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Metabolism of Purine Nucleotides

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Metabolism of Purine Nucleotides
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The pyrimidine nucleotides found in highest concentrations in cells are those containing uracil and cytosine. The structures of the bases are shown in Figure 12.4. Uracil and cytosine nucleotides are the major pyrimidine components of RNA; cytosine and thymine are the major pyrimidine components of DNA. As with purine derivatives, the pyrimidine nucleosides or nucleotides contain either ribose or 2­deoxyribose. The sugar moiety is linked to the pyrimidine in a b ­N­glycosidic bond at N­1. Nucleosides of pyrimidines are uridine, cytidine, and thymidine (Figure 12.5). Phosphate esters of pyrimidine nucleosides are UMP, CMP, and TMP. In cells the major pyrimidine derivatives are tri­ and diphosphates (Figure 12.6).
See the Appendix for a summary of the nomenclature and chemistry of the purines and pyrimidines.
Figure 12.4 Pyrimidine bases.
Properties of Nucleotides
Cellular components containing either purine or pyrimidine bases can be easily detected because of their strong absorption of UV light. Purine bases, nucleosides, and nucleotides have stronger absorptions than pyrimidines and their derivatives. The wavelength of light at which maximum absorption occurs varies with the particular base component, but in most cases the UV maximum is close to 260 nm. The UV spectrum for each derivative responds differently to changes in pH. The UV absorptions provide the basis for sensitive methods in assaying these compounds. For example, deamination of adenine nucleosides or nucleotides to the corresponding hypoxanthine derivatives causes a marked shift in lmax from 265 to 250 nm, which is easily determined. Because of the high molar extinction coefficients of the purine and pyrimidine bases and their high concentrations in nucleic acids, the absorbance at 260 nm can be used to quantitate the amount of nucleic acid in RNA and DNA preparations.
The N­glycosidic bond of nucleosides and nucleotides is stable to alkali. However, stability of this bond to acid hydrolysis differs markedly. The N­glycosidic bond of purine nucleosides and nucleotides is easily hydrolyzed by dilute acid at elevated temperatures (e.g., 60°C) to yield free purine base and sugar or sugar phosphate. On the other hand, the N­glycosidic bond of uracil, cytosine, and thymine nucleosides and nucleotides is very stable to acid treatment. Strong conditions, such as perchloric acid (60%) and 100°C, releases free pyrimidine but with complete destruction of the sugar. The N­glycosidic bond of dihydrouracil nucleoside and dihydrouracil nucleotide is labile in mild acid.
Because of the highly polar phosphate group, purine and pyrimidine nucleotides are much more soluble in aqueous solutions than are their nucleosides and free bases. In general, nucleosides are more soluble than free bases.
Purine and pyrimidine bases and their nucleoside and nucleotide derivatives can be easily separated by a variety of techniques. These methods include paper chromatography; thin­layer chromatography (TLC), utilizing plates with cellulose or ion­exchange resins, electrophoresis; and ion­exchange column chromatography. With high­performance liquid chromatography (HPLC) nanomole quantities of these components are easily and quickly separated and detected.
12.4— Metabolism of Purine Nucleotides
The purine ring is synthesized de novo in mammalian cells utilizing amino acids as carbon and nitrogen donors and also CO2 as a carbon donor. The de novo pathway for purine nucleotide synthesis leading to inosine 5¢­monophosphate (IMP) consists of ten metabolic steps. Hydrolysis of ATP is required to drive several reactions in this pathway. Overall, the de novo pathway for purine nucleotide synthesis is expensive in terms of moles of ATP utilized per mole of IMP synthesized.
Figure 12.5 Pyrimidine nucleosides.
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Figure 12.6 Uracil nucleotides.
Purine Nucleotides Are Synthesized by a Stepwise Buildup of the Ring to Form IMP
All enzymes involved in synthesis of purine nucleotides are found in the cytosol of the cell. However, not all cells (e.g., red cells) are capable of de novo purine nucleotide synthesis. In the de novo pathway, a stepwise series of reactions leads to synthesis of IMP, which in turn serves as the precursor for both adenosine 5¢­
monophosphate (AMP) and guanosine 5¢­monophosphate (GMP). Since IMP serves as the common precursor for AMP and GMP and this pathway is highly regulated by AMP and GMP, IMP is not normally found to any extent in cells.
