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Cytidine monophosphate

Cytidine monophosphate (CMP), also known as 5'-cytidylic acid, is a ribonucleotide consisting of the pyrimidine nucleobase cytosine attached to a ribose sugar via a β-N1-glycosidic bond, with a phosphate group esterified at the 5' position of the ribose.^[1] Its chemical formula is C₉H₁₄N₃O₈P, and it has a molecular weight of 323.2 g/mol.^[1] CMP serves as a fundamental building block in the synthesis of RNA, where it is incorporated as one of the four canonical nucleotides alongside adenosine monophosphate (AMP), guanosine monophosphate (GMP), and uridine monophosphate (UMP).^[2] In nucleotide metabolism, CMP is synthesized primarily through the de novo pyrimidine biosynthesis pathway, involving the conversion of uridine triphosphate (UTP) to cytidine triphosphate (CTP) by CTP synthase, followed by stepwise dephosphorylation to CMP.^[2] It can also be generated via salvage pathways, such as the phosphorylation of cytidine to CMP by uridine-cytidine kinase.^[3] CMP itself is more commonly derived from higher phosphates.^[2] Biochemically, CMP functions as a precursor for the production of higher-energy nucleotides like CDP and CTP, which are essential for nucleic acid synthesis, phospholipid biosynthesis, and energy transfer processes.^[4] The enzyme UMP/CMP kinase catalyzes the phosphorylation of CMP to CDP using ATP as the phosphate donor, with reported kinetic parameters including a Km for CMP of 0.028 mM and a kcat of 91.9 s⁻¹ in bacterial systems.^[4] Deoxy forms, such as dCMP, arise from CDP via ribonucleotide reductase and support DNA replication.^[2] Beyond its core metabolic roles, CMP has been studied for potential therapeutic applications, including its administration alongside uridine monophosphate (UMP) to improve exercise performance in animal models by facilitating glucose uptake into muscles and preserving hepatic glycogen stores.^[5] It is naturally present in biological fluids such as saliva and feces, and has been detected in studies of conditions like colorectal cancer and neurodegenerative diseases including Alzheimer's.^[1]

Definition and Properties

Nomenclature and Formula

Cytidine monophosphate (CMP) is a ribonucleotide composed of the pyrimidine base cytosine linked to a ribose sugar through a β-N1-glycosidic bond, with a phosphate group attached via esterification at the 5' position of the ribose.^[1] This structure positions CMP as a key building block for RNA, where it serves as one of the four canonical monomers alongside adenosine monophosphate (AMP), guanosine monophosphate (GMP), and uridine monophosphate (UMP).^[6] The compound is commonly referred to as cytidylic acid, cytidine 5'-monophosphate (CMP), or 5'-CMP, reflecting its role as the 5'-phosphorylated derivative of cytidine.^[7] Its systematic IUPAC name is (2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-ylmethyl dihydrogen phosphate, which precisely describes the stereochemistry and atomic connectivity of the molecule.^[7] The molecular formula of cytidine monophosphate is C₉H₁₄N₃O₈P, with a molar mass of 323.198 g/mol.^[1] Historically, it has been termed cytidylic acid in early biochemical literature to denote the phosphoric acid ester of cytidine, a naming convention that parallels other nucleotides like adenylic acid; this distinguishes it from deoxycytidine monophosphate (dCMP), which features a deoxyribose sugar instead of ribose and functions primarily in DNA.^[6]

Physical and Chemical Properties

Cytidine monophosphate (CMP) appears as a white crystalline powder.^[8] It exhibits high solubility in water, approximately 100 mg/mL at 20°C, forming clear solutions, while it is sparingly soluble in ethanol and other organic solvents.^[9]^[10] The pKa values of CMP are 0.8 for the first dissociation of the phosphate group, 4.5 for protonation at the N3 position of the cytosine base, and 6.3 for the second dissociation of the phosphate group.^[11] These pKa values influence its ionization state at physiological pH, where the phosphate is predominantly dianionic.^[11] CMP displays ultraviolet absorption with a maximum at 271 nm and a molar extinction coefficient (ε) of 8,740 M⁻¹ cm⁻¹ at neutral pH.^[12] The compound is stable in neutral aqueous solutions but undergoes hydrolysis under acidic or alkaline conditions, leading to cleavage of the phosphate ester or glycosidic bonds. It is also sensitive to enzymatic degradation by phosphatases that target the phosphate group.^[13] In terms of chemical reactivity, the phosphate group of CMP serves as a leaving group in phosphorylation reactions catalyzed by kinases, facilitating the transfer to form diphosphates.^[13] Additionally, the cytosine base is susceptible to hydrolytic deamination, converting it to uracil under certain conditions.^[14]

