Nucleotide Metabolism Dr.

Pichayada Somboon

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 Outline
❖ Synthesis of Purine Nucleotides
❖ Other Purine Nucleotides are Synthesized from IMP
❖ Synthesis of Pyrimidine Nucleotides
❖ CTP synthesis
❖ Reduction of Ribonucleotides to Deoxyribonucleotides
❖ Methylation of dUMP Produces dTMP
❖ Salvage of Purines and Pyrimidines
❖ Purine Catabolism
❖ The Purine Nucleotide Cycle in Muscle
❖ Pyrimidine Catabolism
 Synthesis of Purine Nucleotides
❖ carbon from carbon dioxide was incorporated into
C-6
❖ carbon from formate into C-2 and C-8 of the purines
❖ sources of the ring atoms were shown to be
❖ N-1, aspartate

Sources of the ring atoms
in purines synthesized
❖ C-2 and C-8, formate via 10-formyltetrahydrofolate
❖ N-3 and N-9, amide groups from glutamine
❖ C-4, C-5, and N-7, glycine
❖ C-6, carbon dioxide
Synthesis of Purine Nucleotides
1. Synthesis of 5-phosphoribosyl-1-pyrophosphate

❖ The purine ring structure is not synthesized as a free base but as a

substituent of ribose 5-phosphate

❖ The ribose 5-phosphate for purine biosynthesis comes from 5-

phosphoribosyl-1-pyrophosphate (PRPP)

❖ PRPP is synthesized from ribose 5-phosphate and ATP in a reaction

catalyzed by PRPP synthetase

❖ PRPP is also a precursor for the biosynthesis of pyrimidine

nucleotides, although in that pathway it reacts with a
preformed pyrimidine to form a nucleotide

❖ PRPP is also used in the nucleotide salvage pathways and in

the biosynthesis of histidine
 Synthesis of Purine Nucleotides
2. Synthesis of 5-phosphoribosylamine

❖ Synthesis of 5-phosphoribosylamine from PRPP and glutamine

❖ initial product of the purine nucleotide biosynthetic pathway is inosine 5’-monophosphate (IMP, or inosinate), a
nucleotide containing hypoxanthine, or 6-oxopurine, as its base
❖ in Escherichia coli, these steps are catalyzed by two proteins; in eukaryotes, they are catalyzed by a multifunctional enzyme
❖ synthesis of IMP consumes considerable energy. ATP is converted to AMP during the synthesis of PRPP.
Other purine nucleotides synthesis

❖ inosine 5’-monophosphate (IMP) can be converted to adenosine 5’-

monophosphate (AMP) or guanosine 5’-monophosphate (GMP)

❖ use of GTP as a cosubstrate in the synthesis of AMP from IMP, and of ATP in the
synthesis of GMP from IMP, helps balance the formation of the two products
Feedback inhibition in purine nucleotide biosynthesis

❖ purine nucleotide synthesis is probably regulated in cells by

feedback inhibition

❖ several enzymes that catalyze steps in the biosynthesis of

purine nucleotides exhibit allosteric behavior in vitro. PRPP
synthetase is inhibited by several purine

❖ glutamine–PRPP amidotransferase (step 1), is allosterically

inhibited by 5’-ribonucleotide end products (IMP, AMP, and
GMP) at intracellular concentrations

❖ this step appears to be the principal site of regulation of

this pathway

❖ end products inhibit two of the initial common steps as well

as steps leading from IMP at the branch point
Synthesis of Pyrimidine Nucleotides
❖ Uridine 5’-monophosphate is the precursor of other pyrimidine nucleotides
❖ pathway for the biosynthesis of UMP is simpler than the purine pathway and consumes
fewer ATP molecules
❖ pyrimidine ring atoms come from bicarbonate, which contributes C-2; the amide group of
glutamine (N-3); and aspartate, which contributes the remaining atoms
Synthesis of Pyrimidine Nucleotides

❖ Six-step pathway for the synthesis of UMP in prokaryotes

❖ In eukaryotes, steps 1 through 3 are catalyzed by a multifunctional

protein called dihydroorotate synthase, and steps 5 and 6 are
catalyzed by a bifunctional enzyme, UMP synthase

❖ In addition to being an intermediate in pyrimidine synthesis,

carbamoyl phosphate is a metabolite in the pathway for the
biosynthesis of arginine via citrulline

❖ In prokaryotes, the same carbamoyl phosphate synthetase is

used in both pyrimidine and arginine biosynthetic pathways
 CTP synthesis
❖ UMP is converted to CTP in three steps

(1) (2)

(3)
 CTP synthesis

❖ Cytidine triphosphate (CTP) is a pyrimidine nucleoside

triphosphate

❖ CTP, much like ATP, consists of a ribose sugar, and three

phosphate groups. The major difference between the two
molecules is the base used, which in CTP is cytosine.

