GO:0017076 purine nucleotide binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0017076 purine nucleotide binding describes the molecular function of selectively binding purine nucleotides such as ATP, GTP, cAMP, and cGMP.
• Purine nucleotide binding is central to signal transduction, energy metabolism, and ion channel regulation [1,5].
• Key protein families include nucleotidyl cyclases, uncoupling proteins (UCP1), annexins, and low-molecular-mass purine-binding proteins [1,2,3,6,7,8].
• Structural studies have revealed the atomic basis of purine nucleotide binding to UCP1, showing how ATP and GTP inhibit proton transport [6,8].
• Dysregulated purine nucleotide binding contributes to metabolic disorders, cancer, and cardiovascular disease [1,6].
• CRISPR knockout, point mutation, and knock-in models enable functional dissection of purine nucleotide binding sites in disease-relevant genes [1,6].
Description
Purine nucleotide binding (GO:0017076) is a fundamental molecular function that mediates the interaction of proteins with purine nucleotides, including adenosine triphosphate (ATP), guanosine triphosphate (GTP), cyclic adenosine monophosphate (cAMP), and cyclic guanosine monophosphate (cGMP). This binding event is essential for numerous cellular processes, ranging from energy transduction and signal transduction to enzyme regulation and ion channel gating [1,5]. The ability of proteins to specifically recognize purine nucleotides underlies their roles in diverse physiological contexts, such as thermogenesis in brown adipose tissue and hormonal signaling [2,4]. Researchers study purine nucleotide binding to understand how cells sense and respond to changes in energy status and signaling cues. For example, mammalian nucleotidyl cyclases contain nucleotide binding sites that are critical for catalyzing the formation of cyclic nucleotides. Similarly, plant purine nucleotide cyclases play roles in development and stress responses. The binding of purine nucleotides to uncoupling protein 1 (UCP1) inhibits proton leak, thereby regulating thermogenesis [6,8]. These examples highlight the broad biological significance of this molecular function. Given its involvement in health and disease, purine nucleotide binding is a target for therapeutic intervention and a focus of structural and functional studies [1,6]. Understanding the precise mechanisms of nucleotide recognition and the consequences of altered binding is essential for developing drugs that modulate these interactions.
purine nucleotide binding At A Glance
| GO ID | GO:0017076 |
|---|---|
| GO term | purine nucleotide binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to purine nucleotides such as ATP, GTP, cAMP, and cGMP |
| Definition | Binding to a purine nucleotide, a compound consisting of a purine nucleoside esterified with (ortho)phosphate. |
| Related proteins | Nucleotidyl cyclases, UCP1, annexins, low-molecular-mass purine-binding proteins |
| Disease relevance | Metabolic disorders, cancer, cardiovascular disease |
What Is GO:0017076?
GO:0017076 purine nucleotide binding is defined as the selective interaction of a protein or biomolecule with a purine nucleotide, which is a compound consisting of a purine nucleoside esterified with orthophosphate. This function encompasses the non-covalent binding of purine nucleotides such as ATP, GTP, cAMP, and cGMP, and is distinct from binding to pyrimidine nucleotides.
Why Is purine nucleotide binding Important in Cell Biology?
Purine nucleotide binding is crucial for cellular energy homeostasis, signal transduction, and metabolic regulation [1,5]. Proteins that bind purine nucleotides act as molecular switches, sensors, and enzymes that control diverse processes, including thermogenesis, hormone signaling, and cell proliferation [2,4,6]. Dysregulation of these binding events is linked to diseases such as obesity, diabetes, and cancer [1,6]. Therefore, understanding the structural and functional basis of purine nucleotide binding is essential for both basic biology and therapeutic development [7,8].
• Regulates energy metabolism through ATP and GTP binding.
• Mediates signal transduction via cyclic nucleotides like cAMP and cGMP [1,5].
• Controls thermogenesis by purine nucleotide inhibition of UCP1 [6,8].
• Involved in plant development and stress responses.
• Annexins bind nucleotides to regulate membrane dynamics and calcium signaling.
• Low-molecular-mass purine-binding proteins may modulate cellular processes.
• Altered binding contributes to metabolic disorders such as obesity.
• Target for drugs modulating nucleotide-dependent enzymes.
• Essential for mitochondrial function and brown adipose tissue activity [2,4].
• Provides a paradigm for studying protein-ligand interactions [6,8].
Molecular Mechanism of purine nucleotide binding
Nucleotide Recognition and Binding Site Architecture
In simple terms: Proteins have specific pockets that fit purine nucleotides like a lock and key.