Structure

Molecular Components

Cytidine monophosphate (CMP) consists of three primary molecular components: the nucleobase cytosine, the pentose sugar ribose, and a single phosphate group, which are covalently linked to form the ribonucleotide structure. The nucleobase is cytosine, a pyrimidine ring derivative described as 4-aminopyrimidin-2(1H)-one, featuring an exocyclic amino group at the C4 position and a keto group at the C2 position. This nucleobase connects to the sugar moiety through an N-glycosidic bond, specifically between the nitrogen at position N1 of cytosine and the anomeric carbon C1' of ribose.^[15] The sugar component is β-D-ribofuranose, the five-membered furanose ring form of D-ribose, which includes hydroxyl groups at the 2', 3', and 5' positions. The 2' and 3' hydroxyls are particularly important, as they participate in phosphodiester linkages that form the RNA backbone. In contrast to deoxycytidine monophosphate (dCMP), which uses 2-deoxyribose lacking the 2'-OH group, CMP retains this hydroxyl substituent, distinguishing it as a ribonucleotide.^[16] The phosphate is a monophosphate group (–OPO₃H₂), attached via a phosphoester bond to the 5'-CH₂OH of the ribose, forming a 5'-ester linkage. At physiological pH (approximately 7.4), the phosphate exists predominantly in its dianionic ionization state (–OPO₃²⁻), due to the pKa values of the phosphate group (pKa₁ ≈ 0.9, pKa₂ ≈ 6.3).^[17] These components assemble into CMP through the specified N-glycosidic and 5'-phosphoester bonds, yielding the canonical ribonucleotide with the formula C₉H₁₄N₃O₈P.^[7]

Stereochemistry and Conformation

Cytidine monophosphate (CMP) exhibits chirality primarily through its ribose sugar moiety, which contains four chiral centers at the C1', C2', C3', and C4' positions, configured as β-D-ribofuranose with absolute stereochemistry (2R,3S,4R,5R).^[18] This β-D configuration positions the cytosine base above the plane of the furanose ring on the β-face at the anomeric C1', while the hydroxyl groups at C2' and C3' are cis-oriented, essential for the molecule's incorporation into RNA structures.^[7] The phosphate group attached to the C5' methylene is achiral, consisting of a dihydrogen phosphate ester that does not introduce additional stereocenters.^[18] The cytosine base in CMP predominantly exists in the amino-keto tautomeric form (4-amino-2(1H)-pyrimidinone), which is stabilized by intramolecular hydrogen bonding and is the form observed in most biological contexts.^[19] The rare imino-enol tautomer (4-imino-2-hydroxypyrimidine) occurs at low populations, estimated at less than 0.1% in neutral aqueous solution, but can influence base pairing fidelity when transiently populated.^[19] In protonated states, such as at low pH, keto-iminol tautomerism becomes more accessible, with the C⁺-iminol form detectable via spectroscopic methods and implicated in altered base recognition.^[20] Conformational preferences of CMP are dominated by the glycosidic torsion angle (χ, defined as O4'-C1'-N1-C6), which favors the anti range (χ ≈ -120° to -180°) in aqueous solution and crystalline states, positioning the base away from the sugar for optimal stacking in nucleic acids.^[21] The syn conformation (χ ≈ 0° to 60°) is energetically disfavored but can appear under specific conditions like protonation. The ribose sugar adopts a C3'-endo pucker (North conformation) as the predominant form in solution, characterized by pseudorotation phase angle P ≈ 0°-36°, which shortens the C1'-C4' distance and aligns with A-form RNA helices.^[22] In contrast, C2'-endo (South) puckering is minor in ribonucleotides like CMP but more common in deoxy forms. The phosphate backbone exhibits flexibility around the P-O5'-C5'-C4' torsion (γ), allowing gauche⁺ (≈60°) and trans (≈180°) rotamers, with gauche preferred to minimize steric clashes.^[23] Nuclear magnetic resonance (NMR) studies in aqueous solution reveal dynamic ensembles where CMP maintains an average anti/C3'-endo conformation, with coupling constants (³J_{H1'-H2'} ≈ 5-6 Hz and ³J_{H2'-H3'} ≈ 5 Hz) consistent with a conformational equilibrium between North and South puckers.^[24] Space-filling models derived from crystal structures (e.g., PDB entries with CMP ligands) depict a compact overall shape, approximately 10 Å in length, with the extended cytosine base (planar and aromatic) stacked perpendicular to the ribofuranose ring and the pendant phosphate projecting outward for ionic interactions.^[18] Environmental factors modulate CMP conformation; at low pH (below 4), protonation of the N3 site in cytosine shifts the glycosidic torsion toward syn (χ ≈ 0°-90°), as evidenced by UV resonance Raman spectroscopy, potentially disrupting base pairing.^[20] Solvent polarity influences sugar puckering, with polar protic solvents like water stabilizing the C3'-endo form through hydrogen bonding to the 2'-OH, while nonpolar environments may favor C2'-endo.^[23] These shifts underscore the role of cellular conditions in fine-tuning CMP's structural adaptability for RNA helix formation.

