Nucleoside diphosphate kinase specificity

Jong, A.Y. Ma, J.J. Saccharomyces cerevisiae nucleoside-diphosphate kinase purification, characterization, and substrate specificity. Arch. Biochem. Biophys., 291, 241-246 (1991)... 

Schaertl, S. Konrad, M. Geeves, M.A. Substrate specificity of human nucleoside-diphosphate kinase revealed by transient kinetic analysis. J. Biol. Chem., 273, 5662-5669 (1998)... 

Shankar, S. Hershberger, C.D. Chakrabarty, A.M. The nucleoside diphosphate kinase of Mycobacterium smegmatis identification of proteins that modulate specificity of nucleoside triphosphate synthesis by the enzyme. Mol. Microbiol., 24, 477-487 (1997)... 

Nucleoside diphosphates (NDP) are synthesized from the corresponding nucleoside monophosphates (NMP) by base-specific nucleoside monophosphate kinases (Figure 22.9). [Note These kinases do not discriminate between ribose or deoxyribose in the substrate.] ATP is generally the source of the transferred phosphate, because it is present in higher concentrations than the other nucleoside triphosphates. Adenylate kinase is particularly active in liver and muscle, where the turnover of energy from ATP is high. Its function is to maintain an equilibrium among AMP, ADP, and ATP. Nucleoside diphosphates and triphosphates are interconverted by nucleoside diphosphate kinase—an enzyme that, unlike the monophosphate kinases, has broad specificity. 

Nucleoside diphosphates (NDP) are synthesized from the corresponding nucleoside monophosphates (NMP) by base-specific nucleoside monophosphate kinases. NDPs and nucleoside triphosphates (NTP) are interconverted by nucleoside diphosphate kinase—an enzyme that, unlike the monophosphate kinases, has broad specificity. 

Kandeel M, Kitade Y (2010) Substrate specificity and nucleotides binding properties of NM23H2/nucleoside diphosphate kinase homolog from Plasmodium falciparum. J Bioenerg Biomembr 42(5) 361-369... 

Thus, uridine-cytidine kinase converts uridine and cytidine to UMP and CMP, respectively thymidine kinase converts thymidine to dTMP and adenosine kinase converts adenosine to AMP. Specific kinases convert monophospho-nucleotides to dinucleotides using ATP as a phosphate donor. The conversion of diphosphonucleotides to triphosphonucleotides is carried out by a nonspecific nucleoside diphosphate kinase. This includes both the ribo- and deoxy-ribonucleotides. Cytosine and its nucleoside and nucleotide transformations are often associated with the metabolism of uracil and its nucleosides and nucleotides. Note that UTP can give rise to CTP (Figure 10.9), and also that, in the presence of cytidine deaminase, cytidine can be converted to uridine. 

Nucleoside diphosphates and triphosphates are interconverted by nucleoside diphosphate kinase, an enzyme that has broad specificity, in contrast with the monophosphate kinases. X and Y can represent any of several ribonucleosides or even deoxyribonucleosides. 

The diphosphates are converted to the triphosphates by the ubiquitous enzyme nucleoside diphosphate kinase. Remarkably, the lack of base or sugar specificity applies to the phosphate acceptor and the phosphate donor. Hence, the general reaction is... 

GMP and AMP are converted to diphosphates (see here) in reactions catalyzed by guanylate kinase and adenylate kinase, respectively. Conversion of nucleoside diphosphates to nucleoside triphosphates is catalyzed by nucleoside diphosphate kinase (see here). The reaction is reversible, thus providing a way to make both ATP and GTP. The enzyme is highly active, but has broad specificity for its phosphoryl group donor (nucleoside triphosphate) and receptor (nucleoside diphosphate). 

AMP and GMP can be phosphorylated to the di- and triphosphate levels. The production of nucleoside diphosphates requires specific nucleoside monophosphate kinases, whereas the production of nucleoside triphosphates requires nucleoside diphosphate kinases, which are active with a wide range of nucleoside diphosphates. The purine nucleoside triphosphates are also used for energy-requiring processes in the cell and also as precursors for RNA synthesis (see Fig. 41.2). 

The nucleoside diphosphate kinase from human erythrocytes was of low specificity and would react with nucleoside triphosphates and nucleoside diphosphates which contained either ribose or deoxyribose and any of the natural purine or pyrimidine bases. The finding that alternative substrates, such as GTP and ATP, were competitive inhibitors, is consistent with the low substrate specificity... 