Formation of IMP is shown in Figure 12.7. Several points should be emphasized about this pathway: phosphoribosylpyrophosphate (PRPP) is synthesized from ribose 5­phosphate generated by the hexose monophosphate pathway; the equivalent of 6 moles of ATP are utilized per mole of IMP synthesized; formation of 5­
phosphoribosylamine (the first step) is the committed step. In formation of 5­phosphoribosylamine, the N–C bond is formed that will ultimately be the N­glycosidic bond of the purine nucleotide; there are no known regulated steps between 5­phosphoribosylamine and IMP. Tetrahydrofolate serves as a ''C1" carrier (N10­formyl H4folate, Figure 12.8) in this pathway.
The enzyme activities catalyzing several steps in the pathway reside on separate domains of multifunctional proteins. The activities of 5 ­phosphoribosylglycinamide synthetase, 5 ­phosphoribosylglycinamide transformylase, and 5 ­phosphoribosylaminoimidazole synthetase form part of a trifunctional protein. 5 ­
Phosphoribosylaminoimidazole carboxylase and 5 ­phosphoribosyl­4­(N­succinocarboxamide)­5­aminoimidazole synthetase activities are on a bifunctional protein. 5 ­Phosphoribosyl­4­carboxamide­5­aminoimidazole transformylase and IMP cyclohydrolase activities are present on another bifunctional protein.
To summarize, de novo synthesis of purine nucleotides requires amino acids as carbon and nitrogen donors, CO2 as a carbon source, and "C1 units" transferred via H4folate. The contributions of these sources to the purine ring are shown in Figure 12.9. Several amino acids including serine, glycine, tryptophan, and histidine can yield "C1 units" to H4folate (Chapter 11) and therefore they can contribute to C­2 and C­8 of the ring. 5 ­Phosphoribosyl­5­aminoimidazole carboxylase, which catalyzes the reaction in which CO2 is used to introduce C­6 of the ring, is not a biotin­dependent carboxylase.
IMP Is the Common Precursor for AMP and GMP
IMP, the first ribonucleotide formed in the de novo pathway, serves as the common precursor for AMP and GMP synthesis (Figure 12.10). AMP and GMP are converted to ATP and GTP, respectively, utilizing nucleoside 5 ­monophos­
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Figure 12.7 De novo synthesis of purine ribonucleotides. The enzymes catalyzing the reactions are: glutamine PRPP amidotransferase; GAR synthetase; GAR transformylase; FGAM synthetase; AIR synthetase; AIR carboxylase; SAICAR synthetase; adenylosuccinate lyase; AICAR transformylase; and IMP cyclohydrolase.
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Figure 12.8 Structure of N10­formyl H4folate.
Figure 12.9 Sources of carbon and nitrogen atoms in the purine ring. C­4, C­5, and N­7 are from glycine; N­3 and N­9 from glutamine; C­2 and C­8 from "C1"­H4folate; N­1 from aspartate; and C­6 from CO2.
Figure 12.10 Formation of AMP and GMP from IMP branch point.
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Figure 12.11 Effects of allosteric modulators on molecular forms of glutamine PRPP amido­transferase.
phate kinases and nucleoside 5¢­diphosphate kinases. Conversion of IMP to AMP and GMP, from this branch point, does not occur randomly. Formation of GMP from IMP requires ATP as the energy source, whereas formation of AMP from IMP requires GTP as the energy source. This can be thought of as a reciprocal relationship. That is, when there is sufficient ATP in the cell, GMP will be synthesized and when there is sufficient GTP, AMP will be synthesized.
Figure 12.12 Glutamine PRPP amidotransferase activity as a function of glutamine or PRPP concentrations.