Biosynthesis

De Novo Pathway

The de novo biosynthesis of cytidine monophosphate (CMP) occurs as part of the pyrimidine nucleotide synthesis pathway, which assembles the pyrimidine ring from simple precursors such as aspartate, glutamine, bicarbonate, and 5-phosphoribosyl-1-pyrophosphate (PRPP), ultimately yielding uridine monophosphate (UMP) as the first committed nucleotide product.^[25] UMP is then converted to CMP through sequential phosphorylation to uridine triphosphate (UTP) and amination to cytidine triphosphate (CTP), followed by dephosphorylation.^[25] This pathway ensures the cell's supply of pyrimidines for nucleic acid synthesis without relying on preformed bases or nucleosides.^[26] The core steps leading to UMP are catalyzed by a series of enzymes, beginning with the multifunctional CAD complex—a hexameric protein comprising carbamoyl-phosphate synthetase II (CPSII), aspartate transcarbamoylase (ATCase), and dihydroorotase (DHOase).^[25] CPSII condenses glutamine, bicarbonate, and two ATP molecules to form carbamoyl phosphate; ATCase then transfers the carbamoyl moiety to aspartate, yielding N-carbamoyl-L-aspartate; and DHOase cyclizes this intermediate to L-dihydroorotate.^[25] Dihydroorotate is oxidized to orotate by the flavin-dependent dihydroorotate dehydrogenase (DHODH), an enzyme anchored to the inner mitochondrial membrane in eukaryotes.^[25] Orotate subsequently combines with PRPP via orotate phosphoribosyltransferase (OPRT) to produce orotidine 5'-monophosphate (OMP), which is decarboxylated by OMP decarboxylase (ODCase) to generate UMP; OPRT and ODCase form a bifunctional UMP synthase in mammals.^[25] Conversion of UMP to CMP proceeds through kinase-mediated phosphorylations: UMP is first converted to UDP by UMP/CMP kinase, then to UTP by nucleoside diphosphate kinase using ATP.^[25] CTP synthetase then catalyzes the ATP- and glutamine-dependent amination of UTP at the C4 position of the uracil ring, producing CTP as the direct precursor to CMP.^[25] CTP is dephosphorylated in two steps—first to CDP by nucleoside triphosphate pyrophosphohydrolase (e.g., apyrase-like enzymes) and then to CMP by nonspecific phosphatases—to maintain nucleotide pools for various cellular needs. Regulation of the de novo pathway occurs primarily at CPSII within the CAD complex, where CTP exerts allosteric feedback inhibition to prevent overproduction of pyrimidines, while PRPP acts as an activator.^[27] Additional control involves phosphorylation of CAD by kinases such as protein kinase A and MAPK, enhancing activity during cell proliferation.^[25] In eukaryotes, the pathway is mostly cytosolic, with CAD and UMP synthase in the cytoplasm and nucleus (the latter during S phase), except for the mitochondrial localization of DHODH, which links pyrimidine synthesis to cellular respiration.^[25]

Salvage Pathway

The salvage pathway for cytidine monophosphate (CMP) enables the recycling of pre-existing pyrimidine nucleosides and bases into nucleotides, circumventing the more energy-demanding de novo biosynthesis route. This process is particularly vital in tissues exhibiting high rates of nucleotide turnover, such as the liver and intestine, where it supports efficient maintenance of cellular nucleotide pools for RNA synthesis and other metabolic needs. By reutilizing components from degraded nucleic acids or external sources, the pathway conserves phosphoribosyl pyrophosphate (PRPP) and ATP, providing a rapid response to fluctuating demands when de novo activity is insufficient.^[25] The primary route in this pathway converts cytidine directly to CMP through phosphorylation. The enzyme uridine-cytidine kinase 2 (UCK2), often the rate-limiting step, catalyzes the reaction: cytidine + ATP → CMP + ADP, with UCK1 providing complementary activity.^[28] UCK2, a homotetrameric enzyme, achieves specificity via hydrogen bonding interactions at residues His117 and Tyr112 with cytidine's 4-amino group, while a magnesium cofactor facilitates phosphate transfer.^[29] Substrates like cytidine originate from dietary intake, RNA turnover within cells, or contributions from gut microbial flora, entering cells via nucleoside transporters such as hENT1 and hENT2. Direct salvage from the pyrimidine base cytosine is not significant in mammals, as mammalian tissues lack cytosine phosphoribosyltransferase and cytosine deaminase activities. In contrast, such base salvage routes are more prominent in certain microorganisms. Instead, any cytosine would require conversion via other pathways, but pyrimidine salvage in mammals primarily occurs at the nucleoside level.^[30]^[31] Regulation of the pathway occurs primarily at the level of UCK enzyme stability and activity, with UCK2 expression and half-life modulated by mTORC1 signaling to match cellular growth states.^[32] Feedback inhibition by downstream products like cytidine triphosphate (CTP) and uridine triphosphate (UTP) prevents overaccumulation, while the pathway activates under conditions of low de novo flux. Notably, UCK2 exhibits broader substrate tolerance, also phosphorylating deoxycytidine and deoxyuridine to their monophosphates, aiding deoxyribonucleotide salvage. Evolutionarily, this pathway confers an energy-conserving advantage by recycling abundant nucleosides, reducing reliance on glutamine- and aspartate-intensive de novo steps, which is especially beneficial in nutrient-limited environments. Defects in salvage enzymes, such as UCK2 mutations or inhibition, result in intermediate accumulation, replication stress, and heightened sensitivity to nucleoside analogs in clinical contexts like cancer therapy. When salvage substrates are scarce, cells may integrate this route with de novo synthesis for balanced CMP production.

