Pyrimidine nucleoside diphosphates

Less than 3% of soil organic phosphorus is present as nucleic acids and derivatives derived from the decomposition of living organisms (Dalai, 1977). The four bases of DNA have been identified in humic acids (Anderson, 1961). The presence of nucleic acids and derivatives in the soil was confirmed by the isolation of two pyrimidine nucleoside diphosphates (Anderson, 1970). Nucleic acids are rapidly mineralized, re-synthesized and combined with other soil constituents, or incorporated into microbial biomass (Anderson and Malcolm, 1974). Nevertheless, the interaction of nucleases with soil constituents can inhibit DNA hydrolysis, with important environmental consequences related to extracellular gene uptake by bacteria (Demanfeche et al., 2001). 

The ability of nucleoside triphosphates, singly, or in combination, to effect changes in the catalytic properties of the reductase have been explored systematically by Reichard and his co-workers the complicated pattern of results is summarized in Table 16-11. These findings have been interpreted in terms of four states of activity for the reductase. In the presence of ATP, the reductase prefers as substrates pyrimidine nucleoside diphosphates. In the presence of dGTP, a purine-specific state is assumed and dTTP causes the enzyme to be in a condition in which both purine and pyrimidine ribonucleoside diphosphates are reduced. 

Ribonucleic acid is thought to possess a highly branched structure. Cleavage about a branch point in the manner illustrated in (VIII) would give the pyrimidine nucleoside diphosphates discussed above. Ribonucleic acid also contains a number of phospho-monoester end groups which are susceptible to acid prostatic phosphatase and certain other monoesterases. A great deal has been learned of ribonucleic acid structure... 

While mammahan cells reutilize few free pyrimidines, salvage reactions convert the ribonucleosides uridine and cytidine and the deoxyribonucleosides thymidine and deoxycytidine to their respective nucleotides. ATP-dependent phosphoryltransferases (kinases) catalyze the phosphorylation of the nucleoside diphosphates 2 "-de-oxycytidine, 2 -deoxyguanosine, and 2 -deoxyadenosine to their corresponding nucleoside triphosphates. In addition, orotate phosphoribosyltransferase (reaction 5, Figure 34-7), an enzyme of pyrimidine nucleotide synthesis, salvages orotic acid by converting it to orotidine monophosphate (OMP). 

In view of the difficulty of hydrolyzing the pyrimidine nucleosidic linkages, ribonucleic acids have been hydrolyzed to a mixture of purine bases and pyrimidine nucleotides which is then separated by paper chromatography.132, 163 164 This method has been employed extensively for the analysis of ribonucleic acids, and gives reproducible results,166 but it has not been used to any great extent for deoxyribonucleic acids, probably because, under these conditions of hydrolysis, they yield some pyrimidine deoxy-ribonucleoside diphosphates.166... 

Hydrolysis of ribonucleic acids by snake venom was found to yield inorganic phosphate, nucleosides, and pyrimidine ribonucleoside diphosphates.197 These diphosphates were shown by their behavior toward various enzymes to be mixtures of 2,5- and 3,5-diphosphates, and it therefore seems likely that they were formed through intermediate, cyclic phosphates. Thus, although this evidence confirms the existence of 2(or 3) — 5 linkages, it does not distinguish between the 2- and 3-positions. 

DNA and RNA synthesis De novo formation of purine and pyrimidine nucleotide Nucleoside diphosphate reductase Thymidylate synthase Polymerase reactions Chapter 20... 

Although there are a number of inefficient steps in most proposed prebiotic syntheses of ribotides, the major objection to RNA as the primogenitor of life has been the relatively small yield of ribose in the formose reaction, a simple condensation of glycoaldehyde. Muller et a/.,18 however, have discovered a variation of the formose reaction that produces a limited mix of pentose diphosphates in which the ribose forms predominate (52 14 23 11, ribose arabinose lyxose xylose). Although many critical chemical roadblocks remain (such as the extremely low yield of pyrimidine nucleosides following the condensation of ribose and free bases), this advance belies the previously held view that products of the formose reaction are necessarily so chemically diverse that they are the carbohydrate analog of petroleum. 19... 

Fig. 15-15 The de novo pyrimidine biosynthetic pathway. CAP, carbamoyl phosphate CA-asp, /V-carbamoyl-L-aspartate DHO, L-dihydroorotate Oro, orotate OMP, orotidine 5 -monophosphate. Enzymes (1) carbamoyl phosphate synthetase II (2) aspartate transcarbamoylase (3) dihydroorotase, (4) dihydroorotate dehydrogenase (5) orotate phosphoribosyltransferase (6) OMP decarboxylase (7) nucleoside monophosphate kinase (8) nucleoside diphosphate kinase (9) CTP synthetase.

Cytarabine is a pyrimidine nucleoside related to idoxuridine (43). It is used primarily as an anticancer rather than an antiviral agent. Cytarabine acts by blocking the utilization of deoxycytidine, thereby inhibiting the repiication of viral DNA. The drug is first converted to mono-, di-, and triphosphates, which interfere with DNA synthesis by inhibiting both DNA polymerase and the reductase that promotes the conversion of cytidine diphosphate into its deoxy derivatives. 

NOTE 4 These enzymes (2.4.2.1 - 2.4.2.23) generally catalyze the reactions Purine or pyrimidine nucleoside + orthophosphate or pyrophosphate = purine or pyrimidine + a ribose or ribosyl phosphate, ribosyl diphosphate, or ribosyl pyrophosphate.]... 

Cytidine phosphates cytidine S -monophosphate (CMP, cytidylic acid, M, 323.2), cytidine 5 -diphos-phate (CDP, M, 403.19) and cytidine 5 -triphosphate (CTP, M, 483.16). For structure, see e. g. Pyrimidine biosynthesis. CTP is a precursor of RNA synthesis, while deoxy-CTP is a precursor of DNA synthesis. CDP may be regarded as the coenzyme of phospholipid biosynthesis (see Membrane lipids) (activated choline is CDP-choline). Glycerol and the sugar alcohol, ribitol, are also activated by bonding to CDP (see Nucleoside diphosphate sugars). Reduction of ribose... 

With the advent of an adequate nucleotide technology and the development of widespread interest in nucleotide metabolism, many free nucleotides have been found in cells however, no comprehensive survey has appeared since the 1958 report of Henderson and LePage (17), which lists over 100 nucleotides, and the list has probably more than doubled since. A large number of free nucleoside diphosphate conjugates have been isolated from cells and characterized many such compounds serve as coenzymes in group-transfer reactions, for example, CDP-X and UDP-X derivatives participate, respectively, in phospholipid and polysaccharide synthesis (see Chapter 3). As well, many new nucleotides have been recognized as metabolites of nucleoside antibiotics and of synthetic purine and pyrimidine analogues. 

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... 

The existence of a very active, widely distributed nucleoside diphosphate kinase has been demonstrated repeatedly (see Chapter 4 and reference S5). This enzyme has been prepared in crystalline form from yeast (36), and Mourad and Parks (37) have isolated the enzyme in high purification from human erythrocytes. The latter enzyme reacts with nucleoside di-and triphosphates which contain either ribose or deoxyribose and any of the natural purine or pyrimidine bases, including thymine. 

An excellent separation of twelve mono-, di- and tri-phosphorylated purine and pyrimidine nucleosides was achieved in 50 min on a hydrophilic strong anion exchange resin in the fninate form eluted with a volatile buffer (HCOjH - HCO2NH4). It was applied to the purification of [U- C]adenosine-S -diphosphate and other radiolabelled nucleotides and their analogues. ... 

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