Purine Nucleotide Synthesis Is Highly Regulated
The committed step of a metabolic pathway is generally the site of metabolic regulation. In the de novo pathway of purine nucleotide synthesis, formation of 5­
phosphoribosylamine from glutamine and 5­phosphoribosyl­1­pyrophosphate is the committed step in IMP formation. The enzyme catalyzing this reaction, glutamine PRPP amidotransferase, is rate­limiting and is regulated allosterically by the end products of the pathway—IMP, GMP, and AMP. These nucleotides serve as negative effectors. On the other hand, PRPP is a positive effector. Glutamine PRPP amidotransferase is a monomer of 135 kDa that is enzymatically active. In the presence of IMP, AMP, or GMP, the enzyme forms a dimer that is much less active. The presence of PRPP favors the active monomeric form of the enzyme (Figure 12.11).
The enzyme from human tissues has distinct nucleotide­binding sites. One site specifically binds oxypurine nucleotides (IMP and GMP) while the other site specifically binds aminopurine nucleotides (AMP). When AMP and GMP or IMP are simultaneously present, the enzyme activity is synergistically inhibited. Glutamine PRPP amidotransferase displays hyperbolic kinetics with respect to glutamine as the substrate and sigmoidal kinetics with respect to PRPP (Figure 12.12). Since the intracellular concentration of glutamine is close to its Km and the concentration varies relatively little, the glutamine concentration has little effect in regulating IMP synthesis. The intracellular concentration of PRPP, however, varies widely and can be 10 to 100 times less than the Km for PRPP. As a result, the concentration of PRPP plays an important role in regulating synthesis of purine nucleotides.
Between the formation of 5­phosphoribosylamine and IMP, there are no known regulated steps. However, there is regulation at the branch point of IMP to AMP and IMP to GMP. From IMP to GMP, IMP dehydrogenase is the rate­limiting enzyme and it is regulated by GMP acting as a competitive inhibitor. Adenylosuccinate synthetase is the rate­limiting enzyme in conversion of IMP to AMP with AMP acting as a competitive inhibitor.
Figure 12.13 Regulation of purine nucleotide synthesis. The dashed lines represent sites of active or inhibition .
There must be other as yet unknown mechanisms that regulate the ATP/GTP ratio within relatively narrow limits. In most cells the total cellular concentration of adenine nucleotides (ATP plus ADP plus AMP) is four to six times that of guanine nucleotides (GTP plus GDP plus GMP). The overall regulation of purine nucleotide synthesis is summarized in Figure 12.13. Defects in the metabolic pathway that lead to loss of regulation of purine nucleotide synthesis result in overproduction of purine nucleotides and the end product, uric acid.
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This results in a relatively common clinical condition known as gout (see Clin. Corr. 12.1).
Purine Bases and Nucleosides Can Be Salvaged to Reform Nucleotides
The efficiency of normal metabolism is shown by the presence of two distinct "salvage pathways." One pathway utilizes the bases, hypoxanthine, guanine, and adenine as substrates while the other pathway utilizes preformed nucleosides as the substrates. In each pathway there is specificity with respect to the base or nucleoside being "salvaged." The ''salvage" of bases requires the activity of phosphoribosyl transferases. There are two distinct phosphoribosyl transferases. Hypoxanthine–guanine phosphoribosyltransferase (HGPRTase) catalyzes the reactions
and
and adenine phosphoribosyltransferase (APRTase) catalyzes
CLINICAL CORRELATION 12.1 Gout
Gout is characterized by elevated uric acid levels in blood and urine due to a variety of metabolic abnormalities that lead to overproduction of purine nucleotides via the de novo pathway. Many, if not all, of the clinical symptoms associated with elevated levels of uric acid arise because of the very poor solubility of uric acid in the aqueous environment. Sodium urate crystals deposit in joints of the extremities and in renal interstitial tissue, and these events tend to trigger the sequelae. Hyperuricemia from overproduction of uric acid via the de novo pathway can be distinguished from hyperuricemia that results from kidney disease or excessive cell death (e.g., increased degradation of nucleic acids from radiation therapy). Feeding of [15N]glycine to a patient who is an overproducer will result in uric acid excreted in urine that is enriched in 15N at the N­7 of uric acid while in a patient who is not an overproducer, there will be no enrichment of 15N in uric acid from these patients.
