterization of dATP-binding proteins, as demonstrated for eIF4A and the cap-binding complex. This method is useful for identifying novel dATP-binding proteins and studying binding specificity.
Structural Biology
Cryo-EM and X-ray crystallography have revealed how proteins like Apaf-1 and plant NLRs bind dATP and undergo conformational changes. These techniques provide atomic-level insights into dATP-binding mechanisms.
Biochemical Assays
ATPase and dATP-binding assays can measure nucleotide hydrolysis and binding affinity, as shown for Cryopyrin/NALP3. Such assays are essential for functional characterization.
CRISPR Screening
Genome-wide CRISPR knockout screens can identify genes required for dATP-dependent processes such as apoptosis or inflammasome activation. This approach enables unbiased discovery of dATP-binding regulators.
How CRISPR Can Be Used to Study GO:0032564 dATP binding
Knockout
CRISPR knockout of genes such as APAF1, NLRP3, or CASP9 can abolish dATP-dependent processes, providing causal evidence for their roles. Knockout cell lines are valuable for dissecting apoptosis and inflammation pathways.
Point Mutation
Introducing point mutations that disrupt dATP binding (e.g., in APAF1 or NLRP3) allows precise testing of the functional significance of dATP binding without affecting protein expression. Such models are critical for distinguishing binding-dependent from independent functions.
Knock-in
Knock-in of tagged or mutant versions of dATP-binding proteins (e.g., GFP-APAF1) enables live-cell imaging and biochemical purification. This approach helps track protein localization and complex assembly.
Overexpression
Overexpression of dATP-binding proteins such as EIF4A or NLRP3 can amplify signaling and reveal gain-of-function phenotypes. This is useful for studying downstream effects and identifying interacting partners.
How EDITGENE Supports dATP binding Research
Researchers studying dATP binding-related genes often need to determine whether a candidate gene is causally involved in apoptosis, inflammation, or immunity. EDITGENE provides comprehensive CRISPR services to generate precisely engineered cell models, enabling functional validation of dATP-binding proteins.
Contact EDITGENE today to design your custom CRISPR model for dATP binding research.
Frequently Asked Questions About dATP binding
What is dATP binding?
dATP binding (GO:0032564) is a molecular function defined as the binding to deoxyadenosine triphosphate (dATP), a nucleotide involved in DNA synthesis and signaling.
What genes are involved in dATP binding?
Key genes include APAF1, CASP9, NLRP3, ZAR1, and EIF4A, which bind dATP to mediate apoptosis, inflammation, immunity, and translation.
How is dATP binding studied?
Methods include photoaffinity labeling, cryo-EM, ATPase assays, and CRISPR screens.
What diseases are associated with dATP binding?
Dysregulation of dATP binding is linked to cancer, cryopyrin-associated periodic syndromes, viral infections, and neurodegeneration.
What is the difference between ATP and dATP binding?
ATP binding (GO:0005524) involves adenosine triphosphate, while dATP binding (GO:0032564) specifically involves deoxyadenosine triphosphate, which lacks the 2'-hydroxyl group.
Which proteins bind dATP in apoptosis?
Apaf-1 binds dATP to assemble the apoptosome and activate caspase-9.
Does NLRP3 bind dATP?
Yes, Cryopyrin/NALP3 binds ATP/dATP and requires ATP binding for inflammatory signaling.
How can I knockout a dATP-binding gene?
CRISPR knockout services from EDITGENE can generate APAF1, NLRP3, or CASP9 knockout cell lines.
What is the role of dATP in plant immunity?
Plant NLR resistosomes bind dATP/dADP to trigger immune signaling.
Can dATP binding be targeted therapeutically?
Yes, targeting dATP-binding proteins is a potential strategy for cancer and inflammatory diseases.
Conclusion
dATP binding (GO:0032564) is a fundamental molecular function that governs critical cellular processes including apoptosis, inflammation, and antiviral immunity. The integration of QuickGO annotation with verified literature reveals a conserved mechanism across species, from plants to humans. Understanding dATP binding provides a foundation for developing therapeutic interventions in cancer, autoinflammatory diseases, and infections.
References
- 1. Wang J et al.. 2019. Reconstitution and structure of a plant NLR resistosome conferring immunity.. Science 364(6435) PMID: 30948527
- 2. Srinivasula SM et al.. 1998. Autoactivation of procaspase-9 by Apaf-1-mediated oligomerization.. Mol Cell 1(7):949-57 PMID: 9651578
- 3. Kuida K. 2000. Caspase-9.. Int J Biochem Cell Biol 32(2):121-4 PMID: 10687948
- 4. Rousset F et al.. 2023. A conserved family of immune effectors cleaves cellular ATP upon viral infection.. Cell 186(17):3619-3631.e13 PMID: 37595565
- 5. Sarkar G et al.. 1985. Photoaffinity labeling of the cap-binding protein complex with ATP/dATP. Differential labeling of free eukaryotic initiation factor 4A and the eukaryotic initiation factor 4A component of the cap-binding protein complex with [alpha-32P]ATP/dATP.. J Biol Chem 260(25):13831-7 PMID: 4055759
- 6. Duncan JA et al.. 2007. Cryopyrin/NALP3 binds ATP/dATP, is an ATPase, and requires ATP binding to mediate inflammatory signaling.. Proc Natl Acad Sci U S A 104(19):8041-6 PMID: 17483456
- 7. Dalton A et al.. 1992. Characterization and purification of a novel dATP-binding protein in eukaryotes.. Biochem J 287 ( Pt 3)(Pt 3):871-9 PMID: 1445246
- 8. Shi Y. 2008. Apoptosome assembly.. Methods Enzymol 442:141-56 PMID: 18662568