Purine nucleotide binding proteins typically contain conserved binding pockets that recognize the purine ring and phosphate groups of nucleotides such as ATP or GTP. For example, mammalian nucleotidyl cyclases possess nucleotide binding sites that accommodate ATP or GTP for cyclic nucleotide synthesis. Structural studies of UCP1 have revealed the atomic details of how purine nucleotides bind to the protein, involving interactions with specific amino acid residues [6,8]. These binding sites are often characterized by hydrogen bonding and electrostatic interactions with the phosphate moieties.
Conformational Changes and Functional Consequences
In simple terms: When a nucleotide binds, the protein changes shape to perform its function.
Binding of purine nucleotides induces conformational changes in target proteins, which can activate or inhibit their activity [1,6]. In UCP1, purine nucleotide binding inhibits proton conductance, thereby reducing thermogenesis [6,8]. Similarly, binding of cAMP to protein kinase A triggers a cascade of signaling events. These conformational changes are critical for translating nucleotide binding into biological outcomes.
Regulation by Nucleotide Concentration and Post-translational Modifications
In simple terms: The amount of nucleotide available and chemical tags on the protein can affect binding.
The binding of purine nucleotides is influenced by cellular nucleotide concentrations, which fluctuate with metabolic state. Post-translational modifications, such as phosphorylation, can modulate the affinity of proteins for nucleotides. For instance, annexins undergo calcium-dependent membrane binding that may affect their nucleotide-binding properties. These regulatory mechanisms ensure that purine nucleotide binding is tightly controlled in response to cellular needs [1,5].
Physiological Roles in Thermogenesis and Metabolism
In simple terms: Purine nucleotide binding helps control body heat and energy use.
In brown adipose tissue, purine nucleotide binding to UCP1 is a key regulator of thermogenesis [2,4,6]. Cold acclimation increases purine nucleotide binding in brown fat mitochondria, enhancing heat production. The isolated purine nucleotide binding protein from brown fat mitochondria has been characterized, showing its role in energy dissipation. These findings link purine nucleotide binding directly to metabolic regulation [6,8].
Key Genes Involved in GO:0017076 purine nucleotide binding
The following genes and proteins are representative examples of purine nucleotide binding function, based on published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| UCP1 | Mitochondrial uncoupling protein; binds purine nucleotides to inhibit proton leak | Thermogenesis, obesity, metabolic studies [6,8] |
| ADCY1 | Adenylyl cyclase; binds ATP to synthesize cAMP | Signal transduction, cAMP signaling |
| GUCY1A1 | Guanylyl cyclase; binds GTP to synthesize cGMP | Cardiovascular signaling, cGMP pathways |
| ANXA1 | Annexin; calcium-dependent nucleotide binding | Membrane dynamics, inflammation |
| ANXA2 | Annexin; nucleotide-binding protein | Cell motility, cancer |
| NME1 | Nucleoside diphosphate kinase; binds purine nucleotides | Metastasis suppression, nucleotide metabolism |
| NME2 | Nucleoside diphosphate kinase; binds purine nucleotides | Transcription regulation, nucleotide metabolism |
| RAB1A | Small GTPase; binds GTP | Vesicle trafficking |
| RAB5A | Small GTPase; binds GTP | Endocytosis |
| RHO A | Small GTPase; binds GTP | Cytoskeleton dynamics |
| KRAS | Small GTPase; binds GTP | Cancer signaling |
| HRAS | Small GTPase; binds GTP | Cancer signaling |
| ATP1A1 | Na+/K+-ATPase; binds ATP | Ion transport, energy metabolism |
| ATP2A1 | SERCA; binds ATP | Calcium transport |
| PRKACA | Protein kinase A; binds cAMP | Signal transduction |
| PRKACG | Protein kinase A; binds cAMP | Signal transduction |
| CNGA1 | Cyclic nucleotide-gated channel; binds cAMP/cGMP | Sensory signaling |
| HCN1 | Hyperpolarization-activated cyclic nucleotide-gated channel; binds cAMP | Pacemaker activity |
How Is purine nucleotide binding Regulated?