Metabolism

Anabolic Pathways

Cytidine monophosphate (CMP) functions as a key precursor in anabolic pathways, where it undergoes sequential phosphorylation to generate cytidine diphosphate (CDP) and cytidine triphosphate (CTP), providing high-energy nucleotides for nucleic acid synthesis, lipid membrane formation, and glycosylation processes.^[33] These activation steps occur primarily through salvage mechanisms, utilizing ATP as the phosphate donor to elevate the energy state of the nucleotide for downstream biosynthetic incorporation. The first phosphorylation step converts CMP to CDP and is catalyzed by cytidylate kinase (EC 2.7.4.14), with two distinct isoforms in human cells: the cytosolic UMP/CMP kinase 1 (CMPK1) and the mitochondrial UMP/CMP kinase 2 (CMPK2). CMPK1, a bifunctional enzyme, efficiently transfers the γ-phosphate from ATP to CMP (or UMP) in the reaction CMP + ATP → CDP + ADP, supporting general pyrimidine nucleotide pools in the cytoplasm and nucleus.^[34] CMPK2 performs an analogous reaction in the mitochondrial matrix, CMP + ATP → CDP + ADP, but is specialized for local nucleotide supply within mitochondria.^[35] Subsequent conversion of CDP to CTP is mediated by nucleoside diphosphate kinases (NDPKs), a family of enzymes encoded by the NME genes (NME1–NME9 in humans), which catalyze the reversible phosphotransfer CDP + ATP ⇌ CTP + ADP. These hexameric proteins exhibit broad substrate specificity, preferentially phosphorylating CDP among pyrimidine diphosphates, and are essential for equilibrating nucleoside triphosphate pools across cellular compartments. CMPK2 holds particular significance in mitochondrial anabolic processes, where it sustains CDP levels for deoxynucleotide triphosphate (dNTP) synthesis required for mitochondrial DNA (mtDNA) replication and repair, thereby maintaining mitochondrial genome stability and oxidative phosphorylation efficiency.^[37] Dysregulation of CMPK2 leads to mtDNA depletion and elevated reactive oxygen species, underscoring its role in mitochondrial homeostasis.^[38] Additionally, CMPK2 contributes to antiviral defense by bolstering nucleotide availability that restricts viral replication, independent of or in concert with interferon signaling.^[37] Regulation of these anabolic steps emphasizes transcriptional control, particularly for CMPK2, which is induced as an interferon-stimulated gene (ISG) through the JAK-STAT pathway in response to type I interferons, enhancing its expression during innate immune activation against pathogens like dengue virus and coronaviruses.^[37]^[39] CMPK1 operates more constitutively to meet basal demands, with overall pathway flux influenced by cellular ATP availability and nucleotide pool balances rather than direct allosteric feedback from CTP on the kinases themselves.^[33] The anabolic progression from CMP remains largely confined to the cytidine nucleotide lineage, with minimal direct interconversion to uridine counterparts like UDP at the monophosphate stage.^[35]

Catabolic Pathways

The catabolism of cytidine monophosphate (CMP) involves a series of enzymatic reactions that dismantle the nucleotide to its base, sugar, and phosphate components, preventing cellular accumulation and enabling recycling through salvage pathways to maintain purine and pyrimidine nucleotide balance.^[40] This process begins in the cytosol and proceeds through dephosphorylation followed by deglycosylation and base degradation, with products such as uracil and ribose-1-phosphate feeding back into salvage mechanisms for reuse.^[41] The initial step is the dephosphorylation of CMP to cytidine and inorganic phosphate (Pi), catalyzed by cytosolic 5'-nucleotidases such as NT5C2, which exhibit broad specificity for ribonucleoside monophosphates.^[42] This reaction occurs primarily in the cytoplasm, though surface ecto-5'-nucleotidase (NT5E) can contribute in extracellular contexts.^[43] Subsequent deglycosylation of cytidine is mediated by cytidine deaminase (CDA), which hydrolyzes cytidine to uridine and ammonia (NH₃) in an irreversible reaction essential for pyrimidine salvage and catabolism.^[44] Uridine is then cleaved by uridine phosphorylase 1 (UPP1) into uracil and ribose-1-phosphate via phosphorolysis, a reversible step that supports nucleotide recycling.^[45] Further breakdown of uracil occurs through the action of dihydropyrimidine dehydrogenase (DPYD), the rate-limiting enzyme that reduces uracil to dihydrouracil, ultimately yielding β-alanine and CO₂ in a multi-step process.^[46] Meanwhile, ribose-1-phosphate is converted to ribose-5-phosphate by phosphopentomutase (PGM2), which integrates the sugar into central metabolic pathways like the pentose phosphate route.^[47] Pyrimidine catabolic pathways, including CMP degradation, are upregulated during catabolic states such as fasting or tissue breakdown to manage nucleotide turnover.^[48] Polymorphisms in the CDA gene, such as the 79A>C variant, influence enzyme activity and are associated with altered gemcitabine metabolism, leading to increased drug toxicity in affected individuals.^[49] End products like β-alanine and ammonium (NH₄⁺) are primarily excreted via urine, while mitochondrial nucleotide pools may link to catabolism through enzymes like CMP kinase 2 (CMPK2), which modulates CMP levels for mtDNA maintenance.^[50]

