Purine and Pyrimidine Synthesis

De Novo Purine Synthesis

• Begins with PRPP (5-phosphoribosyl-1-pyrophosphate) as the activated ribose sugar donor; PRPP synthetase catalyzes this critical step
• Purine ring is built on the ribose backbone through 10 enzymatic steps, beginning with glutamine-PRPP amidotransferase (the rate-limiting enzyme)
• Sequential addition of carbons and nitrogens from glutamine, glycine, formate, aspartate, and CO₂ creates the purine skeleton
• Final products are IMP (inosine monophosphate), which is then converted to AMP and GMP through separate branches
• Rate-limiting step is catalyzed by glutamine-PRPP amidotransferase, which is feedback-inhibited by AMP, GMP, and IMP (negative feedback regulation)
• All purine nucleotides eventually catabolize to uric acid in humans (the end product of purine metabolism)

De Novo Pyrimidine Synthesis

• Begins with carbamoyl phosphate synthetase II (CPS II) in the cytoplasm (distinct from CPS I in the urea cycle)
• Carbamoyl phosphate combines with aspartate to form carbamoyl aspartate, initiating a linear (not a ring) construction pathway
• The pyrimidine ring is completed in 6 enzymatic steps to form orotate, then orotate undergoes orotidine formation and decarboxylation to yield UMP
• UMP is then converted to CTP and dTMP (for DNA synthesis)
• Rate-limiting enzyme is CPS II, which is feedback-inhibited by UTP and CTP (negative feedback)
• Pyrimidine catabolism yields β-alanine and ammonia (not uric acid like purines)

Salvage Pathways

• HGPRT (hypoxanthine-guanine phosphoribosyltransferase) recovers hypoxanthine and guanine directly to their respective nucleotides
• Adenine phosphoribosyltransferase (APRT) salvages adenine
• Cytidine deaminase and deoxycytidine kinase recycle pyrimidine bases
• Salvage pathways are highly efficient and conserve energy; deficiency in salvage enzymes shifts metabolism toward catabolism

Purine and Pyrimidine Catabolism

• Purines undergo deamination (adenosine deaminase converts adenosine to inosine; ADA is crucial) and oxidation via xanthine oxidase to eventually form uric acid
• Accumulation of purine metabolites (adenosine, deoxyadenosine, inosine) is toxic to lymphocytes due to their high metabolic rates
• Pyrimidines are degraded to β-alanine and ammonia, then converted to CO₂ and H₂O

Acute Leukemia (Excessive Nucleotide Synthesis)

• Rapid cell division and nucleotide synthesis lead to massive uric acid production, causing hyperuricemia
• Patients present with acute uric acid nephropathy (crystal obstruction in renal tubules) → acute kidney injury with oliguria
• Tumor lysis syndrome occurs classically when initiating chemotherapy
• Hyperkalemia, hyperphosphatemia, and hypocalcemia accompany nucleotide breakdown

Gout (Chronic Hyperuricemia)

• Chronic elevation of uric acid leads to monosodium urate crystal deposition in joints and soft tissues
• Acute flares present with sudden-onset, severe monoarticular arthritis (typically first metatarsophalangeal joint), erythema, and warmth
• Chronic presentation includes tophi (subcutaneous urate deposits), chronic arthritis, and uric acid nephrolithiasis

Adenosine Deaminase (ADA) Deficiency

• SCID (Severe Combined Immunodeficiency) phenotype: absent T cells, B cells, and NK cells
• Presents in infancy with recurrent severe infections (bacterial, viral, fungal, opportunistic)
• Failure to thrive, diarrhea, hepatosplenomegaly, developmental delay
• Accumulation of deoxyadenosine is particularly toxic to lymphocytes (high deoxycytidine kinase activity)

HGPRT Deficiency (Lesch-Nyhan Syndrome)

• Complete deficiency causes Lesch-Nyhan syndrome: severe hyperuricemia, gout in childhood, renal failure, neurological manifestations
• Neurological symptoms include dystonia, spasticity, intellectual disability, behavioral problems (self-injurious behavior including self-biting)
• Severe gout and uric acid nephrolithiasis in young children (unusual presentation of gout)
• Partial deficiency (HGPRT-) causes mild hyperuricemia and early-onset gout without neurological features

Orotic Aciduria (Type I — UMPS Deficiency)

