Purine De Novo Synthesis (IMP synthesis through to AMP/GMP)

1. 1

   Ribose 5-phosphate → 5-phosphoribosyl-1-pyrophosphate (PRPP)

   Ribose-phosphate pyrophosphokinase (PRPP synthetase) 2.7.6.1 ST-0191 Irreversible ATP PRPP
   In Ribose-5-phosphate

   Out PRPP
   › Notes

   Ribose-phosphate pyrophosphokinase (PRPP synthetase) transfers pyrophosphate from ATP to ribose 5-phosphate: ribose 5-phosphate + ATP → PRPP + AMP. Mg2+ and inorganic phosphate are required/activating; this reaction consumes two high-energy phosphate equivalents because ATP is converted to AMP. It is irreversible in vivo and is a major control point that supplies PRPP to both de novo and salvage pathways, but it is not the committed step of purine synthesis.

2. 2

   PRPP → 5-phosphoribosylamine (5-PRA)

   Glutamine-PRPP amidotransferase 2.4.2.14 ST-0192 Irreversible rate-limiting H2O PPi PRPP
   In PRPP

   Out 5-Phosphoribosylamine
   › Notes

   Glutamine-PRPP amidotransferase catalyzes PRPP + glutamine + H2O → 5-PRA + glutamate + PPi. The enzyme uses an internal glutaminase domain to generate ammonia, which is channeled to the phosphoribosyl-transferase domain; PPi hydrolysis drives the reaction forward. This is the committed, rate-limiting, and effectively irreversible step of de novo purine synthesis.

3. 3

   5-PRA → glycinamide ribonucleotide (GAR)

   Phosphoribosylamine--glycine ligase (GAR synthetase) ST-0193 Irreversible/directional ATP Pi
   In 5-Phosphoribosylamine

   Out Glycinamide ribonucleotide (GAR)
   › Notes

   Phosphoribosylamine--glycine ligase (GAR synthetase) catalyzes 5-PRA + glycine + ATP → GAR + ADP + Pi. Mg2+ is required; glycine contributes C4, C5, and N7 of the future purine ring.

4. 4

   GAR → formylglycinamide ribonucleotide (FGAR)

   GAR transformylase (GART) 2.1.2.2 ST-0194 Irreversible/directional THF (folate)
   In Glycinamide ribonucleotide (GAR)

   Out Formylglycinamide ribonucleotide (FGAR)
   › Notes

   GAR transformylase transfers a formyl group: GAR + 10-formyl-THF → FGAR + THF. This is the first of two folate-dependent one-carbon transfer steps and introduces C8 of the purine ring.

5. 5

   FGAR → formylglycinamidine ribonucleotide (FGAM)

   FGAM synthetase 6.3.5.3 ST-0195 Irreversible/directional ATP H2O Pi
   In Formylglycinamide ribonucleotide (FGAR)

   Out Formylglycinamidine ribonucleotide (FGAM)
   › Notes

   FGAM synthetase catalyzes FGAR + glutamine + ATP + H2O → FGAM + glutamate + ADP + Pi. The glutamine-derived nitrogen becomes N3 of the purine ring; ATP activates the formyl group before amidination.

6. 6

   FGAM → 5-aminoimidazole ribonucleotide (AIR)

   AIR synthetase 6.3.3.1 ST-0196 Irreversible ATP Pi
   In Formylglycinamidine ribonucleotide (FGAM)

   Out 5-Aminoimidazole ribonucleotide (AIR)
   › Notes

   AIR synthetase catalyzes ATP-dependent ring closure: FGAM + ATP → AIR + ADP + Pi. This irreversible cyclization forms the imidazole portion of the purine nucleus.

7. 7

   AIR → carboxyaminoimidazole ribonucleotide (CAIR)

   AIR carboxylase 4.1.1.21 ST-0197 Irreversible/directional Bicarbonate/CO2
   In 5-Aminoimidazole ribonucleotide (AIR)

   Out Carboxyaminoimidazole ribonucleotide (CAIR)
   › Notes

   AIR carboxylase catalyzes AIR + CO2 (derived from bicarbonate) → CAIR. In mammalian cells, the class II AIR carboxylase activity of PAICS performs direct carboxylation and does not require ATP; this differs from the two-enzyme, ATP-dependent bacterial route. The carboxyl carbon becomes C6 of the purine ring.

8. 8

   CAIR → succinylaminoimidazolecarboxamide ribonucleotide (SAICAR)

   SAICAR synthetase 6.3.2.6 ST-0198 Irreversible/directional ATP Pi
   In Carboxyaminoimidazole ribonucleotide (CAIR)

   Out SAICAR
   › Notes

   SAICAR synthetase catalyzes CAIR + aspartate + ATP → SAICAR + ADP + Pi. Aspartate donates N1 of the purine ring, while its carbon skeleton is later released as fumarate.

9. 9

   SAICAR → 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR)

   Adenylosuccinate lyase (ADSL) 4.3.2.2 ST-0199 Irreversible/directional
   In SAICAR

   Out AICAR
   › Notes

   Adenylosuccinate lyase catalyzes SAICAR → AICAR + fumarate. This nonhydrolytic elimination releases the aspartate carbon skeleton as fumarate, linking purine synthesis to the tricarboxylic acid cycle.