Biological Functions

Role in Nucleic Acid Synthesis

Cytidine monophosphate (CMP) serves as a precursor that is phosphorylated to cytidine triphosphate (CTP), which acts as a fundamental building block in RNA synthesis. During transcription, RNA polymerase incorporates CTP into the growing RNA chain, where the cytidine base pairs with guanine in the DNA template through three hydrogen bonds: the N3 of cytosine bonds to N1 of guanine, the O2 of cytosine to the N2 amino group of guanine, and the N4 amino group of cytosine to the O6 of guanine.^[51] This base-pairing specificity ensures accurate sequence complementarity in RNA production.^[52] The polymerization process involves the nucleotidyl transfer reaction catalyzed by RNA polymerases, such as RNA polymerase II and III in eukaryotes, where CTP reacts with the 3'-hydroxyl end of the growing RNA chain (ppRNA) to form a phosphodiester bond: CTP + ppRNA → CMP-RNA + pyrophosphate (PPi). This reaction maintains high fidelity through mechanisms including base-pairing selection and proofreading, where mismatched incorporations are corrected via backtracking and cleavage by the polymerase's intrinsic RNase activity. CMP itself is not directly incorporated but must first be activated to CTP by UMP/CMP kinase and nucleoside diphosphate kinase.^[53] In various RNA types, cytidine residues derived from CTP play critical roles; in transfer RNA (tRNA), they are essential components of anticodon loops for codon-anticodon recognition during translation, while in messenger RNA (mRNA), they contribute to codon sequences and splicing signals, such as in branch point recognition motifs like UACUAAC. In ribosomal RNA (rRNA), cytidine residues support structural stability and functional domains necessary for ribosome assembly and protein synthesis. Unlike in RNA, CMP does not contribute directly to DNA synthesis; instead, the deoxy form dCTP is produced via reduction of CDP to dCDP by ribonucleotide reductase, followed by phosphorylation.^[54]^[55]^[56] In many organisms, cytidine constitutes approximately 25% of RNA bases, reflecting typical GC content levels, and isotopic labeling studies demonstrate rapid turnover of RNA molecules, with half-lives ranging from minutes for mRNA to hours or days for rRNA and tRNA, highlighting the dynamic nature of nucleic acid synthesis. Errors in cytidine incorporation can occur through deamination, converting cytidine to uridine (CMP to UMP equivalent in RNA), mediated by APOBEC family enzymes during RNA editing, which alters codon specificity and gene expression without changing the genomic sequence.^[57]^[58]^[59]

Role in Glycosylation and Other Processes

Cytidine monophosphate (CMP) serves as a critical activated donor in glycosylation pathways, particularly through its conversion to CMP-N-acetylneuraminic acid (CMP-Neu5Ac), the activated form of sialic acid. This activation occurs via CMP-Neu5Ac synthetase (CMAS), which catalyzes the reaction between CTP and sialic acid (Neu5Ac) in the nucleus or cytoplasm, depending on the organism.^[60] The resulting CMP-Neu5Ac is transported to the Golgi apparatus, where it acts as the sugar donor for sialyltransferases that incorporate sialic acid onto glycoproteins and glycolipids. For instance, sialyltransferases such as ST6Gal-I transfer sialic acid from CMP-Neu5Ac to N-linked glycans on glycoproteins like mucins, influencing their stability and function, while other sialyltransferases add sialic acid to gangliosides, complex glycolipids essential for neural cell recognition. In bacteria, CMP-Neu5Ac similarly supports sialylation of cell wall components, including lipopolysaccharides and capsules, aiding in immune evasion and structural integrity. Sialylation processes are evolutionarily conserved but unique to animals among eukaryotes, with the full pathway emerging in deuterostomes; bacteria independently acquired CMP-Neu5Ac synthetases for similar purposes. Beyond glycosylation, CMP participates in lipid metabolism through its role in generating cytidine diphosphate (CDP) intermediates. CMP is phosphorylated by cytidylate kinases to CDP, which is further utilized in the synthesis of CDP-diacylglycerol (CDP-DAG) by CDP-DAG synthase, using CTP and phosphatidic acid as precursors. CDP-DAG serves as a branch point for phospholipid biosynthesis, including phosphatidylinositol and cardiolipin, which are vital for membrane integrity. In the Kennedy pathway for phosphatidylcholine synthesis, CMP contributes indirectly via the nucleotide pool to form CDP-choline from phosphocholine and CTP, which then reacts with diacylglycerol to produce phosphatidylcholine, a major membrane lipid regulating lipid droplet formation and cellular growth. CMP also plays a minor role in coenzyme A (CoA) biosynthesis, where cytidine nucleotides support the CTP-dependent formation of phosphopantothenoylcysteine, an intermediate in the pantothenate pathway essential for acyl carrier functions in fatty acid metabolism. In cellular signaling, CMP is phosphorylated by cytidine monophosphate kinase 2 (CMPK2), a mitochondrial enzyme that maintains nucleotide triphosphate pools for mitochondrial DNA replication and repair. CMPK2-mediated phosphorylation of CMP to CDP enhances mitochondrial reactive oxygen species (ROS) production, linking to innate immune responses; during viral infections, CMPK2 activation promotes type I interferon (IFN) production through IFN-dependent and independent pathways, including cGAS-STING signaling and NLRP3 inflammasome activation. This process is conserved across vertebrates, with CMPK2 ensuring deoxyribonucleotide availability for mtDNA maintenance in post-mitotic cells. CMP-Neu5Ac levels further regulate cellular processes, with fluctuations modulating sialylation extent to influence cell adhesion and migration; elevated CMP-Neu5Ac enhances sialyltransferase activity, promoting migratory phenotypes in cancer cells via altered glycan interactions, while depletion impairs adhesion in neural development.