Studies of "gouty" patients have shown that multiple and heterogeneous defects are the cause of overproduction of uric acid. In some cases, biochemical defects have not been defined. Examples of biochemical defects that result in increased purine nucleotide synthesis include the following:
1. Increased PRPP synthetase activity: Increased PRPP synthetase activity results in increased intracellular levels of PRPP. As discussed in the section on regulation of purine nucleotide synthesis, PRPP acts as a positive effector of glutamine–PRPP amidotransferase, leading to increased flux through the de novo pathway since activity of the rate­limiting step is markedly increased.
2. Partial HGPRTase activity: Partial decrease in HGPRTase activity has two fallouts with respect to the de novo pathway for purine nucleotide synthesis. First, since there is decreased salvage of hypoxanthine and guanine, PRPP is not consumed by the HGPRTase reaction and PRPP can activate glutamine–PRPP amidotransferase activity. Second, with decreased salvage of hypoxanthine and guanine, IMP and GMP are not formed via this pathway so that regulation of the PRPP amidotransferase step by IMP and GMP as negative effectors is compromised.
3. Glucose 6­phosphatase deficiency: In patients who have glucose 6­phosphatase deficiency (von Gierke's disease, type I glycogen storage disease) there is frequently hyperuricemia and gout as well. Loss of glucose 6­phosphatase activity results in more glucose 6­phosphate being shunted to the hexose monophosphate shunt. As a result of increased hexose monophosphate shunt activity, more ribose 5­phosphate is generated and the intracellular level of PRPP is increased. PRPP is a positive effector of PRPP amidotransferase.
These examples show that factors that increase the rate­limiting step in de novo synthesis of purine nucleotide synthesis lead to increased synthesis and degradation to uric acid.
There are different approaches to the treatment of gout that include colchicine, antihyperuricemic drugs, and allopurinol. Allopurinol and its metabolite, alloxanthine, are effective inhibitors of xanthine oxidase and will cause a decrease in uric acid levels. In "overproducers" who do not have a severe deficiency of HGPRTase activity, allopurinol treatment inhibits xanthine oxidase, thereby increasing the concentrations of hypoxanthine and xanthine. These purine bases are then salvaged to form IMP and XMP. These reactions consume PRPP and generate inhibitors of PRPP amidotransferase. The overall effect is that allopurinol treatment decreases both uric acid formation and de novo synthesis of purine nucleotides.
Becker, M. A., and Roessler, B. J. Hyperuricemia and gout. In: C. R. Scriver, A. L. Beaudet, W. S. Sly, and D. Valle (Eds.), The Metabolic and Molecular Bases of Inherited Disease, 7th ed., Vol. II, Chap. 49. New York: McGraw­Hill, 1995, pp. 1655–1677.
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These two enzymes do not overlap in substrate specificity. The phosphoribosyl­transferase reactions are regulated by the end products of the reactions. IMP and GMP are competitive inhibitors, with respect to PRPP, of HGPRTase while AMP is a competitive inhibitor, with respect to PRPP, of APRTase. In this way, salvage of purine bases is regulated.
The hypoxanthine and guanine for salvage arise from degradation of endogenous or exogenous purine nucleotides. On the other hand, the source of adenine utilized in the APRTase reaction appears to be mainly from synthesis of polyamines (see p. 473). For each molecule of spermine synthesized, two molecules of 5¢­
methylthioadenosine are generated that are degraded to 5­methylthioribose­1­phosphate and adenine via the 5¢­methylthioadenosine phosphorylase­
catalyzed reaction. The adenine base is salvaged through the APRTase reaction.
Generation of AMP and GMP through these phosphoribosyltransferase reactions effectively inhibits the de novo pathway at the PRPP amidotransferase step. First, PRPP is consumed, decreasing the rate of formation of 5­phosphoribosylamine; and second, AMP and GMP serve as feedback inhibitors at this step.
HGPRTase activity is markedly depressed in the Lesch–Nyhan syndrome (see Clin. Corr. 12.2), which is characterized clinically by hyperuricemia, mental retardation, and self­mutilation.
CLINICAL CORRELATION 12.2 Lesch–Nyhan Syndrome
The Lesch–Nyhan syndrome is characterized clinically by hyperuricemia, excessive uric acid production, and neurological problems, which may include spasticity, mental retardation, and self­mutilation. This disorder is associated with a very severe or complete deficiency of HGPRTase activity. The gene for HGPRTase is on the X chromosome, hence the deficiency is virtually limited to males. In a study of the available patients, it was observed that if HGPRTase activity was less than 2% of normal, mental retardation was present, and if the activity was less than 0.2% of normal, the self­mutilation aspect was expressed. This defect also leads to excretion of hypoxanthine and xanthine.
