GO:0047507 deoxynucleoside phosphate kinase activity, ATP as phosphate donor: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0047507 describes the molecular function of transferring the terminal phosphate of ATP to a 2'-deoxyribonucleoside 5'-monophosphate, yielding the corresponding 5'-diphosphate and ADP.
• This activity is the first committed step in the salvage pathway that recycles deoxynucleosides into DNA precursors, and it is essential for maintaining balanced dNTP pools.
• Enzymes with this activity include deoxyguanosine kinase, deoxycytidine kinase, thymidine kinase and related deoxynucleoside kinases, which show broad substrate tolerance and can use alternative phosphate donors such as UTP or polyphosphate in vitro.
• Kinetic and mutational studies have revealed that single amino-acid changes in deoxynucleoside kinases can alter phosphate-donor preference and cause mitochondrial DNA depletion syndromes.
• The activity is a validated drug target and biomarker axis: nucleoside analogues used in cancer and antiviral therapy are activated by these kinases, and serum thymidine kinase 1 is used as a diagnostic biomarker.
• CRISPR-based knockout, point-mutation, knock-in and overexpression models enable causal dissection of GO:0047507 in dNTP homeostasis, mitochondrial function and chemoresistance.
Description
GO:0047507, deoxynucleoside phosphate kinase activity, ATP as phosphate donor, is a molecular function defined in the Gene Ontology as the catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + ATP = a 2'-deoxyribonucleoside 5'-diphosphate + ADP. In practical terms, it is the phosphorylation step that converts a deoxynucleoside monophosphate into a deoxynucleoside diphosphate, using ATP as the phosphate donor. This reaction sits at the gateway of the deoxynucleoside salvage pathway, which allows cells to recycle deoxynucleosides derived from DNA turnover or from extracellular sources into the dNTP pool needed for DNA replication and repair. The activity is carried out by a family of deoxynucleoside kinases that differ in substrate specificity, subcellular localization and kinetic properties. For example, deoxyguanosine kinase from Bacillus subtilis and pig skin has been purified and characterized, and its ability to use UTP as an alternative phosphate donor has been documented. In human cells, deoxyguanosine kinase and deoxycytidine kinase are key enzymes for purine and pyrimidine salvage, respectively, and their dysfunction is linked to mitochondrial DNA depletion. Because dNTP pool imbalance is a hallmark of cancer, viral infection and mitochondrial disease, understanding GO:0047507 is central to both basic nucleotide metabolism and translational research. This article integrates the QuickGO definition with verified PubMed literature to describe the mechanism, key genes, disease links and experimental strategies for studying GO:0047507. It is intended for researchers who need a concise, citable overview of this molecular function and who wish to design CRISPR-based models to interrogate it.
deoxynucleoside phosphate kinase activity, ATP as phosphate donor At A Glance
| GO ID | GO:0047507 |
|---|---|
| GO term | deoxynucleoside phosphate kinase activity, ATP as phosphate donor |
| Ontology | molecular_function |
| Synonym | ATP:deoxynucleoside-phosphate phosphotransferase activity; deoxynucleoside-5'-monophosphate kinase activity; deoxynucleoside monophosphate kinase activity; deoxynucleoside-phosphate kinase activity; deoxyribonucleoside monophosphokinase activity |
| Major function | Phosphorylation of 2'-deoxyribonucleoside 5'-monophosphates to the corresponding 5'-diphosphates using ATP as the phosphate donor |
| Reaction | a 2'-deoxyribonucleoside 5'-phosphate + ATP = a 2'-deoxyribonucleoside 5'-diphosphate + ADP |
| Pathway context | Deoxynucleoside salvage and dNTP biosynthesis |
| Representative enzymes | Deoxyguanosine kinase, deoxycytidine kinase, thymidine kinase and related deoxynucleoside kinases |
| Alternative donors in vitro | UTP and inorganic tripolyphosphate can substitute for ATP in some enzyme preparations |
What Is GO:0047507?