Physiological and Clinical Significance

In Human Health

Cytidine monophosphate (CMP) is integral to maintaining pyrimidine nucleotide homeostasis in human cells, where it balances synthesis and degradation to support nucleic acid production and metabolic stability. Intracellular CMP concentrations reflect tight regulation that prevents imbalances in pyrimidine pools essential for cellular function. This homeostasis is achieved through coordinated anabolic and catabolic processes, including phosphatase-mediated dephosphorylation of CMP to nucleosides for recycling or excretion. In human development, CMP contributes to fetal RNA synthesis and glycosylation pathways, particularly by activating sialic acid into CMP-sialic acid, a key donor for sialoglycans that facilitate neural tissue formation and neuronal network maturation. During embryogenesis, sialylation patterns involving CMP-sialic acid are dynamically regulated to promote brain development, with deficiencies potentially disrupting polysialic acid structures critical for synaptic plasticity and cognitive growth. Maternal sialic acid supplementation, which relies on CMP activation, has been shown to enhance offspring brain sialic acid content and cognitive outcomes, underscoring CMP's role in prenatal neural health. Nutritionally, CMP can be supported via the salvage pathway using dietary cytidine from RNA-rich sources such as yeast extracts and organ meats, which provide nucleosides for endogenous nucleotide replenishment. Breastfeeding further aids CMP availability, as human milk contains significant levels of CMP among its nucleotides, with concentrations varying by lactation stage but consistently supporting infant metabolic needs. These dietary inputs help sustain CMP pools during periods of high demand, such as rapid growth. Aging is associated with mitochondrial dysfunction that may involve impaired CMP-related pathways, as loss of cytidylate kinase 2 (CMPK2)—which phosphorylates CMP—leads to reduced mitochondrial integrity and energy production. In malnutrition, nucleotide deficiencies, including low CMP availability, compromise immune function by limiting RNA synthesis for immune cell proliferation and antibody production. Urinary cytidine, a degradation product of CMP, serves as a biomarker for RNA turnover rates, with elevated levels indicating increased cellular degradation often linked to metabolic stress. Sex and gender differences influence CMP-dependent glycosylation, particularly in reproduction, where hormones like follicle-stimulating hormone regulate sialylation patterns on glycoproteins to modulate ovarian function and embryo implantation. Estrogen and progesterone fluctuations during the menstrual cycle and pregnancy alter CMP-sialic acid utilization, enhancing sialoglycan expression on reproductive tissues to support fertility and immune tolerance at the maternal-fetal interface.

Medical Applications and Disorders

Orotic aciduria, also known as hereditary orotic aciduria, results from defects in uridine monophosphate synthase (UMPS), which impairs de novo pyrimidine biosynthesis and leads to reduced levels of UMP and downstream nucleotides including CMP. This deficiency manifests as megaloblastic anemia, growth retardation, and orotic acid crystalluria due to the accumulation of orotic acid, with uridine or uridine triacetate supplementation used therapeutically to bypass the enzymatic block and restore pyrimidine pools.^[61] Cytidine deaminase (CDA) deficiency is a rare autosomal recessive disorder that causes severe combined immunodeficiency through the toxic accumulation of deoxycytidine and its metabolites, which inhibit lymphocyte proliferation and DNA synthesis. Affected individuals present with recurrent infections, failure to thrive, and profoundly low T-cell counts, highlighting CDA's role in pyrimidine salvage to prevent nucleotide imbalances that disrupt immune cell development.^[62] Mutations in the CMPK2 gene, encoding cytidine/uridine monophosphate kinase 2, are linked to mitochondrial dysfunction and familial brain calcification, leading to energy deficits. CMPK2 upregulation promotes progression in hepatocellular carcinoma by enhancing mitochondrial metabolism and antiviral signaling, while its role in restricting hepatitis C virus (HCV) replication underscores its involvement in viral resistance pathways. Loss-of-function variants exacerbate neuroinflammation in conditions like acute brain injury via dysregulated cGAS-STING activation.^[63] Deficiency in thymidine phosphorylase (TYMP), which catalyzes the reversible phosphorolysis of pyrimidine nucleosides, results in elevated levels of thymidine and deoxyuridine, contributing to neurological disorders such as mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) through toxic nucleotide imbalances. This salvage pathway disruption leads to demyelination, gastrointestinal dysmotility, and cachexia.^[64] CMP plays a role in chemotherapy resistance, particularly in leukemias, where altered salvage kinase activity reduces the activation of nucleoside analogs, allowing cancer cells to evade DNA damage. Therapeutically, cytarabine (Ara-C), a CMP analog, is activated via phosphorylation to Ara-CMP by deoxycytidine kinase and further by CMP kinase, incorporating into DNA to inhibit polymerase and treat acute myeloid leukemia.^[65] Gemcitabine, another analog, relies on CMP kinase (CMPK1) for conversion to its diphosphate form, which inhibits ribonucleotide reductase and DNA synthesis in pancreatic and other solid tumors.^[66] In muscular dystrophy, defects in CMP-sialic acid synthetase impair sialic acid activation for glycosylation, leading to muscle degeneration; sialic acid supplementation serves as a therapeutic strategy to restore CMP-Neu5Ac levels and alleviate symptoms in GNE myopathy.^[67]

