Purine Ribonucleotide Metabolism (Molecular Biology)

1. Biosynthesis of the Purine Ring

The biosynthetic pathway for the purine ring was described in the 1950s, in a classic series of experiments carried out in the laboratories of John Buchanan and G. Robert Greenberg. Birds excrete most of their nitrogen in the form of uric acid, an oxidized purine. Therefore, by feeding radiolabeled precursors to pigeons and then chemically degrading the uric acid crystallized from their droppings, it was possible to identify precursors to each position in the ring, and this led to identification of the reactions and isolation of the enzymes involved. This pathway is called the de novo pathway because it involves synthesis of the purine ring from low-molecular-weight precursors. A separate set of pathways is referred to as salvage pathways because they involve reutilization of preformed purine ring-containing compounds, usually nucleosides or nucleobases released by nucleic acid degradation (see Salvage Pathways To Nucleotide Biosynthesis).

2. De Novo Biosynthesis of Purine Nucleotides

2.1. Biosynthesis of Inosinic Acid

The early radiolabeling studies identified the precursors of the purine ring (Fig. 1) as glycine, glutamine amide nitrogen, CO2, aspartate amino nitrogen, along with the "one-carbon pool," which included formate or the b-carbon of serine but which is now known to come directly from the formyl group of N10-formyltetrahydrofolate (10-formyl-THF). The pathway is sensitive to inhibition by folate antagonists, such as methotrexate, and glutamine antagonists, such as azaserine, and this sensitivity largely explains the chemotherapeutic efficacy of these classes of antimetabolites. Aside from a number of parasitic protozoans, which lack the capacity for purine ring synthesis and depend on salvage pathways, the de novo purine synthetic pathway is virtually identical among all organisms examined to date.


Figure 1. Metabolic sources of the atoms of the purine ring, as determined by administration of labeled precursors.

Metabolic sources of the atoms of the purine ring, as determined by administration of labeled precursors.

That pathway, summarized in Figure 2, involves the stepwise assembly of the purine ring at the nucleotide level, on a ribose 5-phosphate backbone. In the first committed reaction (step 1), the glutamine amide group displaces the pyrophosphate at C-1 of 5-phosphoribosyl-1-pyrophosphate (PRPP), to give 5-phosphoribosylamine, the simplest possible nucleotide (its base is ammonia). The enzyme, PRPP amidotransferase , is the principal point for control of the overall pathway. There follows the ATP-dependent incorporation of glycine (step 2), the first of two formyltransferase reactions involving N10-formyltetrahydrofolate (step 3), a second glutamine amidotransferase reaction (step 4), and a ring closure (step 5), yielding the imidazole portion of the bicyclic purine ring. The next reaction (step 6) is a CO2-fixation reaction unusual in that it does not require biotin as a cofactor. Next (step 7), an ATP-dependent reaction links the aspartate amino nitrogen to the carboxyl group formed in the previous reaction. There follows an a,b-elimination reaction (step 8) in which the carbon skeleton of aspartate is released as fumarate, with its nitrogen becoming part of a carboxamide group. A second formyltransferase (step 9) creates a product that undergoes an intramolecular condensation (step 10), yielding inosinic acid (IMP), the first completed purine nucleotide. IMP has hypoxanthine as its purine base.

Figure 2. The de novo biosynthetic pathway to inosinic acid. Enzyme names: 1, PRPP amidotransferase; 2, GAR synthe’ FGAR amidotransferase; 5, FGAM cyclase; 6, AIR carboxylase; 7, SAICAR synthetase; 8, SAICAR lyase; 9, AICAR tr synthase.

 The de novo biosynthetic pathway to inosinic acid. Enzyme names: 1, PRPP amidotransferase; 2, GAR synthe' FGAR amidotransferase; 5, FGAM cyclase; 6, AIR carboxylase; 7, SAICAR synthetase; 8, SAICAR lyase; 9, AICAR tr synthase.