GO:0047507 is the molecular function of catalyzing the transfer of a phosphate group from ATP to a 2'-deoxyribonucleoside 5'-monophosphate, producing a 2'-deoxyribonucleoside 5'-diphosphate and ADP. The term is defined by the reaction: a 2'-deoxyribonucleoside 5'-phosphate + ATP = a 2'-deoxyribonucleoside 5'-diphosphate + ADP. It is synonymous with ATP:deoxynucleoside-phosphate phosphotransferase activity, deoxynucleoside-5'-monophosphate kinase activity, deoxynucleoside monophosphate kinase activity, deoxynucleoside-phosphate kinase activity and deoxyribonucleoside monophosphokinase activity. The activity is a subset of nucleoside monophosphate kinase chemistry but is restricted to 2'-deoxyribonucleoside substrates and explicitly uses ATP as the phosphate donor in the GO definition.
Why Is deoxynucleoside phosphate kinase activity, ATP as phosphate donor Important in Cell Biology?
GO:0047507 is important because it controls the first committed step of deoxynucleoside salvage, a pathway that supplies DNA precursors when de novo synthesis is insufficient or when cells are under replication stress. The activity directly determines the balance of dNTP pools, and its perturbation causes mitochondrial DNA depletion, altered sensitivity to nucleoside analogue drugs and changes in cell proliferation. Because many anticancer and antiviral nucleoside analogues require phosphorylation by deoxynucleoside kinases to become active, the enzymes carrying GO:0047507 are both drug targets and determinants of drug response. In addition, serum thymidine kinase 1, an enzyme with related deoxynucleoside kinase activity, is used as a diagnostic biomarker in veterinary and human oncology, illustrating the translational value of this function.
• Provides the first phosphorylation step in deoxynucleoside salvage, feeding the dNTP pool for DNA replication and repair.
• Maintains mitochondrial dNTP pools; defects cause mitochondrial DNA depletion syndromes.
• Activates nucleoside analogue prodrugs used in cancer and antiviral therapy.
• Serves as a biomarker axis: thymidine kinase 1 serum levels reflect cell proliferation.
• Shows broad substrate tolerance and alternative phosphate-donor usage, which complicates inhibitor design.
• Is a target for CRISPR knockout and point-mutation studies to separate catalytic from non-catalytic functions.
• Links nucleotide metabolism to chemoresistance and to viral replication.
• Enables comparative enzymology across species, from bacteria to mammals.
• Supports metabolic engineering of ATP regeneration when coupled to polyphosphate kinases.
• Provides a tractable model for studying enzyme kinetics and allostery in nucleotide kinases.
Molecular Mechanism of deoxynucleoside phosphate kinase activity, ATP as phosphate donor
Substrate recognition and binding
In simple terms: The enzyme first grabs the deoxynucleoside monophosphate and ATP in its active site.
Deoxynucleoside kinases that carry GO:0047507 bind a 2'-deoxyribonucleoside 5'-monophosphate and ATP in a ternary complex. Purified deoxyguanosine kinase from Bacillus subtilis and pig skin shows strict preference for deoxyguanosine monophosphate as the phosphate acceptor, while ATP is the preferred donor under physiological conditions. The enzyme active site accommodates the deoxyribose moiety and the base, explaining why ribonucleoside monophosphates are poor substrates.
Phosphoryl transfer and product release
In simple terms: The terminal phosphate of ATP is moved onto the deoxynucleoside monophosphate, making a diphosphate and ADP.
The catalytic step follows an in-line phosphoryl-transfer mechanism in which the gamma-phosphate of ATP is transferred to the 5'-hydroxyl of the deoxynucleoside monophosphate, generating a 2'-deoxyribonucleoside 5'-diphosphate and ADP. Kinetic analyses of deoxyguanosine kinase show Michaelis-Menten behavior with respect to both substrates, and product inhibition by ADP can modulate flux through the reaction.
Alternative phosphate donors and donor plasticity
In simple terms: Some versions of the enzyme can use UTP or polyphosphate instead of ATP.
Although GO:0047507 specifies ATP as the phosphate donor, in vitro studies have shown that deoxyguanosine kinase from Bacillus subtilis prefers UTP over ATP, and human deoxyribonucleoside kinases can use inorganic tripolyphosphate as a phosphate donor. Polyphosphate kinases can also act as nucleoside diphosphate kinases, regenerating ATP from polyphosphate and AMP, which indirectly supports deoxynucleoside phosphorylation. This donor plasticity is relevant when designing assays and interpreting cellular data.
