Pyrimidine nucleotides, biosynthesis

Figure 34-7 summarizes the roles of the intermediates and enzymes of pyrimidine nucleotide biosynthesis. The catalyst for the initial reaction is cytosolic carbamoyl phosphate synthase II, a different enzyme from the mitochondrial carbamoyl phosphate synthase I of urea synthesis (Figure 29-9). Compartmentation thus provides two independent pools of carbamoyl phosphate. PRPP, an early participant in purine nucleotide synthesis (Figure 34-2), is a much later participant in pyrimidine biosynthesis.

Reaction 12 of Figure 34—7 is the only reaction of pyrimidine nucleotide biosynthesis that requires a tetrahydrofo-late derivative. The methylene group of A A Tmethyl-ene-tetrahydrofolate is reduced to the methyl group that is transferred, and tetrahydrofolate is oxidized to dihydro-... 

Certain Pyrimidine Analogs Are Substrates for Enzymes of Pyrimidine Nucleotide Biosynthesis... 

The activities of the first and second enzymes of pyrimidine nucleotide biosynthesis are controlled by allosteric... 

Purine Pyrimidine Nucleotide Biosynthesis Are Coordinately Regulated... 

Purine and pyrimidine biosynthesis parallel one another mole for mole, suggesting coordinated control of their biosynthesis. Several sites of cross-regulation characterize purine and pyrimidine nucleotide biosynthesis. The PRPP synthase reaction (reaction 1, Figure 34-2), which forms a precursor essential for both processes, is feedback-inhibited by both purine and pyrimidine nucleotides. 

Excess carbamoyl phosphate exits to the cytosol, where it stimulates pyrimidine nucleotide biosynthesis. The resulting mild orotic aciduria is increased by high-nitrogen foods. 

Goordinated regulation of purine and pyrimidine nucleotide biosynthesis ensures their presence in proportions appropriate for nucleic acid biosynthesis and other metabolic needs. 

A common intermediate for all the nucleotides is 5-phosphoribosyl-l-diphosphate (PRPP), produced by successive ATP-dependent phosphorylations of ribose. This has an a-diphosphate leaving group that can be displaced in Sn2 reactions. Similar Sn2 reactions have been seen in glycoside synthesis (see Section 12.4) and biosynthesis (see Box 12.4), and for the synthesis of aminosugars (see Section 12.9). For pyrimidine nucleotide biosynthesis, the nucleophile is the 1-nitrogen of uracil-6-carboxylic acid, usually called orotic acid. The product is the nucleotide orotidylic acid, which is subsequently decarboxylated to the now recognizable uridylic acid (UMP). 

The common pyrimidine ribonucleotides are cytidine 5 -monophosphate (CMP cytidylate) and uridine 5 -monophosphate (UMP uridylate), which contain the pyrimidines cytosine and uracil. De novo pyrimidine nucleotide biosynthesis (Fig. 22-36) proceeds in a somewhat different manner from purine nucleotide synthesis the six-membered pyrimidine ring is made first and then attached to ribose 5-phosphate. Required in this process is carbamoyl phosphate, also an intermediate in the urea cycle (see Fig. 18-10). However, as we noted... 

FIGURE 22-36 De novo synthesis of pyrimidine nucleotides biosynthesis of UTP and CTP via orotidylate. The pyrimidine is constructed from carbamoyl phosphate and aspartate. The ribose 5-phosphate is then added to the completed pyrimidine ring by orotate phosphori-bosyltransferase. The first step in this pathway (not shown here see Fig. 18-11a) is the synthesis of carbamoyl phosphate from C02 and NH), catalyzed in eukaryotes by carbamoyl phosphate synthetase II. 

Pyrimidine Nucleotide Biosynthesis Is Regulated by Feedback Inhibition... 

The biosynthetic pathway to pyrimidine nucleotides is simpler than that for purine nucleotides, reflecting the simpler structure of the base. In contrast to the biosynthetic pathway for purine nucleotides, in the pyrimidine pathway the pyrimidine ring is constructed before ribose-5-phosphate is incorporated into the nucleotide. The first pyrimidine mononucleotide to be synthesized is orotidine-5 -monophosphate (OMP), and from this compound, pathways lead to nucleotides of uracil, cytosine, and thymine. OMP thus occupies a central role in pyrimidine nucleotide biosynthesis, somewhat analogous to the position of IMP in purine nucleotide biosynthesis. Like IMP, OMP is found only in low concentrations in cells and is not a constituent of RNA. 

One inhibitor of those shown in table 23.3 specifically interferes with a step in pyrimidine nucleotide biosynthesis. Af-(Phosphonacet T)-L-aspartate (PALA) is a powerful inhibitor of the carbamoyl transferase reaction. PALA was synthesized to act as an analog of the transition state intermediate (see chapter 9) postulated to be formed in the aspar-... 

