Deoxycytidine kinase

Last updated
DCK
Protein DCK PDB 1p5z.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases DCK , entrez:1633, deoxycytidine kinase
External IDs OMIM: 125450 MGI: 102726 HomoloGene: 616 GeneCards: DCK
Orthologs
SpeciesHumanMouse
Entrez

1633

13178

Ensembl

ENSG00000156136

ENSMUSG00000029366

UniProt

P27707

P43346

RefSeq (mRNA)

NM_000788

NM_007832

RefSeq (protein)

NP_000779

NP_031858

Location (UCSC) Chr 4: 70.99 – 71.03 Mb Chr 5: 88.91 – 88.93 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Deoxycytidine kinase (dCK) is an enzyme which is encoded by the DCK gene in humans. [5] dCK predominantly phosphorylates deoxycytidine (dC) and converts dC into deoxycytidine monophosphate. dCK catalyzes one of the initial steps in the nucleoside salvage pathway [6] and has the potential to phosphorylate other preformed nucleosides, specifically deoxyadenosine (dA) and deoxyguanosine (dG), and convert them into their monophosphate forms. [7] There has been recent biomedical research interest in investigating dCK's potential as a therapeutic target for different types of cancer. [6] [7] [8]

Structure

dCK homodimer with highlighted Glu53 DCK homodimer with highlighted Glu53.png
dCK homodimer with highlighted Glu53

dCK is a homodimer where each monomer subunit consists of multiple alpha helices surrounding a beta sheet core. [9] [7] [10] Each subunit includes a nucleotide donor binding site, nucleoside acceptor binding site, nucleotide base sensing loop (240-254 residues), insert region (12-15 residues) that connects helices 2 and 3. [9] [10] dCK has several different protein conformations but its conformation depends on the nucleoside or nucleotide it binds to. dCK can bind to ADP, ATP, UDP or UTP (phosphoryl group donors) but UDP/UTP binding changes the enzyme's conformation by rearranging the nucleotide base sensing loop as compared to the dCK's conformation when bound to ATP. This change in conformation when a specific phosphoryl donor is bound in the nucleotide binding site determines which nucleoside can bind in the nucleoside binding site. [9] [10] For example, it has been observed that when dCK binds to ADP, dCK takes on a "closed" conformation or more compact nucleoside binding site where glutamic acid 53 (Glu53) is brought into closer proximity to directly interact with the nucleoside's 5' hydroxyl group. [9] [10]

Function

Deoxycytidine kinase (dCK) phosphorylates several deoxyribonucleosides and their nucleoside analogues (a nucleoside with a sugar and a different nucleic acid base substitute or analogue that has unique properties when modified) using phosphate groups from ATP and UTP. [9] [10] More specifically, dCK adds the first phosphoryl group to preformed nucleosides and is usually the rate-limiting enzyme of the overall process of converting nucleosides to their deoxynucleoside triphosphate form, or nucleotide form, in the nucleoside salvage pathway. [10] Below is a simplified pathway that displays dCK's role in synthesizing nucleotides using the nucleoside salvage pathway. [8] [11]

dCK's Role in the Nucleoside Salvage Pathway Nucleoside Salvage Pathway.png
dCK's Role in the Nucleoside Salvage Pathway

Glu53 performs base catalysis to deprotonate the hydroxyl group, which allows the now nucleophilic oxygen from the nucleoside 5' hydroxyl group to attack the end of the phosphate chain (gamma phosphate) on the phosphoryl donor (e.g. ATP or UTP). This has deemed the "closed" conformation as the catalytically active conformation since it catalyzes the phosphoryl transfer between phosphoryl donors and receiving nucleosides. [9] Similarly, "open" conformation is generally referred to as the catalytically inactive form since Glu53 is not in close proximity to nucleoside 5' hydroxyl group and will not catalyze the phosphoryl transfer. [9]

Regulation

One method of to regulate both catalytic activity and substrate specificity is a post-translational modification on Serine 74, a residue in the insert region on each of the individual dCK subunits. [9] Although serine 74 is far from dCK's active site, phosphorylation of serine 74 (Ser74) on dCK causes a change in enzyme conformation and influences enzyme kinetics. More specifically, phosphorylation of Ser74 favors dCK to adopt its open (inactive) conformation and allow dCK to become more competent in binding and releasing nucleosides but restricts dCK from transferring phosphoryl groups. dCK's closed (active) conformation allows dCK to transfer phosphoryl groups, but not bind or release nucleosides. The "open" and "closed" states refer to the nucleoside binding site on dCK. [9]