There are more than a hundred disease­related mutations defined in the HGPRTase gene from Lesch–Nyhan patients. These have led to the loss of HGPRTase protein, loss of HGPRTase activity, "Km mutants," HGPRTase protein with a short half­life, and so on.
The role of HGPRTase is to catalyze reactions in which hypoxanthine and guanine are converted to nucleotides. The hyperuricemia and excessive uric acid production that occur in patients with the Lesch–Nyhan syndrome are easily explained by the lack of HGPRTase activity. Hypoxanthine and guanine are not salvaged, leading to increased intracellular pools of PRPP and decreased levels of IMP or GMP. Both of these factors promote de novo synthesis of purine nucleotides without regard for proper regulation of this pathway.
It is not understood why a severe defect in this salvage pathway leads to neurological problems. Adenine phosphoribosyltransferase activity in these patients is normal or elevated. With this salvage enzyme, presumably the cellular needs for purine nucleotides could be met by conversion of AMP to GMP via IMP if the cell's de novo pathway were not functioning. The normal tissue distribution of HGPRTase activity perhaps could explain the neurological symptoms. The brain (frontal lob, basal ganglia, and cerebellum) has 10–20 times the enzyme activity found in liver, spleen, or kidney and from 4 to 8 times that found in erythrocytes. Individuals who have primary gout with excessive uric acid formation and hyperuricemia do not display neurological problems. It is argued that products of purine degradation (hypoxanthine, xanthine, and uric acid) cannot be toxic to the central nervous system (CNS). However, it is possible that these metabolites are toxic to the developing CNS or that lack of this enzyme leads to an imbalance in the concentrations of purine nucleotides at critical times during development.
If IMP dehydrogenase activity in brain were extremely low, lack of HGPRTase could lead to decreased levels of intracellular GTP due to decreased salvage of guanine. Since GTP is a precursor of tetrahydrobiopterin, a required cofactor in the biosynthesis of neurotransmitters, and is required in other functions such as signal transduction via G­
proteins and protein synthesis, low levels of GTP during development could be the triggering factor in the observed neurological manifestations.
Treatment of Lesch–Nyhan patients with allopurinol will decrease the amount of uric acid formed, relieving some of the problems caused by sodium urate deposits. However, since the Lesch–Nyhan patient has a marked reduction in HGPRTase activity, hypoxanthine and guanine are not salvaged, PRPP is not consumed, and consequently de novo synthesis of purine nucleotides is not shut down. There is no treatment for the neurological problems. These patients usually die from kidney failure, resulting from high sodium urate deposits.
Rossiter, B. J. F., and Caskey, C. T. Hypoxanthine­guanine phosphoribosyl­transferase deficiency: Lesch–Nyhan syndrome and gout. In: C. R. Scriver, A. L. Beaudet, W. S. Sly, and D. Valle (Eds.), The Metabolic and Molecular Bases of Inherited Disease, 7th ed., Vol II, Chap. 50. New York: McGraw Hill, 1995, pp. 1679–1706.
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Overall, these salvage reactions not only conserve energy but also permit cells to form nucleotides from the bases. The erythrocyte, for example, does not have glutamine PRPP amidotransferase and hence cannot synthesize 5­phosphoribosylamine, the first unique metabolite in the pathway of purine nucleotide synthesis. As a consequence, red cells must depend on purine phosphoribosyltransferases and 5 ­phosphotransferase to replenish their nucleotide pools.
