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Deoxyribonucleotide Formation

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Deoxyribonucleotide Formation
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reactions that will either result in degradation and excretion or reutilization of the bases. For example, when normal liver is presented with uracil, it is rapidly degraded to b ­alanine, whereas proliferating tumor cells would convert uracil to UMP. This is the result of the availability of PRPP, enzyme levels, and metabolic state of the animal.
12.6— Deoxyribonucleotide Formation
As indicated previously, the concentrations of deoxyribonucleotides are extremely low in nonproliferating cells. Only at the time of DNA replication (S phase) does the deoxyribonucleotide pool increase to support the required DNA synthesis.
Deoxyribonucleotides Are Formed by Reduction of Ribonucleoside Diphosphates
Nucleoside 5¢­diphosphate reductase (ribonucleotide reductase) catalyzes the reaction in which 2 ­deoxyribonucleotides are synthesized from the corresponding ribonucleoside 5 ­diphosphate. The reaction is controlled not only by the amount of enzyme present in cells but also by a very finely regulated allosteric control mechanism. The reaction can be summarized as shown in Figure 12.23. Reduction of a particular substrate requires the presence of a specific nucleoside 5 ­
triphosphate as a positive effector. For example, reduction of CDP or UDP requires ATP as the positive effector, while reduction of ADP and GDP require the presence of dGTP and dTTP, respectively. A small molecular weight protein, thioredoxin or glutaredoxin, is involved in reduction at the 2 position through oxidation of its sulfhydryl groups. To complete the catalytic cycle, NADPH is used to regenerate free sulfhydryl groups on the protein. Thioredoxin reductase, a flavoprotein, is required if thioredoxin is involved; glutathione and glutathione reductase are involved if glutaredoxin is the protein.
Mammalian ribonucleotide reductase consists of two nonidentical protein subunits (heterodimer), neither of which alone has enzymatic activity. The larger subunit has at least two different effector­binding sites. The smaller subunit contains a nonheme iron and a stable tyrosyl free radical. The two subunits make up the active site of the enzyme. The two subunits are encoded by different genes on separate chromosomes. The mRNAs for these subunits, and consequently the proteins, are differentially expressed as cells transit the cell cycle.
As mentioned earlier, the activity of ribonucleotide reductase is under allosteric control. While reduction of each substrate requires the presence of a specific positive effector, the products serve as potent negative effectors of the enzyme. DeoxyATP is a potent inhibitor of the reduction of all four substrates: CDP, UDP, GDP, and ADP; dGTP inhibits reduction of CDP, UDP, and GDP; dTTP inhibits reduction of CDP, UDP, and ADP. From this it is seen that dGTP
Figure 12.23 De novo synthesis of 2 ­deoxyribonucleotides from ribonucleotides. This reaction is catalyzed by ribonucleotide reductase.
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Figure 12.24 Role of ribonucleotide reductase in DNA synthesis. The enzymes catalyzing the reactions are (1) ribonucleotide reductase, (2) nucleoside 5 ­diphosphate kinase, (3) deoxycytidylate deaminase, (4) thymidylate synthase, and (5) DNA polymerase.
and dTTP can serve as either positive or negative effectors of ribonucleotide reductase. Effective inhibition of ribonucleotide reductase by dATP, dGTP, or dTTP explains the toxicity of deoxyadenosine, deoxyguanosine, and thymidine to a variety of mammalian cells.
Ribonucleotide reductase is uniquely responsible for catalyzing the rate­limiting reactions by which 2 ­deoxyribonucleoside 5 ­triphosphates are synthesized de novo for DNA replication as summarized in Figure 12.24. Effective inhibitors of ribonucleotide reductase are potent inhibitors of DNA synthesis and hence of cell replication.
Figure 12.25 Structure of N5,N10­methylene H4folate.
Deoxythymidylate Synthesis Requires N5,N10­Methylene H4Folate
Deoxythymidylate (dTMP) is formed from 2 ­deoxyuridine 5 ­monophosphate (dUMP) in a reaction that is unique. Thymidylate synthase catalyzes the reaction in which a one­carbon unit from N5,N10­methylene H4folate (Figure 12.25) is transferred to dUMP and simultaneously reduced to a methyl group. The reaction is presented in Figure 12.26. In this reaction, N5,N10­methylene H4folate serves as the one­carbon donor and as a reducing agent. This is the only reaction in which H4folate, acting as a one­carbon carrier, is oxidized to H2folate. There are no known regulatory mechanisms for this reaction.
The substrate for this reaction can come from two different pathways as shown below:
In both pathways deoxyribonucleotides, dCDP or dUDP, are generated by ribonucleotide reductase. In one pathway, dUMP is generated from dUDP while in the other pathway, dCMP is deaminated to dUMP. From labeling studies it
Figure 12.26 Synthesis of deoxythymidine nucleotide.
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appears that the major pathway for formation of dUMP involves deamination of dCMP by dCMP deaminase, an enzyme that is subject to allosteric regulation by dCTP (positive) and dTTP (negative) (Figure 12.27).
Figure 12.27 Regulation of dCMP deaminase.
Pyrimidine Interconversions with Emphasis on Deoxyribopyrimidine Nucleosides and Nucleotides
As shown in Section 12.4, there are metabolic pathways for interconversions of purine nucleotides and these pathways are regulated to maintain an appropriate balance of adenine and guanine nucleotides. Pathways also exist for interconversion of pyrimidine nucleotides and these pathways are of particular importance for pyrimidine deoxyribonucleosides and deoxyribonucleotide as summarized in Figure 12.28. Note that dCTP and dTTP are major positive and negative effectors of the interconversions and salvage of deoxyribonucleosides.
Pyrimidine Nucleotides Are Degraded to b ­Amino Acids
Turnover of nucleic acids results in release of pyrimidine nucleotides and purine nucleotides (discussed previously). Degradation of pyrimidine nucleotides follows the pathways shown in Figure 12.29. In these degradative pathways the pyrimidine nucleotides are converted to nucleosides by nonspecific phosphatases. Cytidine and deoxycytidine are deaminated to uridine and deoxyuridine by pyrimidine nucleoside deaminase. Uridine phosphorylase catalyzes phosphorolysis of uridine, deoxyuridine, and thymidine resulting in formation of uracil and thymine as pyrimidine base products.
Uracil and thymine are then further degraded by analogous reactions, although the final products are different as shown in Figure 12.30. Uracil is degraded to b ­
alanine, NH4+, and CO2. None of these products is unique to uracil degradation, and consequently the turnover of cytosine or uracil nucleotides cannot be estimated from the end products of this pathway. Thymine degradation proceeds to b ­aminoisobutyric acid, NH4+, and CO2. b ­Aminoisobutyric acid is excreted in urine of humans and originates exclusively from degradation of thymine. Thus it is possible to estimate the turnover of DNA or thymidine nucleotides by measurement of b ­
aminoisobutyric acid excretion. Increased levels of b ­aminoisobutyric acid are excreted in cancer patients undergoing chemotherapy or radiation therapy in which large numbers of cells are killed and DNA is degraded.
Figure 12.28 Interconversions of pyrimidine nucleotides with emphasis on deoxyribonucleotide metabolism. The solid arrows indicate enzyme­catalyzed reactions; the dashed lines represent sites of activation .
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Figure 12.29 Pathways for degradation of pyrimidine nucleotides.
Figure 12.30 Degradation of uracil and thymine to end products.
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