Nucleotide biosynthesis

dCK is a key enzyme in the nucleoside salvage pathway (NSP). More specifically, this pathway recycles preformed nucleosides from degrading DNA molecules to synthesize dNTPs for the cell. The nucleoside salvage pathway can act as an alternative path to produce nucleotides (dNTP's) in case of de novo pathway downregulation. [6] That is, the salvage pathway (and thus dCK) is upregulated when the de novo pathway is downregulated or inhibited in order to compensate for the loss in nucleotide production. Both the de novo pathway (DNP) and the nucleoside salvage pathway (NSP) are anabolic pathways that produce deoxyribonucleotide triphosphates (dNTP's) or nucleotides, the monomers that make up DNA.

Therapeutic implications

Deficiency of dCK is associated with resistance to antiviral and anticancer chemotherapeutic agents. Conversely, increased deoxycytidine kinase activity is associated with increased activation of these agents to cytotoxic nucleoside triphosphate derivatives. dCK is clinically important because of its relationship to drug resistance and sensitivity. [5] Manipulating dCK's enzymatic activity has been shown to have a strong correlation in sensitizing cells to the effects of other drugs (e.g. RNR inhibitors, [6] gemcitabine) or treatments (e.g. ionizing radiation) [11] and so more combination therapies are currently been studied to reduce biological resistance mechanisms and drug tolerance in patients. [6] [11] [12]

For example, gemcitabine is a FDA-approved pyrimidine nucleoside analogue and a dCK activity based prodrug that has been used to treat pancreatic, breast, bladder and non-small cell lung cancer. [8] [11] Mechanistically, dCK, which uptakes preformed nucleosides, adds the first phosphoryl group on dFdC (gemcitabine's original form as a deoxycytidine analog) to convert it into dFdCMP, its monophosphate form. [8] [11] Cytidylate kinase or UMP-CMP kinase then adds the second phosphoryl group to form dFdCDP (gemcitabine diphosphate form), which can inhibit ribonucleotide reductase. Nucleoside-diphosphate kinase or nucleoside kinase A adds the third phosphoryl group to form dFdCTP (gemcitabine triphosphate form) which is gemcitabine's active form which inhibits both deoxycytidylate deaminase and DNA polymerase. [8] Although gemcitabine has widely used to treat solid tumors for over a decade, patients taking gemcitabine alone (monotherapy) have been observed to develop chemoresistance to the drug. [8] [11]

See also

Related Research Articles

<span class="mw-page-title-main">Kinase</span> Enzyme catalyzing transfer of phosphate groups onto specific substrates

In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule donates a phosphate group to the substrate molecule. This transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and ADP gains a phosphate group. These two processes, phosphorylation and dephosphorylation, occur four times during glycolysis.

<span class="mw-page-title-main">Adenosine monophosphate</span> Chemical compound

Adenosine monophosphate (AMP), also known as 5'-adenylic acid, is a nucleotide. AMP consists of a phosphate group, the sugar ribose, and the nucleobase adenine; it is an ester of phosphoric acid and the nucleoside adenosine. As a substituent it takes the form of the prefix adenylyl-.

<span class="mw-page-title-main">Phosphatase</span> Enzyme which catalyzes the removal of a phosphate group from a molecule

In biochemistry, a phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol. Because a phosphatase enzyme catalyzes the hydrolysis of its substrate, it is a subcategory of hydrolases. Phosphatase enzymes are essential to many biological functions, because phosphorylation and dephosphorylation serve diverse roles in cellular regulation and signaling. Whereas phosphatases remove phosphate groups from molecules, kinases catalyze the transfer of phosphate groups to molecules from ATP. Together, kinases and phosphatases direct a form of post-translational modification that is essential to the cell's regulatory network.

A salvage pathway is a pathway in which a biological product is produced from intermediates in the degradative pathway of its own or a similar substance. The term often refers to nucleotide salvage in particular, in which nucleotides are synthesized from intermediates in their degradative pathway.