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6–10 day deliveryAppearance (Color)White. UV spectrophotometry98 to 102 % (lambda max. 280 nm, pH 2). Loss on drying=<7 % (105°C, 5 hrs). Appearance (Form)Crystalline powder.
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Cytosine is an aminopyrimidine that is pyrimidin-2-one having the amino group located at position 4. It has a role as a human metabolite, an Escherichia coli ...
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D-Ribofuranose | C5H10O5 | CID 5779 - PubChem
D-ribofuranose is a ribofuranose having D-configuration. It is a ribofuranose and a D-ribose. · D-ribofuranose has been reported in Mycoplasma gallisepticum with ...
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Because of its three pKas, phosphate is dianionic at pH 7, the physiological intracellular pH. Thus, phosphate monoester groups have one full negative ...
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Keto-iminol tautomerism of protonated cytidine monophosphate characterized by ultraviolet resonance Raman spectroscopy: implications of C+ iminol tautomer for base mispairing
### Key Findings on Tautomerism of Cytidine Monophosphate
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Nucleotide Geometry Standards - NAKB
The most common pucker conformation for the ribose sugar in RNA is C3'-endo; the most common pucker conformation for the deoxyribose sugar in DNA is C2'-endo.
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Activated Ribonucleotides Undergo a Sugar Pucker Switch upon ...
Jan 30, 2012 · We found that the sugar pucker of activated ribonucleotides switches from C2′-endo in the free state to C3′-endo upon binding to an RNA template.
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NMR studies of nucleic acids in solution. III. Conformational properties of adenylyl-3' →.5'-adenosine in aqueous solution.
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CMPK1 Gene - GeneCards | KCY Protein | KCY Antibody
### Summary of CMPK1 Gene Content from GeneCards
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KEGG ENZYME: 2.7.4.14
This eukaryotic enzyme is a bifunctional enzyme that catalyses the phosphorylation of both CMP and UMP with similar efficiency.
[30]
CMPK2 - UMP-CMP kinase 2, mitochondrial - UniProt
May 18, 2010 · Mitochondrial nucleotide monophosphate kinase needed for salvage dNTP synthesis that mediates immunomodulatory and antiviral activities.
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Nucleoside diphosphate kinase (NDPK) is defined as an enzyme that functions primarily as a nucleoside diphosphate phosphorylating enzyme, ...Introduction to Nucleoside... · Molecular Structure, Isoforms...
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Biological functions and clinical implications of the CMPK2 across ...
Aug 27, 2025 · CMPK2 maintains mitochondrial homeostasis by catalyzing ATP-dependent phosphorylation of CMP to CDP and UMP to UDP, sustaining mtDNA synthesis ...Missing: CTP | Show results with:CTP
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CMPK2 is a host restriction factor that inhibits infection of multiple ...
Mar 17, 2023 · CMPK2 is a host restriction factor that inhibits infection of multiple coronaviruses in a cell-intrinsic manner.Missing: seminal | Show results with:seminal
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Some unanswered questions about the pyrimidine catabolic pathway
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Purine and Pyrimidine Nucleotide Synthesis and Metabolism - PMC
The salvage cycle interconverts purine bases, nucleosides and nucleotides released as by-products of cellular metabolism or from the catabolism of nucleic acids ...
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Mammalian 5′-Nucleotidases* - Journal of Biological Chemistry
Aug 28, 2003 · 3.6) dephosphorylate non-cyclic nucleoside monophosphates to nucleosides and inorganic phosphate. Seven human 5′-nucleotidases with different ...
[38]
Microbial 5′-nucleotidases: their characteristics, roles in cellular ...
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Entry - *123920 - CYTIDINE DEAMINASE; CDA - OMIM - (OMIM.ORG)
Cytidine deaminase (CDA; EC 3.5.4.5) irreversibly catalyzes the hydrolytic deamination of cytidine and deoxycytidine to uridine and deoxyuridine, respectively.
[40]
UPP1 - Uridine phosphorylase 1 - Homo sapiens (Human) | UniProtKB
Catalyzes the reversible phosphorylytic cleavage of uridine to uracil and ribose-1-phosphate which can then be utilized as carbon and energy sources.
[41]
Functional Characterization of 21 Allelic Variants of ...
Dihydropyrimidine dehydrogenase (DPD, EC 1.3.1.2), encoded by the DPYD gene, is the rate-limiting enzyme in the degradation pathway of endogenous pyrimidine ...
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The PGM3 gene encodes the major phosphoribomutase in the yeast ...
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other genes in the de novo pathway UMP synthase is single copy. 3.1.6. Intracellular Organization of the de novo Pathway. Almost the entire pathway of ...
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impact of the 79A>C cytidine deaminase polymorphism
Mar 6, 2010 · To study the impact of the 79A>C polymorphism in the cytidine deaminase (CDA) gene on the pharmacokinetics of gemcitabine and its metabolite ...
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Human UMP-CMP Kinase 2, a Novel Nucleoside Monophosphate ...