Nucleoside diphosphate kinases exhibit activity over a wide pH range, but usually have optima at or near pH 7. They require the presence of divalent metals for activity, but have a low specificity in this respect, since Mg +, Mn +, Ca +, Co +, and to a lesser extent, Ni + and Zn +, may satisfy this requirement. Magnesium is evidently the physiological ion serving this enzyme s requirement for a divalent ion. The function of magnesium ion in the nucleoside diphosphate kinase reaction is apparent in the work of Colomb et al. (27), who have shown that for the enzyme from beef heart mitochondria, MgATP, but not free ATP, serves as the phosphate donor. Further, free ADP was shown to be preferred over MgADP as the phosphate acceptor. 

In summary, the nucleoside diphosphate kinase reaction is catalyzed by enzymes with broad substrate specificity many tissues show high activities of this enzyme, which is widely distributed in nature. 

Phosphorylation of the monophosphates is effected by a group of enzymes which are specific for the bases phosphorylation of the diphosphates is catalyzed by the ubiquitous nucleoside diphosphate kinase which has low specificity for both the base and pentose portions of its substrates. The latter enzyme occurs in animal cells in such high concentrations that the existence of the first step has been difficult to demonstrate in certain instances. 

The base in the nucleotide may be either guanine or hypoxanthine in the reaction with the heart muscle enzyme, while the spinach enzyme is specific for adenine. In crude heart muscle preparations nucleoside diphosphate kinase permits catalytic amounts of GTP or ITP to support a-ketoglutarate oxidation in the presence of ADP, which is converted to ATP. 

The addition of a third phosphate to any of the nucleoside pyrophosphates, such as UDP, is catalyzed by an enzyme found in yeast and several animal tissues. Since the reaction catalyzed by this enzyme appears to be nonspecific with respect to the base of the nucleotides, it has been named nucleoside diphosphate kinase (nudiki). The phosphate donor in this reaction may be any of the nucleoside triphosphates. As in the case of the nucleoside monophosphate kinases, there are no significant differences in the free energies of hydrolysis of the various nucleoside triphosphates, so all of the reactions are freely reversible with equilibrium constants near 1. Since the phosphorylation of nucleoside diphosphates is reversible, it is necessary that each of the corresponding triphosphates serve as phosphate donor. The phosphorylation of the monophosphates is similarly reversible, but in this case one of the sites on the enz3one appears to react only with adenine, and involves the conversion of ATP to ADP. The complementary reaction involves XMP XDP. Thus the nonadenine nucleotides are never equivalent to ATP, and the reaction is limited to the phosphorylation of a specific nucleoside monophosphate by ATP. 

All of these triphosphates take part in phosphorylations in the cell. Similarly, specific nucleoside monophosphate kinases catalyze the formation of nucleoside diphosphates from the corresponding monophosphates. 

ATP also brings about the formation of other nucleoside diphosphates by the action of a class of enzymes called nucleoside monophosphate kinases. These enzymes, which are generally specific for a particular base but nonspecific for the sugar (ribose or de-oxyribose), catalyze the reaction... 

How is the other major pyrimidine ribonucleotide, cytidine, formed It is synthesized from the uracil base of UMP, but UMP is converted into UTP before the synthesis can take place. Recall that the diphosphates and triphosphates are the active forms of nucleotides in biosynthesis and energy conversions. Nucleoside monophosphates are converted into nucleoside triphosphates in stages. First, nucleoside monophosphates are converted into diphosphates by specific nucleoside monophosphate kinases that utilize ATP as the phosphoryl-group donor (Section 9.4). For example, UMP is phosphorylated to UDP by UMP kinase. 

This enzyme activity is widely distributed in nature, and tissues generally show a higher concentration of this activity than of nucleoside monophosphate kinases. The enzyme has broad specificity purified preparations appear to have only the requirement that the substrates be a nucleoside triphosphate and a nucleoside diphosphate. 

Nucleoside diphosphates may be cleaved, as mentioned above, by inorganic pyrophosphatase, and a phosphatase specific for IDP, GDP, and UDP has also been described. Adenylate kinase also may convert ADP to adenylate (plus ATP). Studies of these enzymes have been reviewed by Keilley (4) and Morton (5). 

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