De novo pyrimidine synthesis

Biosynthesis of pyrimidine nucleotides can occur by a de novo pathway or by the reutilization of preformed pyrimidine bases or ribonucleosides (salvage pathway).
The pyrimidine synthesis is a similar process than that of purines. In the de novo synthesis of pyrimidines, the ring is synthesized first and then it is attached to a ribose-phosphate to for a pyrimidine nucleotide.

Table of Contents

Location

De novo pyrimidine synthesis occurs in the cytosol of cells in all tissues.

Substrates: CO₂; glutamine; ATP; Aspartate; H₂O; NAD⁺; Phosphoribosyl pyrophosphate (PRPP).
Products: UTP; CTP; glutamate; NADH; CO₂

Overview of Pathway:

CO₂ and glutamine are combined to form carbamoyl phosphate. This reaction is catalyzed by carbamoyl phosphate synthetase II, which is the major regulated step for this pathway.
Carbamoyl phosphate is then combined with water and aspartate before being subsequently dehydrogenated in a series of reactions to form orotic acid.
The ribose-5-phosphate ring is then attached to orotic acid by orotate phosphoribosyl transferase to form Orotidine 5′-monophosphate (OMP).
OMP is decarboxylated to form UMP by OMP decarboxylase.
UMP can then be phosphorylated to form UTP.
UTP can subsequently be converted to CTP with the addition of an amino group that is donated by glutamine. The conversion of UTP to CTP is catalyzed by CTP synthetase.

Reactions Involved

(1) The pyrimidine base is synthesized prior to the addition of the ribose moiety.

(a) In the first reaction, glutamine reacts with CO₂ and 2 ATP to form carbamoyl phosphate.

This reaction is analogous to the first reaction of the urea cycle. However, for pyrimidine synthesis, glutamine provides the nitrogen and the reaction occurs in the cytosol, where it is catalyzed by carbamoyl phosphate synthetase II, which is inhibited by UTP.

(b) The entire aspartate molecule adds to carbamoyl phosphate. The molecule closes to yield a ring, which is oxidized, forming orotate.

(c) Orotate reacts with PRPP, producing orotidine 5′-phosphate, which is decarboxylated to form uridine monophosphate (UMP).

(2) UMP is phosphorylated to UTP, which obtains an amino group from glutamine to form CTP. UTP and CTP are used in the synthesis of RNA.

(3) The ribose moiety of CDP is reduced to deoxyribose, forming dCDP. Ribonucleotide reductase is the enzyme.

(a) dCDP is deaminated and dephosphorylated to form dUMP.

(b) dUMP is converted to dTMP by methylene-FH4.

Important enzymes and Regulation

Carbamoyl phosphate synthetase II: Inhibited by UTP; activated by ATP and PRPP.
Orotidylate (OMP) decarboxylase: Inhibited by UMP and CMP.
TP synthetase: Inhibited by CTP.

Pyrimidine synthesis via salvage pathways:

Pyrimidines can be salvaged from orotic acid, uracil, and thymine but not from cytosine. Salvage is accomplished by the enzyme pyrimidine phosphoribosyl transferase.

Associated Disease

Deficiencies in orotate phosphoribosyl transferase or OMP decarboxylase can lead to orotic aciduria which is characterized by growth retardation and anemia.

Significance of Pyrimidine Synthesis

Pyrimidine nucleotides, in common with purine nucleotides, are required for the synthesis of DNA and RNA.
They also participate in intermediary metabolism. For example, pyrimidine nucleotides are involved in the biosynthesis of glycogen and of phospholipids.
Pyrimidines have diverse biological activities such as antimicrobial, CNS depressant, anti-inflammatory, analgesic, anti-convulsant, anticancer, antihelmentic, antioxidant and herbicidal.

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References

Smith, C. M., Marks, A. D., Lieberman, M. A., Marks, D. B., & Marks, D. B. (2005). Marks’ basic medical biochemistry: A clinical approach. Philadelphia: Lippincott Williams & Wilkins.
https://www.slideshare.net/hirapure/de-novo-and-salvage-pathway-of-purines
Rodwell, V. W., Botham, K. M., Kennelly, P. J., Weil, P. A., & Bender, D. A. (2015). Harper’s illustrated biochemistry (30th ed.). New York, N.Y.: McGraw-Hill Education LLC.
John W. Pelley, Edward F. Goljan (2011). Biochemistry. Third edition. Philadelphia: USA.