We have identified a human mitochondrial UMP-CMP kinase (UMP-CMPK, cytidylate kinase; EC 2.7.4.14), designated as UMP-CMP kinase 2 (UMP-CMPK2).Missing: catabolism | Show results with:catabolism
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22.2: Structure and Function of DNA - Biology LibreTexts
Jun 14, 2019 · The base pairs are stabilized by hydrogen bonds ... bonds between them, whereas cytosine and guanine form three hydrogen bonds between them.<|separator|>
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The mechanism of the nucleo-sugar selection by multi-subunit RNA ...
Feb 4, 2021 · DNA polymerases select against NTPs by using steric gates to exclude the 2′OH, but RNAPs have to employ alternative selection strategies.<|separator|>
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Phosphorylation of Cytidine, Deoxycytidine, and Their Analog ...
Phosphorylation of Cytidine, Deoxycytidine, and Their Analog Monophosphates by Human UMP/CMP Kinase Is Differentially Regulated by ATP and Magnesium.
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Biological roles of RNA m5C modification and its implications in ...
Apr 1, 2022 · In tRNA, m5C has been shown to maintain homeostasis, optimize codon–anticodon pairing, regulate stress response, and control translation ...5-Methylcytosine (mc)... · Mc Readers · Abbreviations<|separator|>
[50]
UACUAAC is the preferred branch site for mammalian mRNA splicing.
Remarkably, this distance constraint is so strong that a cytidine or even a uridine residue will serve as the branch- point if the region is devoid of adenosine ...<|control11|><|separator|>
[51]
Deoxyribonucleotide Metabolism in Cycling and Resting Human ...
[3H]Cytidine is phosphorylated to CDP, reduced to dCDP by ribonucleotide reductase and after phosphorylation to dCTP incorporated into DNA.
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High Guanine and Cytosine Content Increases mRNA Levels ... - NIH
May 23, 2006 · In most organisms, the variation in guanine and cytosine (GC) content among genes is modest; for example, 90% of Saccharomyces cerevisiae genes ...
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Metabolic turnover and dynamics of modified ribonucleosides ... - NIH
We developed a 13 C labeling approach, called 13 C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA.Missing: percentage organisms
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Unraveling the Enzyme-Substrate Properties for APOBEC3A ... - NIH
RNA editing by deamination is a crucial event that alters a single nucleotide of a transcript, resulting in the diversification and regulation of the ...Results · A3a Targeted Rna Substrates... · Figure 2. C-To-U Rna Editing...
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A Facile Fluorometric Assay of Orotate Phosphoribosyltransferase ...
Feb 24, 2023 · ... (CMP) and thymidine 5′-monophosphate (TMP). In humans, OPRT, along ... Orotic aciduria is a pathologic condition characterized by ...
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Global Hereditary Orotic Aciduria Market Size & Trends, 2032
Global Hereditary Orotic Aciduria Market Opportunities: ; Segments covered: By Drug Type: Cytidine monophosphate and Uridine monophosphate; By Indication: Type 1 ...
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CYTIDINE DEAMINASE DEFICIENCY AND IMMUNODEFICIENCY ...
Jul 1, 1985 · Enzyme study disclosed a profound deficiency in cytidine deaminase (CDA) in the patient's lymphocytes (10-21-23 pmol.min−1.10−6 cells, normal ...
[58]
Loss of function of CMPK2 causes mitochondria deficiency ... - PMC
Nov 29, 2022 · Brain calcification is a critical aging-associated pathology and can cause multifaceted neurological symptoms.
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Microglial CMPK2 promotes neuroinflammation and brain injury ...
Apr 26, 2024 · Several reports have shown that CMPK2 participates in the progression of diseases, including acute respiratory distress syndrome (ARDS), brain ...
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Landscape of targets within nucleoside metabolism for the ...
TYMP is a pyrimidine nucleoside phosphorylase that regulates pyrimidine nucleoside salvage by controlling the breakdown of thymidine and deoxyuridine. MNGIE ...Missing: CMP | Show results with:CMP
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Pyrimidine Nucleoside Phosphorylase - ScienceDirect.com
It plays a crucial role in pyrimidine nucleoside metabolism, supporting DNA repair and replication. ... There is only one available crystal structure of a human ...
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Gemcitabine Pharmacogenomics: Deoxycytidine Kinase and ...
CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases. J Biol Chem. 1996; 271:2856-2862. Full Text · Full Text (PDF).
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Genetic factors influencing cytarabine therapy. - ClinPGx
The mainstay of acute myeloid leukemia chemotherapy is the nucleoside analog cytarabine (ara-C). Numerous studies suggest that the intracellular concentrations ...
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PharmGKB summary: Gemcitabine Pathway - PMC - NIH
Phosphorylation to gemcitabine di- (dFdCDP) and tri- phosphate (dFdCTP) is catalyzed by UMP/CMP kinase (CMPK1) and nucleoside-diphosphate kinase (NDPK, NME), ...
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Characterization of human UMP/CMP kinase and its ... - PubMed
Pyrimidine nucleoside monophosphate kinase [UMP/CMP kinase (UMP/CMPK);EC 2.7.4.14] plays a crucial role in the formation of UDP, CDP, and dCDP, which are ...