<span class="mw-page-title-main">Adenylate kinase</span> Class of enzymes

Adenylate kinase is a phosphotransferase enzyme that catalyzes the interconversion of the various adenosine phosphates. By constantly monitoring phosphate nucleotide levels inside the cell, ADK plays an important role in cellular energy homeostasis.

<span class="mw-page-title-main">Gemcitabine</span> Chemical compound

Gemcitabine, with brand names including Gemzar, is a chemotherapy medication. It treats cancers including testicular cancer, breast cancer, ovarian cancer, non-small cell lung cancer, pancreatic cancer, and bladder cancer. It is administered by intravenous infusion. It acts against neoplastic growth, and it inhibits the replication of Orthohepevirus A, the causative agent of Hepatitis E, through upregulation of interferon signaling.

<span class="mw-page-title-main">Nucleoside-diphosphate kinase</span>

Nucleoside-diphosphate kinases are enzymes that catalyze the exchange of terminal phosphate between different nucleoside diphosphates (NDP) and triphosphates (NTP) in a reversible manner to produce nucleotide triphosphates. Many NDP serve as acceptor while NTP are donors of phosphate group. The general reaction via ping-pong mechanism is as follows: XDP + YTP ←→ XTP + YDP. NDPK activities maintain an equilibrium between the concentrations of different nucleoside triphosphates such as, for example, when guanosine triphosphate (GTP) produced in the citric acid (Krebs) cycle is converted to adenosine triphosphate (ATP). Other activities include cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor, endocytosis, and gene expression.

<span class="mw-page-title-main">Nucleoside analogue</span> Biochemical compound

Nucleoside analogues are nucleosides which contain a nucleic acid analogue and a sugar. Nucleotide analogs are nucleotides which contain a nucleic acid analogue, a sugar, and a phosphate group with one to three phosphates.

<span class="mw-page-title-main">Purine nucleoside phosphorylase</span> Enzyme

Purine nucleoside phosphorylase, PNP, PNPase or inosine phosphorylase is an enzyme that in humans is encoded by the NP gene. It catalyzes the chemical reaction

<span class="mw-page-title-main">Phosphoglycerate kinase</span> Enzyme

Phosphoglycerate kinase is an enzyme that catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate (1,3-BPG) to ADP producing 3-phosphoglycerate (3-PG) and ATP :

<span class="mw-page-title-main">Deoxyadenosine triphosphate</span> Chemical compound

Deoxyadenosine triphosphate (dATP) is a nucleotide used in cells for DNA synthesis, as a substrate of DNA polymerase. It is classified as a purine nucleoside triphosphate, with its chemical structure consisting of a deoxyribose sugar molecule bound to an adenine and to three phosphate groups. It differs from the energy-transferring molecule adenosine triphosphate (ATP) by a single hydroxyl group, resulting in a deoxyribose instead of a ribose. Two phosphate groups can be hydrolyzed to yield deoxyadenosine monophosphate, which can then be used to synthesize DNA.

<span class="mw-page-title-main">Deoxycytidine diphosphate</span> Chemical compound

Deoxycytidine diphosphate is a nucleoside diphosphate. It is related to the common nucleic acid CTP, or cytidine triphosphate, with the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose removed, and with one fewer phosphoryl group than CTP.

<span class="mw-page-title-main">CTP synthetase</span>

CTP synthase is an enzyme involved in pyrimidine biosynthesis that interconverts UTP and CTP.

<span class="mw-page-title-main">Phosphofructokinase</span> Enzyme in glycolysis

Phosphofructokinase (PFK) is a kinase enzyme that phosphorylates fructose 6-phosphate in glycolysis.

<span class="mw-page-title-main">Diphosphomevalonate decarboxylase</span>

Diphosphomevalonate decarboxylase (EC 4.1.1.33), most commonly referred to in scientific literature as mevalonate diphosphate decarboxylase, is an enzyme that catalyzes the chemical reaction

In enzymology, a nucleoside-phosphate kinase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">UCK2</span>

Uridine-cytidine kinase 2 (UCK2) is an enzyme that in humans is encoded by the UCK2 gene.

<span class="mw-page-title-main">CMPK</span> Protein-coding gene in the species Homo sapiens

UMP-CMP kinase is an enzyme that in humans is encoded by the CMPK1 gene.