Purine nucleotide binding is regulated by cellular nucleotide levels, which are influenced by metabolic state and signaling pathways. For example, the binding of ATP to UCP1 is modulated by the energy status of brown adipocytes [6,8]. Post-translational modifications, such as phosphorylation, can alter the affinity of proteins for nucleotides. Additionally, the expression levels of nucleotide-binding proteins are controlled transcriptionally and translationally in response to environmental cues.
purine nucleotide binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| UCP1 | Obesity, metabolic syndrome | UCP1 knockout mouse, point mutation of nucleotide binding site [6,8] |
| KRAS | Cancer (pancreatic, lung, colorectal) | KRAS G12D knock-in mouse, point mutation |
| ADCY1 | Cardiovascular disease, cAMP signaling | ADCY1 knockout cell line, overexpression |
| ANXA1 | Inflammation, cancer | ANXA1 knockout mouse, knock-in of nucleotide-binding mutant |
| NME1 | Cancer metastasis | NME1 knockout cell line, overexpression |
Metabolic Disorders
Dysregulated purine nucleotide binding contributes to metabolic diseases such as obesity and diabetes [1,6]. In brown adipose tissue, impaired purine nucleotide binding to UCP1 leads to reduced thermogenesis and increased fat accumulation [6,8]. Cold-acclimated rats show increased purine nucleotide binding in brown fat mitochondria, linking this function to adaptive thermogenesis. These findings suggest that modulating purine nucleotide binding could be a therapeutic strategy for metabolic disorders.
Cancer
Purine nucleotide binding proteins, including small GTPases like KRAS and HRAS, are frequently mutated in cancers, leading to constitutive activation. These mutations often impair GTP hydrolysis, locking the proteins in a nucleotide-bound state that drives proliferation. Targeting purine nucleotide binding sites in oncogenic GTPases is an active area of drug discovery.
Cardiovascular Disease
Cyclic nucleotide signaling, mediated by purine nucleotide binding to guanylyl cyclases and cyclic nucleotide-gated channels, is critical for vascular tone and cardiac function. Altered cGMP binding and signaling are implicated in hypertension and heart failure. Annexins, which bind nucleotides, also play roles in cardiovascular biology.
From purine nucleotide binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of purine nucleotide binding affect thermogenesis? | UCP1 knockout mouse [6,8] |
| How do point mutations in the nucleotide binding site alter GTPase activity? | KRAS point mutation knock-in cell line |
| Can overexpression of a purine nucleotide binding protein rescue a phenotype? | Overexpression cell model |
| What is the subcellular localization of a tagged purine nucleotide binding protein? | Tagged knock-in cell line |
| Does a disease-associated mutation alter nucleotide binding affinity? | Point mutation knock-in mouse |
| Can CRISPR library screening identify novel purine nucleotide binding regulators? | Genome-wide CRISPR knockout library |
How to Study the purine nucleotide binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| X-ray crystallography | Atomic structure of protein-nucleotide complex | UCP1-ATP binding |
| Cryo-EM | Structure of large complexes | UCP1-GTP binding |
| Isothermal titration calorimetry | Binding affinity and thermodynamics | Purine nucleotide binding protein |
| Radioligand binding | Binding affinity and specificity | Low-molecular-mass purine-binding protein |
| Proton transport assay | Functional effect of nucleotide binding | UCP1 inhibition [6,8] |
| cAMP accumulation assay | Adenylyl cyclase activity | Nucleotidyl cyclase function |
| CRISPR knockout screen | Genes required for nucleotide binding | Novel regulator discovery |
| Western blot | Protein expression and phosphorylation | Annexin regulation |
Structural Biology
X-ray crystallography and cryo-EM have been used to determine the atomic structures of purine nucleotide binding proteins, such as UCP1 in complex with ATP or GTP [6,8]. These methods reveal the precise interactions between the nucleotide and the binding pocket, informing drug design.
Biochemical Binding Assays
Radioligand binding assays and isothermal titration calorimetry (ITC) measure the affinity and stoichiometry of purine nucleotide binding [2,3]. These techniques have been used to characterize the isolated purine nucleotide binding protein from brown fat mitochondria and low-molecular-mass purine-binding proteins.
Functional Assays
Proton transport assays in mitochondria or liposomes assess the functional consequences of purine nucleotide binding to UCP1 [6,8]. Cyclic AMP accumulation assays measure adenylyl cyclase activity upon nucleotide binding.
CRISPR Screening
Genome-wide CRISPR knockout screens can identify genes that regulate purine nucleotide binding and downstream signaling. This approach is powerful for discovering novel components of nucleotide-binding pathways.
How CRISPR Can Be Used to Study GO:0017076 purine nucleotide binding
Knockout
CRISPR knockout of genes encoding purine nucleotide binding proteins, such as UCP1 or KRAS, allows researchers to study loss-of-function phenotypes in cell models and mice [1,6]. For example, UCP1 knockout mice are used to investigate thermogenesis and metabolic regulation.
Point Mutation
Introducing point mutations in the nucleotide binding site of a protein can reveal the specific residues required for binding and function. For instance, mutating the catalytic glutamine of KRAS affects GTP binding and oncogenic signaling.