❖ CTP is a substrate in the synthesis of RNA.

❖ CTP synthetase is allosterically inhibited by its product, CTP,

and in E. coli is allosterically activated by GTP.

❖ The regulation of ATCase and CTP synthetase balances the

concentrations of endogenous pyrimidine nucleotides.
Reduction of Ribonucleotides to Deoxyribonucleotides
❖ the 2’-deoxyribonucleoside triphosphates are synthesized by the enzymatic reduction of ribonucleotides
❖ in most organisms, this reduction occurs at the nucleoside diphosphate level
Methylation of dUMP Produces dTMP

❖ Deoxythymidylate (dTMP) is formed from UMP

❖ UMP is phosphorylated to UDP, which is reduced to dUDP,
and dUDP is dephosphorylated to dUMP, which is then
methylated
❖ dTMP can also be synthesized via the salvage of thymidine
(deoxythymidine), catalyzed by ATP-dependent thymidine
kinase
Salvage of Purines and Pyrimidines
❖ Breakdown of nucleic acids
❖ During normal cell metabolism, nucleic acids
are degraded to mononucleotides,
nucleosides, and eventually, heterocyclic
bases
❖ Some of the purine and pyrimidine bases
formed in this way are further degraded (e.g.,
purines are converted to uric acid and other
excretory products), but a considerable
fraction is normally salvaged by direct
conversion to 5’-mononucleotides
Interconversions of purine nucleotides and their constituents
Interconversions of pyrimidine nucleotides and their constituents
 Purine Catabolism
❖ Although most free purine and pyrimidine molecules are salvaged, some are catabolized
 Lesch–Nyhan Syndrome and Gout
❖ Lesch–Nyhan Syndrome defects in purine metabolism can have devastating effects
❖ excretion of up to six times the normal amount of uric acid and a greatly increased rate of
purine biosynthesis
❖ Gout is a disease caused by the overproduction or inadequate excretion of uric acid

Lesch–Nyhan Syndrome Gout

 The Purine Nucleotide Cycle in Muscle
❖ Exercising muscle produces ammonia in proportion to the work performed
❖ The ammonia is generated by the activity of a cyclic pathway in vertebrates that supports some of the energy requirements of muscular
work
❖ The sequence of reactions, called the purine nucleotide cycle
❖ When active, the purine nucleotide cycle supplies fumarate to the citric acid cycle, which increases the capacity of the cell to oxidize
acetyl CoA
Pyrimidine Catabolism

The catabolism of pyrimidines ends with intermediates of

central metabolism, so no distinctive excretory products are
formed
 Summary
1. The synthesis of purine nucleotides is a 10-step pathway that leads to IMP
(inosinate). The purine is assembled on a foundation of ribose 5-phosphate donated by
5- phosphoribosyl 1-pyrophosphate (PRPP).
2. IMP can be converted to AMP or GMP.
3. In the six-step synthesis of the pyrimidine nucleotide UMP, PRPP enters the pathway
after completion of the ring structure.
4. CTP is formed by the amination of UTP.
5. Deoxyribonucleotides are synthesized by the reduction of ribonucleotides at C-2’ in a
reaction catalyzed by ribonucleotide reductase.
 Summary
6. Thymidylate (dTMP) is formed from deoxyuridylate (dUMP) by a methylation reaction in which 5,10-
methylenetetrahydrofolate donates both a one-carbon group and a hydride ion. 7,8-Dihydrofolate, the other
product of this methylation, is recycled by NADPH-dependent reduction to the active coenzyme
tetrahydrofolate.

7. PRPP reacts with pyrimidines and purines in salvage reactions to yield nucleoside monophosphates.
Nucleotides and their constituents are interconverted by a variety of enzymes.

8. In birds and some reptiles, nitrogen from amino acids and purine nucleotides is excreted as uric acid.
Primates degrade purines to uric acid. Most other organisms further catabolize uric acid to allantoin, allantoate,
urea, or ammonia.

9. The purine nucleotide cycle generates ammonia and fumarate in muscle.

10. Pyrimidines are catabolized to ammonia, bicarbonate, and either acetyl CoA (from cytosine or uracil) or
succinyl CoA (from thymine).