Purine Nucleotides Can Be Interconverted to Maintain the Appropriate Balance of Adenine and Guanine Nucleotides
De novo synthesis of purine nucleotides is under very fine control, executed at the committed step catalyzed by glutamine PRPP amidotransferase and at the branch point of IMP to AMP and IMP to GMP. Additional enzymes present in mammalian cells allow for interconversions of adenine and guanine nucleotides to maintain the appropriate balance of cellular concentrations of these purine nucleotides. These interconversions occur by indirect steps. There is no direct one­step pathway for conversion of GMP to AMP or AMP to GMP. In each case, AMP or GMP is metabolized to IMP (Figure 12.14). These reactions are catalyzed by separate enzymes, each of which is under separate controls. Reductive deamination of GMP to IMP is catalyzed by GMP reductase. GTP activates this step while XMP is a strong competitive inhibitor of the reaction. GTP, while not required by the enzyme, increases enzyme activity by lowering the Km with respect to GMP and by increasing Vmax.
AMP deaminase (5 ­AMP aminohydrolase) catalyzes deamination of AMP to IMP and is activated by K+ and ATP and inhibited by Pi, GDP, and GTP. In the absence of K+, the u versus [AMP] curve is sigmoidal. The presence of K+ is not required for maximum activity; rather K+ is a positive allosteric effector reducing the apparent Km for AMP.
The net effect of these reactions is that cells can interconvert adenine and guanine nucleotides to meet cellular needs, while maintaining control over these reactions.
GTP Is Precursor of Tetrahydrobiopterin
GTP is the direct precursor for tetrahydrobiopterin synthesis (Figure 12.15). Reactions from GTP to tetrahydrobiopterin are catalyzed by GTP cyclohydrolase I, 6­pyruvoyl­tetrahydropterin synthase, and sepiapterin reductase, with GTP cyclohydrolase I being rate­limiting. Many cell types can synthesize tetrahydrobiopterin. Tetrahydrobiopterin is a required cofactor in hydroxylation reactions involving phenylalanine, tyrosine, and tryptophan (see p. 476) and is involved in the generation of nitric oxide. Inhibitors of IMP dehydrogenase cause a marked reduction in cellular levels of tetrahydrobiopterin, demonstrating the importance of GTP as the precursor of tetrahydrobiopterin and of IMP dehydrogenase as the rate­limiting enzyme in GTP formation.
Figure 12.14 Interconversions of purine nucleotides. The dashed lines represent sites of regulation; inhibition.
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Figure 12.15 Synthesis of tetrahydrobiopterin from GTP.
End Product of Purine Degradation in Humans Is Uric Acid
The degradation of purine nucleotides, nucleosides, and bases funnel through a common pathway leading to formation of uric acid (Figure 12.16). The enzymes involved in degradation of nucleic acids and nucleotides and nucleosides vary in specificity. Nucleases show specificity toward either RNA or DNA and also toward the bases and position of cleavage site at the 3 ,5 ­phosphodiester bonds. Nucleotidases range from those with relatively high specificity, such as 5 ­AMP nucleotidase, to those with broad specificity, such as the acid and alkaline phosphatases, which will hydrolyze any of the 3 ­ or 5 ­nucleotides. AMP deaminase is specific for AMP. Adenosine deaminase is less specific, since not only adenosine but also 2 ­deoxyadenosine and many other 6­amino­purine nucleosides are deaminated by this enzyme.
Purine nucleoside phosphorylase catalyzes the reversible reactions
or
or
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Figure 12.16 Degradation of purine nucleotides.
Deoxyinosine and deoxyguanosine are also excellent substrates for purine nucleoside phosphorylase. This is important for removal of deoxyguanosine to prevent uncontrolled accumulation of dGTP, which is toxic to cells at high concentrations. While the equilibrium constants for reactions catalyzed by purine nucleoside phosphorylase favor the direction of nucleoside synthesis, cellular concentrations of free purine base and ribose 1­phosphate are too low to support nucleoside synthesis under normal conditions. The main function of the enzyme is the degradative rather than synthetic pathway. Deficiencies in adenosine deaminase and purine nucleoside phosphorylase have been correlated with disease states in humans. Adenosine deaminase deficiency is associated with severe combined immunodeficiency, and purine nucleoside phosphorylase deficiency with a defective T­cell immunity but normal B­cell immunity (see Clin. Corr. 12.3).
Formation of Uric Acid
As seen in Figure 12.16, adenine nucleotides end up as hypoxanthine while guanine nucleotides are metabolized to xanthine. These purines are metabolized by xanthine oxidase to form uric acid, a unique end product of purine nucleotide degradation in humans. The reactions are as follows:
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