Kinetic regulation and mutational effects
In simple terms: Changes in the enzyme's sequence can change how fast it works and which donor it prefers.
Kinetic characterization of mutant deoxyguanosine kinase from a patient with reversible hepatic mitochondrial DNA depletion revealed altered substrate affinity and catalytic efficiency, providing a direct link between enzyme kinetics and disease. Similarly, partial purification and characterization of pig skin deoxyguanosine kinase established baseline kinetic parameters that can be compared across species and mutants. These studies show that single amino-acid substitutions can shift phosphate-donor preference and reaction velocity, which is central to understanding GO:0047507 in disease.
Cofactors and metal requirements
In simple terms: The reaction typically needs magnesium ions to help ATP transfer its phosphate.
Like most kinases, enzymes with GO:0047507 require divalent metal ions, typically Mg2+, to neutralize the negative charge of ATP and facilitate phosphoryl transfer. Purification and assay protocols for deoxyguanosine kinase and polynucleotide kinase include Mg2+ in reaction buffers, and removal of metal ions abolishes activity. This requirement is a practical consideration for in vitro kinase assays and for interpreting cellular effects of metal chelators.
Key Genes Involved in GO:0047507 deoxynucleoside phosphate kinase activity, ATP as phosphate donor
The following genes and proteins are experimentally linked to deoxynucleoside phosphate kinase activity with ATP as phosphate donor, based on the verified literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| DGUOK | Encodes deoxyguanosine kinase, a mitochondrial enzyme that phosphorylates deoxyguanosine and deoxyadenosine monophosphates | Mutations cause mitochondrial DNA depletion; kinetic studies link activity to disease |
| DCK | Encodes deoxycytidine kinase, which phosphorylates deoxycytidine and related analogues | Determines activation of nucleoside analogue drugs; target for chemoresistance studies |
| TK1 | Encodes thymidine kinase 1, a cytosolic enzyme that phosphorylates thymidine | Serum TK1 is a proliferation biomarker; relevant to cancer diagnostics |
| TK2 | Encodes thymidine kinase 2, a mitochondrial enzyme for pyrimidine salvage | Defects cause mtDNA depletion; model for GO:0047507 in mitochondria |
| yaaG | Bacillus subtilis gene encoding a deoxynucleoside kinase with deoxyguanosine kinase activity | Model for substrate specificity and UTP preference |
| yaaF | Bacillus subtilis gene encoding a deoxynucleoside kinase | Comparative enzymology of deoxynucleoside kinases |
| PPK | Polyphosphate kinase that can act as a nucleoside diphosphate kinase | Links polyphosphate metabolism to deoxynucleoside phosphorylation |
| ADK | Adenylate kinase involved in ATP regeneration from AMP | Supports coupled assays for deoxynucleoside kinase activity |
| PAP | Polyphosphate:AMP phosphotransferase | Enables ATP regeneration in vitro for kinase assays |
| PNK | Polynucleotide kinase with 5'-kinase activity | Purified from calf thymus; model for phosphate transfer chemistry |
| NDK | Nucleoside diphosphate kinase | Can interconvert deoxynucleoside diphosphates and triphosphates |
| DGUOK (pig) | Pig skin deoxyguanosine kinase | Classic purification and kinetic model for GO:0047507 |
| DGUOK (B. subtilis) | Bacterial deoxyguanosine kinase | Shows UTP as preferred donor, testing donor specificity |
| TK1 (feline) | Feline thymidine kinase 1 | Serum form evaluated as diagnostic biomarker |
| DCK (human) | Human deoxycytidine kinase | Activates cytarabine and other analogues |
| DGUOK (human) | Human deoxyguanosine kinase | Mutant forms studied in reversible hepatic mtDNA depletion |
| PNK (calf) | Calf thymus polynucleotide kinase | Biochemical model for phosphate transfer |
How Is deoxynucleoside phosphate kinase activity, ATP as phosphate donor Regulated?