2.2. Conversion of IMP to Adenine and Guanine Nucleotides

IMP represents a branch point in the synthesis of adenine and guanine nucleotides, as shown in Figure 3. En route to GMP, IMP dehydrogenase oxidizes the hypoxanthine base of IMP to the xanthine base of xanthosine monophosphate (XMP). An ATP-dependent glutamine amidotransferase converts XMP to GMP. En route to AMP, IMP undergoes a reaction sequence involving aspartate, which is very similar to reactions 7 and 8 of the IMP synthetic pathway, except that GTP, not ATP, is the energy cofactor. The release of fumarate is the last step in AMP synthesis.

Figure 3. Pathways from inosinic acid to ATP and GTP. R-P is a ribose 5-phosphate moiety. NDP kinase is nucleoside diphosphate kinase. A few organisms reduce ribonucleotides to deoxyribonucleotides at the triphosphate level rather than, as shown here, the diphosphate level.

Pathways from inosinic acid to ATP and GTP. R-P is a ribose 5-phosphate moiety. NDP kinase is nucleoside diphosphate kinase. A few organisms reduce ribonucleotides to deoxyribonucleotides at the triphosphate level rather than, as shown here, the diphosphate level.

AMP and GMP are converted to the respective 5′-diphosphates by specific nucleotide kinases. The resultant ADP and GDP are converted to the triphosphates by nucleoside diphosphate kinase, an active and nonspecific enzyme that transfers the g-(outermost) phosphate of any nucleoside 5′-triphosphate to any nucleoside 5′-diphosphate. Because the reaction has an equilibrium constant close to 1, the direction of the reaction is determined primarily by concentrations of substrates and products. Because ATP is by far the most abundant nucleotide in most aerobic cells, the principal function of nucleoside diphosphate kinase is to catalyze the ATP-dependent conversion of nucleoside diphosphates to triphosphates, using ATP that was produced by oxidative phosphorylation.

In most organisms, the ribonucleoside diphosphates (purine and pyrimidine) serve as precursors for biosynthesis of deoxyribonucleotides (see Ribonucleotide Reductases and Deoxyribonucleotide Biosynthesis And Degradation). In some organisms, however, those precursors are the respective triphosphates.

2.3. Multifunctional Enzymes and Enzyme Complexes

Vertebrate cells contain a number of the various enzyme activities of IMP biosynthesis in the form of multifunctional enzymes. This was first suspected when cloned vertebrate cDNAs encoding purine synthetic enzymes were found to complement multiple genetic defects in purine synthesis after transformation into Escherichia coli (1). By this means, it was found that a single enzyme catalyzes the second, third, and fifth reactions shown in Figure 2. Similar evidence indicated that the sixth and seventh reactions are catalyzed by a bifunctional enzyme. Moreover, the two transformylase enzymes (reactions 3 and 9) in some animals constitute part of a tightly associated multienzyme complex that also contains several activities of tetrahydrofolate metabolism and single-carbon mobilization. The metabolic rationale for all these enzyme associations has not been established, but it may well involve the cell’s attempt to utilize scarce or unstable intermediates more efficiently by facilitating their transfer from active site to active site within the same reaction sequence.

2.4. Regulation

Control of purine nucleotide synthesis involves both allosteric and genetic regulation. In most cells, PRPP synthetase, which synthesizes the first intermediate in IMP synthesis, is inhibited by AMP, ADP, and GDP, whereas PRPP amidotransferase (reaction 1), the primary control point for the overall reaction (2), is inhibited allosterically by AMP, ADP, GMP, and GDP. In E. coli, biosynthesis of the enzymes of IMP synthesis is inhibited by a repressor encoded by the purR gene. This protein binds either hypoxanthine or guanine, and the resultant protein-purine base complex binds to DNA sites upstream from promoters for several purine (and pyrimidine) biosynthetic enzymes. The crystal structure of the PurR repressor (3) shows it to be closely related to the well-known Lac repressor, which controls the lactose utilization operon by similar mechanisms.

