Purine & Pyrimidine Metabolism

Nucleotide building blocks and de novo synthesis

Purines vs pyrimidines. Purines (adenine, guanine) have a fused double ring; pyrimidines (cytosine, uracil, thymine) have a single ring. Thymine appears in DNA and uracil in RNA. Both classes are built using PRPP (phosphoribosyl pyrophosphate), which PRPP synthetase makes from ribose-5-phosphate supplied by the pentose phosphate pathway.

PURe As Gold: the purines are A and G. CUT the pyrimidines: C, U, T.

Purine synthesis. The purine ring is assembled piece by piece directly on PRPP (ribose-5-phosphate). Its atoms come from glycine, aspartate, glutamine, CO₂, and N10-formyl-tetrahydrofolate, so purine synthesis is folate-dependent. The committed step is glutamine-PRPP amidotransferase. The first finished nucleotide, IMP, is the branch point to AMP and GMP; IMP dehydrogenase opens the guanine branch.

Pyrimidine synthesis. The order is reversed: the ring is made first as free orotic acid and only then joined to PRPP. Carbamoyl phosphate synthetase II (CPS II, cytosolic, rate-limiting) makes carbamoyl phosphate from glutamine and CO₂; it combines with aspartate, the ring closes, and dihydroorotate dehydrogenase yields orotic acid. UMP synthase, a bifunctional enzyme, attaches PRPP to orotate and decarboxylates it to UMP, the parent of UDP, UTP, CTP, and dTMP. CPS II is distinct from mitochondrial CPS I of the urea cycle.

Deoxynucleotides. Ribonucleotide reductase converts ribonucleotides to deoxyribonucleotides (NDP → dNDP) for DNA. Hydroxyurea inhibits it and is used in sickle cell disease (it raises HbF), CML, and polycythemia vera. Thymidylate synthase then methylates dUMP to dTMP using N5,N10-methylene-THF, which is left as dihydrofolate; dihydrofolate reductase (DHFR) must regenerate THF for the next round, which is why dTMP synthesis needs folate.

Purine salvage and degradation

Salvage. Instead of building rings from scratch, cells recycle free bases by reattaching them to PRPP. HGPRT salvages hypoxanthine to IMP and guanine to GMP; APRT salvages adenine to AMP.

Degradation. Adenosine deaminase (ADA) converts adenosine to inosine, and purine nucleoside phosphorylase releases the free bases. Xanthine oxidase catalyzes both final steps, hypoxanthine → xanthine → uric acid (guanine enters at xanthine). Humans lack urate oxidase, so uric acid is the end product and is excreted by the kidney; excess causes gout and urate stones.

Inherited enzyme defects

Lesch-Nyhan syndrome. X-linked recessive absence of HGPRT. Failed salvage sends hypoxanthine and guanine down the degradation pathway, and unused PRPP plus lost IMP/GMP feedback drive extra de novo purine synthesis, so uric acid is massively overproduced. Boys show intellectual disability, self-mutilation (lip and finger biting), aggression, dystonia, gout, and orange uric acid "sand" in the diaper. Allopurinol or febuxostat controls the hyperuricemia but does not reverse the neurologic or behavioral features.

HGPRT: Hyperuricemia, Gout, Pissed off (aggression), Retardation (intellectual disability), dysTonia.

ADA deficiency. An autosomal recessive form of severe combined immunodeficiency (SCID), classically the most common autosomal recessive cause. Without ADA, deoxyadenosine is phosphorylated to dATP, which accumulates and feedback-inhibits ribonucleotide reductase; with no dNTPs, lymphocytes cannot proliferate, so both T and B cells are absent. Infants have recurrent severe infections and no thymic shadow. Definitive therapy is hematopoietic stem cell transplant; enzyme replacement and gene therapy are alternatives.

Orotic aciduria. Hereditary orotic aciduria is a UMP synthase defect: orotic acid is excreted in urine, and blocked pyrimidine (DNA) synthesis causes megaloblastic anemia that B12 and folate do not correct, plus failure to thrive, with no hyperammonemia. Oral uridine bypasses the block. Ornithine transcarbamylase (OTC) deficiency also raises orotic acid, but for a different reason: carbamoyl phosphate that cannot enter the urea cycle spills into pyrimidine synthesis.

Drugs that target nucleotide metabolism

Antifolates and 5-FU. Methotrexate (human), trimethoprim (bacterial), and pyrimethamine (protozoal) inhibit DHFR, depleting THF and therefore dTMP and purines. 5-Fluorouracil is converted to 5F-dUMP, which inhibits thymidylate synthase directly. Both starve dividing cells of dTMP. Leucovorin (folinic acid) supplies reduced folate beyond the DHFR block and rescues methotrexate toxicity; it does not rescue 5-FU and in fact potentiates it (uridine triacetate is the 5-FU antidote).

Purine-synthesis inhibitors. 6-Mercaptopurine (the active metabolite of azathioprine) needs HGPRT for activation, blocks de novo purine synthesis, and is degraded by xanthine oxidase. Mycophenolate and ribavirin inhibit IMP dehydrogenase, cutting guanine nucleotide synthesis, on which lymphocytes depend. Leflunomide inhibits dihydroorotate dehydrogenase, a pyrimidine step. Pentostatin inhibits ADA and exploits the same lymphotoxicity to treat hairy cell leukemia.

Urate-lowering drugs. Allopurinol and febuxostat inhibit xanthine oxidase; they are used for chronic gout and tumor lysis prophylaxis. Rasburicase (recombinant urate oxidase) converts uric acid to soluble allantoin; it generates hydrogen peroxide and is avoided in G6PD deficiency.

Azathioprine or 6-MP given with allopurinol or febuxostat needs a sharp thiopurine dose reduction: with xanthine oxidase blocked, the drug accumulates and causes marrow suppression.