BIOCHEMISTRY - Textbook - Ostapchenko L. I. - 2012

Chapter 10. NUCLEIC ACID METABOLISM

10.5. Biosynthesis of Nucleotides

10.5.2. Biosynthesis of Pyrimidine Nucleotides

De novo Biosynthesis OF PYRIMIDINE NUCLEOTIDES. Like purine nucleotides, Pyrimidine nucleotides are primarily synthesized de novo from simple precursors—CO₂, glutamine, and aspartic acid (Fig. 10.11)—with only 10–20 % of the total amount being produced via Salvage Pathways from nitrogenous bases or nucleosides.

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Fig. 10.11. Sources of pyrimidine atoms

The de novo biosynthesis of pyrimidine nucleotides differs from that of Purines in that the pyrimidine ring is formed first, after which the ribose phosphate moiety is attached to it.

The Synthesis of the pyrimidine ring (Fig. 10.12) takes place in the Cytosol with the participation of carbamoyl phosphate, which is formed from glutamine, CO₂, and ATP in a reaction catalyzed by carbamoyl phosphate synthetase II (CPS II). It is worth noting that carbamoyl phosphate is also produced during urea synthesis in Cell/35.html">Mitochondria via carbamoyl phosphate synthetase I (CPS I), but from CO₂, ATP, and NH₃. In the metabolic pathway of pyrimidine nucleotide synthesis, The activity of the cytosolic regulatory enzyme CPS II is inhibited by the end product UMP, whereas the activity of the mitochondrial enzyme CPS I is not affected by UMP. Thus, the specific intracellular compartmentalization of Enzymes and regulatory mechanisms allows the synthesis of pyrimidine nucleotides and urea to proceed independently and in parallel, According to the physiological needs of the Organism.

Fig. 10.12. Synthesis of uridine-5'-monophosphate

At the next stage, cytosolic carbamoyl phosphate condenses with aspartic acid under the action of aspartate transcarbamylase; then, in a reaction catalyzed by dihydroorotase, a molecule of H₂O is released to form the pyrimidine ring—dihydroorotic acid. The subsequent dehydrogenation of dihydroorotic acid to orotic acid is carried out by dihydroorotate dehydrogenase, using NAD as a coenzyme.

Next, a ribose-5-phosphate residue from 5-phosphoribosyl-1-pyrophosphate (PRPP) is attached to orotic acid. This results in The formation of the nucleotide orotidine-5'-monophosphate (OMP). The conversion of orotate to OMP is catalyzed by orotate phosphoribosyltransferase.

The first true pyrimidine ribonucleotide—uridine-5'-monophosphate (UMP)—is formed through the decarboxylation of OMP by the enzyme OMP decarboxylase. UMP serves as the precursor for all other pyrimidine nucleotides.

Biosynthesis of UDP, UTP, and cytidine nucleotides. The phosphorylation of pyrimidine nucleoside monophosphates to their corresponding di- and triphosphates is mediated by specific nucleoside monophosphate and nucleoside diphosphate Kinases through The transfer of a γ-phosphate group from ATP to the appropriate substrate:

The conversion of uridylic acid into a cytidyl nucleotide must be preceded by the phosphorylation of UMP to uridine-5'-triphosphate. Catalyzed by CTP synthetase, UTP undergoes amidation via an ATP-dependent replacement of its keto group with the amide group of glutamine, yielding cytidine-5'-triphosphate:

The Formation of the third pyrimidine nucleotide, dTTP, will be discussed below.

Synthesis of pyrimidine nucleotides via salvage pathways.

In addition to the aforementioned de novo pathway, free pyrimidine bases and nucleosides can be directly incorporated into nucleotides. For instance, uridine Phosphorylase catalyzes the ribosylation of uracil to form uridine:

uracil + ribose-1-phosphate → uridine + H₃PO₄.

The utilization of pyrimidine ribonucleosides in mammalian Cells is more efficient than that of free nitrogenous bases. The potential reactions for the formation of pyrimidine nucleoside monophosphates from their corresponding nucleosides, catalyzed by nucleoside kinases, are shown below:

Through hydrolytic deamination, a portion of the CMP produced via the salvage pathway can be converted into UMP by cytidine deaminase, thereby replenishing the pool of uridylic nucleotides:

Regulation of Pyrimidine nucleotide synthesis. The pathway of pyrimidine nucleotide biosynthesis is controlled by feedback mechanisms that regulate enzyme activity. For instance, aspartate transcarbamoylase is highly sensitive to the inhibitory action of CTP, yet is activated by ATP. Meanwhile, carbamoyl phosphate synthetase activity is allosterically inhibited by UMP, UTP, and purine nucleotides (Fig. 10.13).

Fig. 10.13. Scheme of regulation of pyrimidine nucleotide synthesis

The activity of CTP synthetase, which catalyzes the conversion of UTP to CTP, is inhibited by its own end product, CTP, but is activated by GTP.

This regulatory mechanism prevents the overproduction not only of UMP but also of other pyrimidine nucleotides, thereby ensuring a balanced supply of all four major purine and pyrimidine nucleotides required for RNA Synthesis.