The activity of enzymes carrying GO:0047507 is regulated at multiple levels. Transcriptional control of deoxynucleoside kinase genes responds to cell-cycle and proliferation signals, and serum thymidine kinase 1 levels reflect this regulation in vivo. Post-translational modifications and allosteric feedback by dNTP products can modulate catalytic efficiency; for example, ADP product inhibition has been observed for deoxyguanosine kinase. Substrate availability, including the balance between de novo synthesis and salvage, also determines flux through the reaction. In mitochondria, the import and assembly of deoxyguanosine kinase and thymidine kinase 2 are regulated by mitochondrial protein quality control, and mutations that impair folding lead to loss of activity. Finally, alternative phosphate donors such as polyphosphate can bypass ATP-dependent regulation in vitro, indicating that donor availability is an additional regulatory layer.
deoxynucleoside phosphate kinase activity, ATP as phosphate donor and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| DGUOK | Mitochondrial DNA depletion syndrome with liver failure | Knockout and point-mutation knock-in in hepatocyte-like cells |
| DCK | Nucleoside analogue resistance in leukemia | CRISPR knockout in leukemia cell lines followed by drug sensitivity assays |
| TK1 | Cancer proliferation biomarker | Overexpression and tagged knock-in for serum secretion studies |
| TK2 | Mitochondrial DNA depletion myopathy | Knockout in myotubes and rescue with wild-type or mutant cDNA |
| PPK/ADK | ATP regeneration and metabolic engineering | Bacterial knockout and overexpression for coupled kinase assays |
Mitochondrial DNA depletion syndromes
Biallelic mutations in DGUOK, which encodes a deoxyguanosine kinase with GO:0047507 activity, cause mitochondrial DNA depletion syndromes characterized by liver failure and neurological symptoms. Kinetic analysis of a mutant deoxyguanosine kinase from a patient with reversible hepatic mtDNA depletion showed altered substrate affinity and catalytic efficiency, directly linking the enzyme's phosphorylation activity to disease severity. This makes GO:0047507 a functional readout for variant interpretation in mitochondrial disease.
Cancer and nucleoside analogue therapy
Deoxynucleoside kinases that carry GO:0047507 activate nucleoside analogue prodrugs such as cytarabine and gemcitabine, which are used in leukemia and solid tumors. Resistance to these drugs often involves loss or mutation of the activating kinase, and thymidine kinase 1 serum levels are used as a proliferation biomarker in cancer. Thus, the activity defined by GO:0047507 is both a therapeutic dependency and a pharmacodynamic marker.
Viral infections and antiviral targeting
Many antiviral nucleoside analogues require phosphorylation by host deoxynucleoside kinases to become active. The same GO:0047507 chemistry is exploited by viruses and by host enzymes, and differences in phosphate-donor preference between viral and host kinases can be targeted for selectivity. Understanding donor specificity is therefore relevant to antiviral drug design.
From deoxynucleoside phosphate kinase activity, ATP as phosphate donor-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of DGUOK alter mitochondrial dNTP pools? | CRISPR knockout of DGUOK in human cell lines followed by dNTP quantification |
| Which residues determine ATP versus UTP preference? | Point-mutation knock-in of candidate residues in DGUOK or bacterial yaaG |
| Can a disease-associated mutation be rescued by wild-type cDNA? | Knock-in of mutant DGUOK plus overexpression of wild-type DGUOK |
| How does thymidine kinase 1 secretion respond to proliferation signals? | Tagged knock-in of TK1 with a secreted reporter |
| Can polyphosphate replace ATP in cellular salvage? | Overexpression of polyphosphate kinase with knockout of endogenous ATP-dependent kinases |
| What is the substrate range of a deoxynucleoside kinase? | Overexpression and purification of wild-type and mutant enzymes for kinetic assays |
How to Study the deoxynucleoside phosphate kinase activity, ATP as phosphate donor Process
| Method | What It Measures | Typical Application |
|---|---|---|
| HPLC-based kinase assay | Conversion of deoxynucleoside monophosphate to diphosphate | Enzyme kinetics and inhibitor testing |
| Coupled ATP regeneration assay | ATP-dependent phosphorylation in real time | High-throughput screening |
| dNTP pool quantification | Cellular deoxynucleoside triphosphate levels | Knockout phenotyping |
| Mitochondrial DNA copy number qPCR | mtDNA depletion | Disease modeling |
| Serum TK1 immunoassay | Thymidine kinase 1 protein levels | Cancer biomarker studies |
| CRISPR knockout screening | Gene essentiality and drug response | Target discovery |
| Site-directed mutagenesis | Effect of single amino-acid changes | Structure-function analysis |
| Protein purification and enzymology | Specific activity and substrate specificity | Comparative enzymology |
Enzymatic kinase assays
Direct measurement of GO:0047507 uses purified enzyme, a deoxynucleoside monophosphate acceptor and ATP as donor, with product detection by HPLC or coupled NADH oxidation. Purification protocols for deoxyguanosine kinase and polynucleotide kinase provide templates for assay development. Coupled ATP regeneration systems using polyphosphate kinase and adenylate kinase can maintain constant ATP levels during kinetic runs.
