Pyrimidine Synthesis and Degradation

Unlike the synthesis of the purine ring, which is constructed on a pre-existing ribose 5-phosphate, the pyrimidine ring is synthesized before being attached to ribose 5-phosphate, which is donated by PRPP. The sources of the atoms in the pyrimidine ring are glutamine, CO2, and aspartate (Fig. 1).

Figure 1:  Sources of the individual atoms in the pyrimidine ring. CO2 = carbon dioxide.
A. Carbamoyl phosphate synthesis
The regulated step of this pathway in mammalian cells is the synthesis of carbamoyl phosphate from glutamine and CO2, catalyzed by carbamoyl phosphate synthetase (CPS) II. CPS II is inhibited by uridine triphosphate (the end product of this pathway, which can be converted into the other pyrimidine nucleotides) and is activated by PRPP. [Note: Carbamoyl phosphate, synthesized by CPS I, is also a precursor of urea . Defects in ornithine transcarbamylase of the urea cycle promote pyrimidine synthesis because of increased availability of carbamoyl phosphate. A comparison of the two enzymes is presented in Figure 2.]

Figure 2:  Summary of the differences between carbamoyl phosphate synthetase (CPS) I and II. PRPP = 5-phosphoribosyl-1-pyrophosphate; UTP = uridine triphosphate.
B. Orotic acid synthesis
The second step in pyrimidine synthesis is the formation of carbamoylaspartate, catalyzed by aspartate transcarbamoylase. The pyrimidine ring is then closed by dihydroorotase. The resulting dihydroorotate is oxidized to produce orotic acid (orotate), as shown in Figure 3. The human enzyme that produces orotate, dihydroorotate dehydrogenase, is a flavin mononucleotide-containing protein of the inner mitochondrial membrane. All other enzymes in pyrimidine biosynthesis are cytosolic. [Note: The first three enzymic activities in this pathway (CPS II, aspartate transcarbamoylase, and dihydroorotase) are actually three different catalytic domains of a single polypeptide known as CAD from the first letter in the name of each domain. This is an example of a multifunctional or multicatalytic polypeptide that facilitates the ordered synthesis of an important compound. Synthesis of the purine nucleotide IMP also involves multifunctional proteins.]

Figure3:  De novo pyrimidine synthesis. ADP = adenosine diphosphate; Pi = inorganic phosphate; FMN(H2) = flavin mononucleotide; CTP = cytidine triphosphate; PRPP = 5-phosphoribosyl-1-pyrophosphate; PPi = pyrophosphate.
C. Pyrimidine nucleotide synthesis
The completed pyrimidine ring is converted to the nucleotide orotidine monophosphate (OMP) in the second stage of pyrimidine nucleotide synthesis (see Fig. 3). As seen with the purines, PRPP is the ribose 5-phosphate donor. The enzyme orotate phosphoribosyltransferase produces OMP and releases pyrophosphate, thereby making the reaction biologically irreversible. [Note: Both purine and pyrimidine synthesis require glutamine, aspartic acid, and PRPP as essential precursors.] OMP (orotidylate) is decarboxylated to uridine monophosphate (UMP) by orotidylate decarboxylase. The phosphoribosyltransferase and decarboxylase activities are separate catalytic domains of a single polypeptide called UMP synthase. Hereditary orotic aciduria (a very rare disorder) may be caused by a deficiency of one or both activities of this bifunctional enzyme, resulting in orotic acid in the urine (see Fig. 3). UMP is sequentially phosphorylated to UDP and UTP. [Note: The UDP is a substrate for
ribonucleotide reductase, which generates dUDP. The dUDP is phosphorylated to dUTP, which is rapidly hydrolyzed to dUMP by UTP diphosphatase (dUTPase). Thus, dUTPase plays an important role in reducing availability of dUTP as a substrate for DNA synthesis, thereby preventing erroneous incorporation of uracil into DNA.]