• Rare autosomal recessive disorder affecting UMP synthase (orotidine 5'-monophosphate decarboxylase)
• Presents with megaloblastic anemia (impaired DNA synthesis due to lack of pyrimidines)
• Developmental delay, immune dysfunction, growth retardation
• Orotic acid crystals in urine (massive orotic acid excretion—key diagnostic finding)

Acute Presentation Pearls

• Tumor lysis syndrome is a medical emergency presenting with acute kidney injury, hyperkalemia, and cardiac arrhythmias
• Gout flares present with acute severe arthritis; chronic gout may be asymptomatic between flares
• ADA and HGPRT deficiencies present in infancy/early childhood with immune deficiency or neurological decline

Laboratory Tests for Purine/Pyrimidine Disorders

• Serum uric acid level (elevated in gout, tumor lysis, HGPRT deficiency, ADA deficiency); normal is <7 mg/dL in men, <6 mg/dL in women
• 24-hour urine uric acid excretion (elevated in overproducers vs. underexcretors); >600 mg/day on purine-free diet or >800 mg/day on regular diet suggests overproduction
• Urine crystals: monosodium urate crystals (needle-shaped, negatively birefringent) in gout; orotic acid crystals (rhomboid) in orotic aciduria
• Serum creatinine and urinalysis to assess kidney function and detect crystalluria (uric acid, urate)
• Uric acid/creatinine ratio in urine (24-hour collection) to differentiate overproduction from underexcretion

Enzyme Assays and Genetic Testing

• HGPRT enzyme activity in red blood cells or fibroblasts (absent in Lesch-Nyhan, reduced in HGPRT-)
• Adenosine deaminase (ADA) activity in red blood cells (absent or severely reduced in ADA deficiency)
• UMPS (UMP synthase) activity for orotic aciduria diagnosis
• Plasma/urine metabolite profiling: elevated deoxyadenosine and dATP in ADA deficiency; elevated

• Orotic acid is the great discriminator: both hereditary orotic aciduria and ornithine transcarbamylase (OTC) deficiency spill orotic acid in urine. OTC deficiency (X-linked) has hyperammonemia and no megaloblastic anemia; orotic aciduria has megaloblastic anemia unresponsive to B12/folate with normal ammonia. Treatment of orotic aciduria is oral uridine (uridine triacetate), which bypasses the UMP synthase block and feedback-inhibits CPS II.
• HGPRT deficiency is X-linked recessive: failed salvage means hypoxanthine/guanine are shunted to uric acid and unused PRPP drives de novo synthesis. Self-mutilation, dystonia, choreoathetosis, hyperuricemia. Xanthine oxidase inhibitors lower urate but do not touch the neurologic disease — the classic distractor.
• ADA deficiency is the most common cause of autosomal recessive SCID; accumulated dATP inhibits ribonucleotide reductase, starving lymphocytes of all dNTPs. Look for an absent thymic shadow and lymphopenia on newborn TREC screening.
• Drug targets worth memorizing: hydroxyurea → ribonucleotide reductase; 5-FU (FdUMP) → thymidylate synthase; methotrexate/trimethoprim/pyrimethamine → dihydrofolate reductase (human/bacterial/protozoal selectivity); 6-mercaptopurine and azathioprine → PRPP amidotransferase; mycophenolate and ribavirin → IMP dehydrogenase; leflunomide → dihydroorotate dehydrogenase.
• The single best next step in a patient on 6-MP or azathioprine started on allopurinol: reduce the thiopurine dose. Xanthine oxidase inhibition blocks thiopurine catabolism and precipitates profound myelosuppression.
• Gout management (ACR 2020 Guideline for Management of Gout): acute flares treated with NSAIDs, colchicine, or glucocorticoids (all acceptable first-line); allopurinol is preferred first-line urate-lowering therapy, including in CKD, titrated to a serum urate <6 mg/dL, with **HLA-B*5801 testing** before allopurinol in patients of Southeast Asian or African descent.
• Tumor lysis syndrome: allopurinol prevents new urate formation but cannot clear existing urate; rasburicase degrades urate to allantoin and is used for high-risk or established TLS. It is contraindicated in G6PD deficiency (hemolysis, methemoglobinemia). Aggressive IV hydration is the backbone; routine urinary alkalinization is no longer recommended.
• Distractor to avoid: pyrimidine catabolism yields β-alanine and ammonia — it never causes hyperuricemia. Only purine turnover does.