Kinetic characterization and mutant analysis
Determination of Km, Vmax and catalytic efficiency for wild-type and mutant enzymes reveals how sequence changes affect phosphate-donor preference and substrate turnover. This approach was used to characterize mutant deoxyguanosine kinase from a patient with reversible hepatic mtDNA depletion. Comparative kinetics across species, such as Bacillus subtilis and pig skin enzymes, helps define conserved and divergent features.
CRISPR-based functional genomics
Knockout, point-mutation and knock-in models allow causal testing of GO:0047507 in cells. For example, knockout of DGUOK can be combined with dNTP measurements and mitochondrial DNA quantification to link enzyme activity to mtDNA maintenance. Overexpression of wild-type or mutant kinases can rescue or exacerbate phenotypes, and tagged knock-in enables localization and interaction studies.
Biomarker and translational assays
Serum thymidine kinase 1 is measured by immunoassays as a proliferation biomarker, providing a non-invasive readout of deoxynucleoside kinase activity in vivo. Such assays can be paired with CRISPR models to validate whether specific kinase isoforms contribute to serum signal.
How CRISPR Can Be Used to Study GO:0047507 deoxynucleoside phosphate kinase activity, ATP as phosphate donor
Knockout
CRISPR knockout of DGUOK, DCK or TK1 creates cell models to test how loss of GO:0047507 affects dNTP pools, mitochondrial DNA maintenance and drug sensitivity. For example, DGUOK knockout cells can be used to measure mtDNA copy number and to test rescue by wild-type or mutant cDNA. Knockout of DCK in leukemia cells can reveal resistance mechanisms to nucleoside analogues.
Point Mutation
Point-mutation knock-in of disease-associated variants, such as those found in DGUOK, allows precise testing of how single amino-acid changes alter kinase activity and phosphate-donor preference. This approach was validated by kinetic characterization of a mutant deoxyguanosine kinase from a patient with reversible hepatic mtDNA depletion. Point mutations can also be introduced into bacterial yaaG to dissect donor specificity.
Knock-in
Knock-in of tagged or reporter versions of deoxynucleoside kinases enables localization, interaction and secretion studies. For instance, a tagged TK1 knock-in can be used to monitor serum secretion and proliferation-dependent expression. Knock-in of wild-type DGUOK into mutant backgrounds can rescue mitochondrial phenotypes and confirm causality.
Overexpression
Overexpression of wild-type or mutant deoxynucleoside kinases provides a gain-of-function system to study substrate range, drug activation and dNTP pool expansion. Overexpression of polyphosphate kinase can also test whether alternative phosphate donors can support deoxynucleoside phosphorylation in cells. Such models are useful for biochemical purification and kinetic analysis.
How EDITGENE Supports deoxynucleoside phosphate kinase activity, ATP as phosphate donor Research
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Frequently Asked Questions About deoxynucleoside phosphate kinase activity, ATP as phosphate donor
What is deoxynucleoside phosphate kinase activity, ATP as phosphate donor?
It is the molecular function defined by GO:0047507, in which ATP donates a phosphate to a 2'-deoxyribonucleoside 5'-monophosphate to form the corresponding 5'-diphosphate and ADP.
What genes are involved in deoxynucleoside phosphate kinase activity, ATP as phosphate donor?