<span class="mw-page-title-main">CTP synthase 1</span> Protein-coding gene in the species Homo sapiens

CTP synthase 1 is an enzyme that is encoded by the CTPS1 gene in humans. CTP synthase 1 is an enzyme in the de novo pyrimidine synthesis pathway that catalyses the conversion of uridine triphosphate (UTP) to cytidine triphosphate (CTP). CTP is a key building block for the production of DNA, RNA and some phospholipids.

Discovery and development of nucleoside and nucleotide reverse-transcriptase inhibitors began in the 1980s when the AIDS epidemic hit Western societies. NRTIs inhibit the reverse transcriptase (RT), an enzyme that controls the replication of the genetic material of the human immunodeficiency virus (HIV). The first NRTI was zidovudine, approved by the U.S. Food and Drug Administration (FDA) in 1987, which was the first step towards treatment of HIV. Six NRTI agents and one NtRTI have followed. The NRTIs and the NtRTI are analogues of endogenous 2´-deoxy-nucleoside and nucleotide. Drug-resistant viruses are an inevitable consequence of prolonged exposure of HIV-1 to anti-HIV drugs.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000156136 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000029366 - Ensembl, May 2017
  3. ↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. 1 2 "Entrez Gene: DCK deoxycytidine kinase".
  6. 1 2 3 4 5 Nathanson DA, Armijo AL, Tom M, Li Z, Dimitrova E, Austin WR, Nomme J, Campbell DO, Ta L, Le TM, Lee JT, Darvish R, Gordin A, Wei L, Liao HI, Wilks M, Martin C, Sadeghi S, Murphy JM, Boulos N, Phelps ME, Faull KF, Herschman HR, Jung ME, Czernin J, Lavie A, Radu CG (March 2014). "Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication". The Journal of Experimental Medicine. 211 (3): 473–86. doi:10.1084/jem.20131738. PMC   3949575 . PMID   24567448.
  7. 1 2 3 Sabini E, Ort S, Monnerjahn C, Konrad M, Lavie A (July 2003). "Structure of human dCK suggests strategies to improve anticancer and antiviral therapy". Nature Structural Biology. 10 (7): 513–9. doi:10.1038/nsb942. hdl: 11858/00-001M-0000-0012-F0B9-8 . PMID   12808445. S2CID   6212685.
  8. 1 2 3 4 5 6 de Sousa Cavalcante L, Monteiro G (October 2014). "Gemcitabine: metabolism and molecular mechanisms of action, sensitivity and chemoresistance in pancreatic cancer". European Journal of Pharmacology. 741: 8–16. doi:10.1016/j.ejphar.2014.07.041. PMID   25084222.
  9. 1 2 3 4 5 6 7 8 9 10 Hazra S, Szewczak A, Ort S, Konrad M, Lavie A (April 2011). "Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release". Biochemistry. 50 (14): 2870–80. doi:10.1021/bi2001032. PMC   3071448 . PMID   21351740.
  10. 1 2 3 4 5 6 Sabini E, Hazra S, Konrad M, Lavie A (July 2008). "Elucidation of Different Binding Modes of Purine Nucleosides to Human Deoxycytidine Kinase". Journal of Medicinal Chemistry. 51 (14): 4219–25. doi:10.1021/jm800134t. PMC   2636677 . PMID   18570408.
  11. 1 2 3 4 5 6 Grégoire V, Rosier JF, De Bast M, Bruniaux M, De Coster B, Octave-Prignot M, Scalliet P (June 2002). "Role of deoxycytidine kinase (dCK) activity in gemcitabine's radioenhancement in mice and human cell lines in vitro". Radiotherapy and Oncology. 63 (3): 329–38. doi:10.1016/s0167-8140(02)00106-8. PMID   12142097.
  12. ↑ Bozic I, Reiter JG, Allen B, Antal T, Chatterjee K, Shah P, Moon YS, Yaqubie A, Kelly N, Le DT, Lipson EJ, Chapman PB, Diaz LA, Vogelstein B, Nowak MA (June 2013). "Evolutionary dynamics of cancer in response to targeted combination therapy". eLife. 2: e00747. doi:10.7554/eLife.00747. PMC   3691570 . PMID   23805382.

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