Acivicin is a potent inhibitor of several steps in purine nucleotide biosynthesis that utilize glutamine. The enzymes it inhibits are glutamine PRPP amidotransferase (step 1, fig. 23.10), phosphoribosyl-A-formylglycinamidine synthase (step 4, fig. 23.10), and GMP synthase (see fig. 23.11). In pyrimidine nucleotide biosynthesis the enzymes inhibited are carbamoyl synthase (step 1, fig. 23.13) and CTP synthase (see fig. 23.14). Acivicin is under trial for the treatment of some forms of cancer. 

In bacteria, the first committed step in pyrimidine nucleotide biosynthesis is the formation of carbamoyl aspartate... 

In eukaryotes, carbamoyl phosphate synthase is inhibited by pyrimidine nucleotides and stimulated by purine nucleotides it appears to be the most important site of feedback inhibition of pyrimidine nucleotide biosynthesis in mammalian tissues. It has been suggested that under some conditions, orotate phosphoribosyltransferase may be a regulatory site as well. 

Jones, M. E., Pyrimidine nucleotide biosynthesis in animals Genes, enzymes and regulation of UMP biosynthesis. Ann. Rev. Biochem. 49 253-279, 1980. Authoritative outline of the regulatory properties of the two multifunctional proteins responsible for pyrimidine nucleotide synthesis in animals. 

Fluorouracil and fluorodeoxyuridine (floxuridine) inhibit pyrimidine nucleotide biosynthesis and interfere with the synthesis and actions of nucleic acids. To exert its effect, fluorouracil (5-FU)... 

Fluorouracil and fluorodeoxyuridine (floxuridine) inhibit pyrimidine nucleotide biosynthesis and interfere with the synthesis and actions of nucleic acids. To exert its effect, fluorouracil (5-FU) must first be converted to nucleotide derivatives such as 5-fluorodeoxyuridylate (5-FdUMP). Similarly, floxuridine (FUdR) is also converted to FdUMP by the following reactions ... 

Figure 10.9 De now pyrimidine nucleotide biosynthesis pathway. Note the numbering of the pyrimidine ring in UMP atoms 2 and 3 come from carbamoyl phosphate and atoms 1, 4, 5, and 6 from aspartate.

Young, J. M., Ransom, J. T. (1995). Leflunomide interferes with pyrimidine nucleotide biosynthesis. Inflamm. Res. 

In eukaryotic cells, two separate pools of carbamoyl phosphate are synthesized by different enzymes located at different sites. Carbamoyl phosphate synthetase I (CPS I) is located in the inner membrane of mitochondria in the liver and, to lesser extent, in the kidneys and small intestine. It supplies carbamoyl phosphate for the urea cycle. CPS 1 is specific for ammonia as nitrogen donor and requires N-acetylglutamate as activator. Carbamoyl phosphate synthetase II (CPS II) is present in the cytosol. It supplies carbamoyl phosphate for pyrimidine nucleotide biosynthesis and uses the amido group of glutamine as nitrogen donor. The presence of physically separated CPSs in eukaryotes probably reflects the need for independent regulation of pyrimidine biosynthesis and urea formation, despite the fact that both pathways require carbamoyl phosphate. In prokaryotes, one CPS serves both pathways. 

PRPP affects purine and pyrimidine nucleotide biosynthesis. PRPP formation is activated by inorganic phosphate and inhibited by several end products of pathways that use PRPP. In the purine de novo pathway, PRPP activates amidophosphoribosyltransferase and is the rate-limiting substrate for the enzyme. In purine... 

So NNC, Wong PCL, Ko RC (1992) Precursors of pyrimidine nucleotide biosynthesis for gravid Angiostrongylus cantonensis (Nematoda Metastrongyloidea). Int J Parasitol 22 427 33 Spector T (1978) Refinement of the coomassie blue method of protein quantitation. Anal Biochem 86 142-146... 

Uridine-cytidine kinase is an important enzyme in pyrimidine nucleotide biosynthesis through the salvage pathway. In addition, this enzyme is also responsible for the 5 -phosphorylation of pyrimidine nucleoside analogs used... 

Aspartate has many fates, too. For example, its nitrogen is used in the biosynthesis of arginine and urea. Similar reactions are involved in purine nucleotide synthesis. The entire aspartate molecule is used in pyrimidine nucleotide biosynthesis. In plants and bacteria, aspartate is a precursor to three other amino acids (i.e., methionine,threonine, and isoleucine) via its conversion to homoserine (see here). Homoserine then leads in separate pathways to methionine and threonine. Threonine, in turn, can be converted to isoleucine. In bacteria, aspartic / -semialdehyde is a precursor to lysine. 

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