10. 10

    AICAR → 5-formamidoimidazole-4-carboxamide ribonucleotide (FAICAR)

    AICAR transformylase (ATIC) 2.1.2.3 ST-0200 Irreversible/directional THF (folate)
    In AICAR

    Out FAICAR
    › Notes

    AICAR transformylase catalyzes AICAR + 10-formyl-THF → FAICAR + THF. The donated formyl carbon becomes C2 of the purine ring.

11. 11

    FAICAR → IMP

    IMP cyclohydrolase ST-0201 Irreversible H2O
    In FAICAR

    Out IMP
    › Notes

    IMP cyclohydrolase catalyzes FAICAR → IMP + H2O (net ring closure with dehydration/rearrangement as represented by the enzyme mechanism). This completes the six-membered ring and is effectively irreversible under cellular conditions. IMP contains hypoxanthine and is the branch point for AMP and GMP.

12. 12

    IMP → adenylosuccinate

    Adenylosuccinate synthetase 6.3.4.4 ST-0202 Irreversible/directional GTP Pi
    In IMP

    Out Adenylosuccinate
    › Notes

    Adenylosuccinate synthetase catalyzes IMP + aspartate + GTP → adenylosuccinate + GDP + Pi. GTP, rather than ATP, drives addition of the amino group donor aspartate; this reciprocal use of GTP favors balanced AMP/GMP production. This is the committed step of the AMP branch.

13. 13

    Adenylosuccinate → AMP

    Adenylosuccinate lyase (ADSL) 4.3.2.2 ST-0203 Irreversible/directional
    In Adenylosuccinate

    Out AMP
    › Notes

    Adenylosuccinate lyase catalyzes adenylosuccinate → AMP + fumarate. The reaction completes AMP synthesis and again releases the aspartate carbon skeleton as fumarate.

14. 14

    IMP → xanthosine monophosphate (XMP)

    IMP dehydrogenase (IMPDH) 1.1.1.205 ST-0204 Irreversible/directional NAD+ NADH H2O
    In IMP

    Out Xanthosine monophosphate (XMP)
    › Notes

    IMP dehydrogenase (IMPDH) catalyzes IMP + NAD+ + H2O → XMP + NADH + H+. This oxidation establishes the 2-keto group needed for subsequent amination and is the committed, regulatory step of the GMP branch.

15. 15

    XMP → GMP

    GMP synthetase 6.3.5.2 ST-0205 Irreversible ATP H2O PPi
    In Xanthosine monophosphate (XMP)

    Out GMP
    › Notes

    GMP synthetase catalyzes XMP + glutamine + ATP + H2O → GMP + glutamate + AMP + PPi. ATP is cleaved to AMP and PPi, and the enzyme channels glutamine-derived ammonia to an adenylated XMP intermediate; thus this step consumes two high-energy phosphate equivalents and is effectively irreversible.

Showing all 15 steps.

Overview

Purine de novo synthesis constructs the purine ring atom-by-atom on ribose 5-phosphate, generating inosine monophosphate (IMP), the common precursor of AMP and GMP. The pathway supplies nucleotides for RNA, DNA (after reduction), energy transfer, second messengers, and activated intermediates, and is especially important in proliferating cells and in tissues with limited salvage capacity. In humans, most early reactions are carried out by multifunctional cytosolic enzymes that can assemble into purinosomes under high purine demand.

Cellular location

The pathway is cytosolic; enzymes are widely expressed, with high flux in liver, intestinal mucosa, bone marrow, developing brain, activated lymphocytes, and rapidly dividing tumor cells. The one-carbon units used in the pathway are supplied as 10-formyltetrahydrofolate (10-formyl-THF), principally from the cytosolic folate-mediated one-carbon network. Ribose 5-phosphate is generated mainly by the oxidative and nonoxidative pentose phosphate pathways.

Net energetics

From ribose 5-phosphate to IMP, human de novo synthesis consumes one ATP → AMP in PRPP formation and four ATP → ADP reactions (GAR synthetase, FGAM synthetase, AIR synthetase, and SAICAR synthetase): six high-energy phosphate equivalents total. It also consumes two glutamine amide nitrogens, one glycine, one aspartate, two 10-formyl-THF one-carbon units, and CO2. Conversion of IMP to AMP consumes one GTP → GDP, making AMP cost six ATP-equivalent bonds plus one GTP-equivalent bond from ribose 5-phosphate; conversion of IMP to GMP consumes one additional ATP → AMP (two high-energy equivalents) and produces one NADH, making GMP cost eight ATP-equivalent bonds; the IMPDH reaction also produces one NADH.

Clinical significance

De novo synthesis is necessary when dietary or intracellular base salvage is insufficient and is a major biosynthetic burden in proliferating tissues. Excess PRPP synthetase activity or diminished feedback inhibition increases purine production and degradation, causing hyperuricemia and gout. Antifolates such as methotrexate and pemetrexed impair the 10-formyl-THF-dependent transformylase reactions, whereas IMPDH inhibitors such as mycophenolate mofetil preferentially suppress guanine nucleotide synthesis in activated lymphocytes. Adenylosuccinate lyase deficiency causes a neurodevelopmental disorder with accumulation of succinylpurines.