Knock-in
Knock-in of a tagged version of a purine nucleotide binding protein enables visualization and biochemical isolation of the protein in its native context. This approach is useful for studying localization and interaction partners.
Overexpression
Overexpression of a purine nucleotide binding protein can amplify signaling pathways and rescue loss-of-function phenotypes. This is commonly used to study adenylyl cyclases and their nucleotide binding properties.
How EDITGENE Supports purine nucleotide binding Research
Researchers studying purine nucleotide binding-related genes often need to determine whether a candidate gene is causally involved in a specific biological process or disease. EDITGENE provides comprehensive CRISPR-based services to accelerate this discovery.
Contact EDITGENE today to design your custom CRISPR model for purine nucleotide binding research.
Frequently Asked Questions About purine nucleotide binding
What is purine nucleotide binding?
Purine nucleotide binding (GO:0017076) is the molecular function of selectively binding purine nucleotides such as ATP, GTP, cAMP, and cGMP.
What genes are involved in purine nucleotide binding?
Genes include UCP1, ADCY1, GUCY1A1, ANXA1, NME1, KRAS, and many others encoding nucleotide-binding proteins [1,3,6,7].
What is the GO term for purine nucleotide binding?
The Gene Ontology term is GO:0017076, defined as binding to a purine nucleotide.
How does purine nucleotide binding regulate thermogenesis?
In brown adipose tissue, purine nucleotide binding to UCP1 inhibits proton leak, thereby reducing thermogenesis [6,8].
What diseases are associated with purine nucleotide binding?
Dysregulated purine nucleotide binding is linked to metabolic disorders, cancer, and cardiovascular disease [1,6].
What methods are used to study purine nucleotide binding?
Methods include X-ray crystallography, cryo-EM, isothermal titration calorimetry, radioligand binding, and functional assays [2,3,6,8].
Can CRISPR be used to study purine nucleotide binding?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are widely used to dissect the function of purine nucleotide binding proteins.
What is the role of UCP1 in purine nucleotide binding?
UCP1 binds purine nucleotides such as ATP and GTP, which inhibits its proton transport activity and regulates thermogenesis [6,8].
How are annexins involved in purine nucleotide binding?
Annexins are calcium-dependent membrane-binding proteins that also bind purine nucleotides, though their exact role is still under investigation.
What is the clinical relevance of purine nucleotide binding?
It is relevant for drug discovery targeting metabolic diseases and cancer, as many nucleotide-binding proteins are druggable [1,6].
Conclusion
Purine nucleotide binding (GO:0017076) is a fundamental molecular function that underpins energy metabolism, signal transduction, and thermogenesis [1,5]. Structural and functional studies have revealed the atomic details of how proteins like UCP1 and nucleotidyl cyclases recognize purine nucleotides [1,6,8]. Dysregulation of this binding is implicated in metabolic disorders, cancer, and cardiovascular disease [1,6]. CRISPR-based models offer powerful tools to dissect the causal roles of purine nucleotide binding proteins in health and disease. EDITGENE provides comprehensive services to support these investigations.
References
- 1. Dove S. 2017. Mammalian Nucleotidyl Cyclases and Their Nucleotide Binding Sites.. Handb Exp Pharmacol 238:49-66 PMID: 27900607
- 2. Lin CS et al.. 1982. Characteristics of the isolated purine nucleotide binding protein from brown fat mitochondria.. Biochemistry 21(12):2950-6 PMID: 7104305
- 3. Gilmour J et al.. 1997. Isolation, cloning and characterization of a low-molecular-mass purine nucleoside- and nucleotide-binding protein.. Biochem J 326 ( Pt 2)(Pt 2):471-7 PMID: 9291120
- 4. Desautels M et al.. 1978. Increased purine nucleotide binding, altered polypeptide composition, and thermogenesis in brown adipose tissue mitochondria of cold-acclimated rats.. Can J Biochem 56(6):378-83 PMID: 667688
- 5. Szmidt-Jaworska A. 2010. [Plant purine nucleotide cyclases].. Postepy Biochem 56(4):409-17 PMID: 21473045
- 6. Kang Y et al.. 2023. Structural basis for the binding of DNP and purine nucleotides onto UCP1.. Nature 620(7972):226-231 PMID: 37336486
- 7. Bandorowicz-Pikula J et al.. 2001. Annexins as nucleotide-binding proteins: facts and speculations.. Bioessays 23(2):170-8 PMID: 11169590
- 8. Jones SA et al.. 2023. Structural basis of purine nucleotide inhibition of human uncoupling protein 1.. Sci Adv 9(22):eadh4251 PMID: 37256948
