Purine and Pyrimidine Metabolism

Purine, Pyrimidine, and Single-Carbon Metabolism

• Purines and pyrimidines are nitrogen-containing molecules.
• Nucleotides function as high-energy substrates, precursors for DNA and RNA synthesis, intracellular signaling molecules, and components of coenzymes.
• Purines and pyrimidines are produced adequately, so dietary intake isn't required.
• Salvage pathways recycle purines and pyrimidines from the diet or metabolic degradation.

Purine Synthesis

• 5-Phosphoribosyl-1-pyrophosphate (PRPP) is the precursor for purine and pyrimidine synthesis and salvage.
• PRPP is produced by pyrophosphorylation of ribose 5-phosphate and consumes two high-energy bonds.
• An amine is added to PRPP by an amidotransferase to form 5-phosphoribosylamine.
• This is the committed and rate-limiting step in purine synthesis, which is subject to feedback regulation by AMP, GMP, and IMP.
• High PRPP concentrations override AMP, GMP, and IMP inhibition via feed-forward regulation
• The purine pathway involves nine reactions, incorporating components to produce IMP.
• The purine ring is composed of the glycine skeleton, aspartate's amino nitrogen, glutamine's amide nitrogen, carbon and O2 from CO2, and two single-carbon additions from tetrahydrofolate.
• IMP is the end product of the pathway and a precursor for both AMP and GMP.
• GMP synthesis requires adenosine triphosphate (ATP)
• AMP synthesis requires guanosine triphosphate.

Purine Salvage

• Salvage pathways recycle purine and pyrimidine bases from RNA and DNA turnover.
• Phosphoribosyl transferase enzymes transfer phosphoribosyl groups from PRPP to free bases, producing mononucleotides.
• Adenine phosphoribosyl transferase produces adenylate from adenine.
• Hypoxanthine-guanine phosphoribosyl transferase produces inosinate and guanylate from hypoxanthine and guanine.
• Purines are assembled on ribose 5-phosphate differently from pyrimidines.
• IMP is the first purine intermediate with an intact ring.
• Increased production leads to more Uric Acid rather than AMP and GMP.

Degradation of Purines to Uric Acid

• Cells degrade unneeded purines which results in uric acid, which is excreted,
• Adenine degradation converges to form inosine, then hypoxanthine
• Xanthine oxidase converts Hypoxanthine to xanthine, and xanthine to uric acid.
• Xanthine oxidase reactions produce hydrogen peroxide, then converted to water and O2.

Pyrimidine Synthesis

• Carbamoyl aspartate contains the components of the final pyrimidine ring.
• Carbamoyl aspartate is formed from aspartate and carbamoyl phosphate
• The pyrimidine products are UTP, CTP, and thymidylate.
• Carbamoyl phosphate is formed by cytoplasmic carbamoyl phosphate synthetase.
• Cytoplasmic carbamoyl phosphate synthetase uses glutamine as a nitrogen source.
• Aspartate transcarbamoylase combines aspartate and carbamoyl phosphate and is regulated to balance purine and pyrimidine production.
• Elevated urate concentrations are treated colchicine or allopurinol.
• Colchicine inhibits inflammation and phagocytosis, while allopurinol inhibits xanthine oxidase.
• N-acetylglutamate doesn't stimulate the cytoplasmic form, and cross-regulation coordinates synthesis through ATP and GTP requirements.

Synthesis of Pyrimidine Nucleotides from Orotate

• Carbamoyl aspartate undergoes ring closure and oxidation to form orotic acid
• Uridylate is formed when PRPP is added to orotate ring structure, followed by decarboxylation.
• UMP gets converted to UTP through phosphorylation by ATP, then converts to CTP through amination with the amido from glutamine.

Thymidylate Synthesis

• DNA requires thymine, therefore UDP is a precursor to thymidylate.
• UTP and CTP is needed for thymidylate production
• UDP converts to deoxyuridine diphosphate (dUDP) by ribonucleotide reductase
• dUDP produces deoxyuridine monophosphate during dephosphorylation.
• Thymidylate synthase transfers a methyl group from 5,10-methylene tetrahydrofolate to form dTMP.
• Thymidylate synthase is irreversibly inactivated by the cancer drug fluorouracil.
• Uracil and thymine are salvaged by pyrimidine phosphoribosyl transferase using PRPP,

Nucleoside Phosphate Interconversion

• Nucleotides are created as monophosphates but converted to diphosphates by nucleoside monophosphate kinase enzymes, and then to triphosphates by nucleoside diphosphate kinase enzymes.

Deoxyribonucleotide Synthesis

• Ribonucleotide diphosphates are converted to deoxyribonucleotide diphosphates by ribonucleotide reductase.
• Ribonucleotide reductase uses reduced thioredoxin as a cofactor.
• Oxidized thioredoxin is recycled back to its reduced form by thioredoxin reductase, requiring reduced nicotine adenine dinucleotide phosphate.
• UMP and TMP synthesis can occur through similar pathways,

Pharmacology

• Methotrexate inhibits dihydrofolate reductase, preventing tetrahydrofolate regeneration and effective antineoplastic activity.
• Nucleotide base analogs enter intracellular pathways and are activated.
• Some purine examples include methylxanthines, 6-thioguanine, and 6-mercaptopurine.
• Some pyrimidine analogs include 5-fluorouracil, bromodeoxyuridine, and anti-HIV drugs like Ara-C and AZT.

Diseases Related to Nucleotide Metabolism

• Several diseases are caused by genetic deficiencies in enzymes associated with nucleotide metabolism.
• Lesch-Nyhan syndrome is caused by a deficiency in hypoxanthine guanine phosphoribosyl transferase, causing uric acid elevations, self-mutilation, and mental retardation.
• Adenosine deaminase deficiency causes severe combined immunodeficiency disease due to deoxy-ATP buildup and inhibited DNA synthesis.
• Gout causes painful joint inflammation and tissue destruction due to urate crystal precipitation, often in distal joints, caused by increased PRPP formation or decreased renal urate clearance.