In de Novo Synthesis, the Pyrimidine Ring Is Assembled from Bicarbonate, Aspartate, and Glutamine

The pyrimidine ring is assembled first and then linked to ribose phosphate to form a pyrimidine nucleotide. PRPP is the donor of the ribose phosphate moiety. The synthesis of the pyrimidine ring starts with the formation of carbamoylaspartate from carbamoyl phosphate and aspartate, a reaction catalyzed by aspartate transcarbamoylase. Dehydration, cyclization, and oxidation yield orotate, which reacts with PRPP to give orotidylate. Decarboxylation of this pyrimidine nucleotide yields UMP. CTP is then formed by the amination of UTP.

Purines Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways

The purine ring is assembled from a variety of precursors: glutamine, glycine, aspartate, N¹⁰-formyltetrahydrofolate, and CO₂. The committed step in the de novo synthesis of purine nucleotides is the formation of 5-phosphoribosylamine from 5-phosphoribosyl-1-pyrophosphate (PRPP) and glutamine. The purine ring is assembled on ribose phosphate, in contrast with the de novo synthesis of pyrimidine nucleotides. The addition of glycine, followed by formylation, amination, and ring closure, yields 5-aminoimidazole ribonucleotide. This intermediate contains the completed five-membered ring of the purine skeleton. The addition of CO₂, the nitrogen atom of aspartate, and a formyl group, followed by ring closure, yields inosinate (IMP), a purine ribonucleotide. AMP and GMP are formed from IMP. Purine ribonucleotides can also be synthesized by a salvage pathway in which a preformed base reacts directly with PRPP.

Deoxyribonucleotides Are Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism

Deoxyribonucleotides, the precursors of DNA, are formed in E. coli by the reduction of ribonucleoside diphosphates. These conversions are catalyzed by ribonucleotide reductase. Electrons are transferred from NADPH to sulfhydryl groups at the active sites of this enzyme by thioredoxin or glutaredoxin. A tyrosyl free radical generated by an iron center in the reductase initiates a radical reaction on the sugar, leading to the exchange of H for OH at C-2′. TMP is formed by methylation of dUMP. The donor of a methylene group and a hydride in this reaction is N⁵,N¹⁰-methylenetetrahydrofolate, which is converted into dihydrofolate. Tetrahydrofolate is regenerated by the reduction of dihydrofolate by NADPH. Dihydrofolate reductase, which catalyzes this reaction, is inhibited by folate analogs such as aminopterin and methotrexate. These compounds and fluorouracil, an inhibitor of thymidylate synthase, are used as anticancer drugs.

Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition

Pyrimidine biosynthesis in E. coli is regulated by the feedback inhibition of aspartate transcarbamoylase, the enzyme that catalyzes the committed step. CTP inhibits and ATP stimulates this enzyme. The feedback inhibition of glutamine-PRPP amidotransferase by purine nucleotides is important in regulating their biosynthesis.

NAD⁺, FAD, and Coenzyme A Are Formed from ATP

Nucleotides are important constituents not only of RNA and DNA, but also of a number of other key biomolecules. Coenzymes NAD⁺ and FAD, prominent in oxidation-reduction reactions, have ADP as an important constituent. The acyl-group activation compound, coenzyme A, is also derived from ATP.

Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions

Purines are degraded to urate in human beings. Gout, a disease that affects joints and leads to arthritis, is associated with the excessive accumulation of urate. The Lesch-Nyhan syndrome, a genetic disease characterized by self-mutilation, mental deficiency, and gout, is caused by the absence of hypoxanthine-guanine phosphoribosyltransferase. This enzyme is essential for the synthesis of purine nucleotides by the salvage pathway.

Key Terms

nucleoside

nucleotide

pyrimidine

carbamoyl phosphate synthetase (CSP)

ATP-grasp fold

5-phosphoribosyl-1-pyrophosphate (PRPP)

orotidylate

purine

salvage pathway

inosinate

hypoxanthine

glutamine phosphoribosyl amidotransferase

ribonucleotide reductase

thymidylate synthase

dihydrofolate reductase