Conversion of IMP to AMP and GMP is also regulated allosterically. GMP inhibits IMP dehydrogenase, the enzyme that converts IMP to GMP, whereas AMP controls its own formation by inhibiting the addition of aspartate to AMP to form adenylosuccinate (Fig. 3). Also, it may have regulatory significance that ATP is involved in the conversion of IMP to GMP, whereas GTP is required for one of the reactions leading from IMP to AMP.

3. Catabolism of purine nucleotides

Nucleotides released by enzymatic digestion of nucleic acids are rather efficiently reutilized for nucleic acid biosynthesis in most cells. However, pathways of nucleotide degradation are significant, as shown by sometimes unexpected and severe consequences of genetic deficiencies in humans of particular enzymes of purine degradation, as dealt with in the next section.

In primates, the end product of purine nucleotide catabolism is uric acid, which is excreted as such. Pathways leading to uric acid vary considerably in different tissues and cells. Most of the reactions involved are shown in Figure 4. Note, for example, that AMP degradation can begin either with deamination, to yield IMP, or with hydrolysis, to yield adenosine. In mammals, the deamination pathway is particularly active in muscle tissue. Both pathways lead to the nucleoside inosine, which is cleaved by inorganic phosphate and purine nucleoside phosphorylase , yielding ribose 1-phosphate and hypoxanthine. Hypoxanthine is oxidized by the versatile molybdenum- and iron-containing enzyme, xanthine oxidase , to xanthine, which is also produced by guanine nucleotide catabolism. Xanthine is also acted on by xanthine oxidase, to give uric acid. As noted, the process ends here in primates. However, most animals further degrade uric acid to allantoin and then to allantoic acid. Some fishes excrete allantoic acid, but most aquatic animals further catabolize allantoic acid to urea and, in the case of marine invertebrates, to ammonia. These latter pathways are summarized in Figure 5.

Figure 4. Pathways of purine nucleotide catabolism to uric acid. R-1-P is ribose 1-phosphate.

Pathways of purine nucleotide catabolism to uric acid. R-1-P is ribose 1-phosphate.

Figure 5. Metabolic degradation of uric acid.

Metabolic degradation of uric acid.

4. Clinical abnormalities of purine metabolism

Six classes of metabolic disorders involving purines have been described (4-9). Three of these conditions—adenine phosphoribosyltransferase deficiency (4), adenylate deaminase deficiency (5), and xanthine oxidase deficiency (6)—are quite rare and will not be discussed here. The three conditions that will be described either are relatively common or their study has revealed important metabolic principles and relationships, or both.

4.1. Hyperuricemia and Gout

Gout refers to a family of diseases in which prolonged elevation of uric acid levels in tissues and blood leads to its crystallization in the joints, causing intermittent attacks of an acute inflammatory arthritis (7). Prolonged hyperuricemia does not always lead to gout attacks; factors leading to the precipitation of urate salts are not thoroughly understood.

Normally, about two-thirds of the uric acid produced in purine catabolism is excreted through the kidneys; the remainder is further broken down by intestinal bacteria. Renal malfunction can lead to elevation of blood uric acid levels, which is a cause of gout. Gout also results from abnormally high purine nucleotide synthesis, which leads to degradation of the excess. Three specific biochemical changes are known to cause this condition. First, hyperactivity of PRPP synthetase elevates intracellular concentrations of PRPP, the substrate for PRPP amidotransferase, the first and rate-controlling step in the de novo pathway (reaction 1, Fig. 2), and this increases flux through the whole pathway.