Key genes include DGUOK, DCK, TK1 and TK2 in humans, and yaaG and yaaF in Bacillus subtilis, all of which encode deoxynucleoside kinases with this activity.
Which enzyme uses ATP as phosphate donor for deoxynucleoside monophosphates?
Deoxyguanosine kinase, deoxycytidine kinase and thymidine kinase 1 are examples that use ATP as the phosphate donor under physiological conditions.
What is the reaction catalyzed by GO:0047507?
The reaction is: a 2'-deoxyribonucleoside 5'-phosphate + ATP = a 2'-deoxyribonucleoside 5'-diphosphate + ADP.
Can deoxynucleoside kinases use UTP instead of ATP?
Yes, in vitro studies show that Bacillus subtilis deoxyguanosine kinase prefers UTP, and human deoxyribonucleoside kinases can use inorganic tripolyphosphate as a donor.
How is deoxynucleoside phosphate kinase activity linked to mitochondrial DNA depletion?
Mutations in DGUOK that reduce kinase activity cause mitochondrial DNA depletion syndromes, as shown by kinetic analysis of patient-derived mutant enzyme.
Why is thymidine kinase 1 used as a cancer biomarker?
Serum thymidine kinase 1 reflects cell proliferation and has been evaluated as a diagnostic biomarker in feline and human oncology.
What experimental models are used to study GO:0047507?
CRISPR knockout, point-mutation knock-in, tagged knock-in and overexpression cell models are used, combined with enzymatic assays and dNTP measurements.
How can I measure deoxynucleoside phosphate kinase activity in the lab?
Purified enzyme assays with HPLC detection, coupled ATP regeneration systems and dNTP pool quantification are standard approaches.
Does polyphosphate kinase contribute to deoxynucleoside phosphorylation?
Polyphosphate kinase can act as a nucleoside diphosphate kinase and can regenerate ATP from polyphosphate and AMP, indirectly supporting deoxynucleoside phosphorylation.
Conclusion
GO:0047507, deoxynucleoside phosphate kinase activity with ATP as phosphate donor, is a central molecular function in deoxynucleoside salvage and dNTP homeostasis. Its enzymes, including deoxyguanosine kinase, deoxycytidine kinase and thymidine kinase 1, are linked to mitochondrial DNA depletion syndromes, cancer drug response and proliferation biomarkers. Understanding their kinetics, substrate specificity and regulation provides a foundation for therapeutic targeting and biomarker development. CRISPR-based knockout, point-mutation, knock-in and overexpression models are powerful tools to dissect the causal roles of these enzymes in health and disease. By combining precise genome editing with enzymatic and metabolic readouts, researchers can translate GO:0047507 biology into new diagnostic and therapeutic strategies.
References
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- 2. Kuroda A et al.. 1997. Polyphosphate kinase as a nucleoside diphosphate kinase in Escherichia coli and Pseudomonas aeruginosa.. Proc Natl Acad Sci U S A 94(2):439-42 PMID: 9012801
- 3. Krawiec K et al.. 2003. Inorganic tripolyphosphate (PPP(i)) as a phosphate donor for human deoxyribonucleoside kinases.. Biochem Biophys Res Commun 301(1):192-7 PMID: 12535661
- 4. Mousson de Camaret B et al.. 2007. Kinetic properties of mutant deoxyguanosine kinase in a case of reversible hepatic mtDNA depletion.. Biochem J 402(2):377-85 PMID: 17073823
- 5. Wang L et al.. 2021. Feline thymidine kinase 1: molecular characterization and evaluation of its serum form as a diagnostic biomarker.. BMC Vet Res 17(1):316 PMID: 34579716
- 6. Resnick SM et al.. 2000. In vitro ATP regeneration from polyphosphate and AMP by polyphosphate:AMP phosphotransferase and adenylate kinase from Acinetobacter johnsonii 210A.. Appl Environ Microbiol 66(5):2045-51 PMID: 10788379
- 7. Green FJ et al.. 1979. Partial purification and characterization of deoxyguanosine kinase from pig skin.. Biochem J 183(3):547-53 PMID: 231969
- 8. Austin GE et al.. 1978. Purification and properties of polynucleotide kinase of calf thymus.. Biochim Biophys Acta 522(2):412-22 PMID: 23843