A second form of gout results from partial or complete deficiency of a purine salvage enzyme, hypoxanthine-guanine phosphoribosyltransferase (HGPRT). This enzyme catalyzes the following reactions:

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It is not yet clear why this deficiency accelerates purine synthesis. One model states that in the absence of these salvage pathways, GMP levels decline which, in turn, modulates the feedback inhibition of PRPP amidotransferase by this nucleotide. Alternatively, it has been proposed that decreased flux through this salvage pathway causes PRPP to accumulate and this, in turn, accelerates flux through PRPP amidotransferase by substrate level control.

The third enzymatic deficiency leading to gout is a deficiency of glucose-6-phosphatase (glycogen storage disease type I). The relationship between this abnormality and uric acid accumulation is still obscure. Whatever the basis for hyperuricemia, the most effective drug for treating the condition is the xanthine oxidase inhibitor allopurinol.

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Inhibition of xanthine oxidase causes hypoxanthine and xanthine—both of which are both more soluble and less toxic than uric acid—to accumulate, thereby preventing uric acid precipitation.

4.2. Lesch-Nyhan Syndrome

As noted, a partial HGPRT deficiency leads to gout. A total deficiency of this enzyme has far more serious consequences. Lesch-Nyhan syndrome (8) involves not only severe hypericemia and gout but, in addition, the nervous system develops abnormally, leading to spasticity and behavioral problems, including aggressive behavior toward others and self-mutilation. Because the gene for HGPRT lies on the X-chromosome, the Lesch-Nyhan syndrome is sex-linked, having been observed only in males. Although the gouty arthritis of Lesch-Nyhan syndrome usually responds well to allopurinol, there is no known cure for the developmental and neurological abnormalities, and afflicted individuals rarely live beyond age 20. Moreover, although it is clear that all symptoms of this condition arise from the HGPRT deficiency, the specific relationship between the enzyme deficiency and the neuropathology is not understood.

4.3. Immunodeficiencies Caused by Purine Abnormalities (9)

In 1972, a patient with an inheritable combined immunodeficiency involving both B and T cells was found to be deficient in the enzyme adenosine deaminase (ADA), which converts adenosine to inosine in purine nucleotide catabolism (see Fig. 4). This surprising finding was followed by the discovery of other families in which the same enzyme deficiency was associated with severe combined immunodeficiency and, by now, several hundred such families have been described. In 1975, a second form of immunodeficiency was found to result from a different purine abnormality, namely, a deficiency of purine nucleoside phosphorylase, an enzyme whose primary function is to degrade guanosine to guanine in purine catabolism. Often, purine nucleoside phosphorylase deficiency involves only defective T-cell function in the immune system.

What is the relationship between deficiencies in two obscure purine catabolic enzymes and defective immune function? A clue came when it was found that erythrocytes of ADA-deficient patients contained high levels of deoxyadenosine and dATP. Since human erythrocytes are without nuclei, the presence of a DNA precursor seemed gratuitous. Subsequently, it was found that dATP accumulates in many tissues. It arises because ADA acts on deoxyadenosine as well as adenosine. Lymphoid tissues have very high activities of purine salvage enzymes, which reutilize products released in nucleic acid breakdown of cells undergoing apoptosis. Accumulation of deoxyadenosine, when its catabolism is blocked, leads to its conversion to dATP in these tissues, and it accumulates in both red and white blood cells. dATP is a potent allosteric inhibitor of ribonucleotide reductase, and its accumulation can block the white cell proliferative response that results from immunochallenge by inhibiting an essential step in replication of DNA—the synthesis of its precursors. There are also indications that excessive accumulation of dATP leads to an ATP deficiency in some cells. By contrast, in PNP-defective cells, the deoxyribonucleotide that accumulates is primarily dGTP, which is a less potent inhibitor of ribonucleotide reductase. This may explain the somewhat milder immune dysfunction associated with PNP deficiency. However, a completely different mechanism for the toxic effect has recently come to light from in vitro studies showing that dATP, in combination with cytochrome c, triggers a chain of protease activation steps leading ultimately to apoptosis (10).

Adenosine deaminase deficiency is the first condition to be treated by gene therapy.

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