Pyrimidine ring, biosynthesis

The major difference between purine and pyrimidine de novo biosynthesis is that the pyrimidine ring is assembled and then added to PRPP (Fig. 20-1). With purines, the purine ring is built directly on the PRPP. 

The major intermediates in the biosynthesis of nucleic acid components are the mononucleotides uridine monophosphate (UMP) in the pyrimidine series and inosine monophosphate (IMP, base hypoxanthine) in the purines. The synthetic pathways for pyrimidines and purines are fundamentally different. For the pyrimidines, the pyrimidine ring is first constructed and then linked to ribose 5 -phosphate to form a nucleotide. By contrast, synthesis of the purines starts directly from ribose 5 -phosphate. The ring is then built up step by step on this carrier molecule. 

In 1972, we elucidated the structure of bleomycin except for the side-chain part of the pyrimidoblamyl moiety (53), and in 1978, we determined the structtire of bleomycin conclxosively, as is shown in Fig. 4 (52). One of the amino acids contained in bleomycin has a pyrimidine ring we named this amino acid "pyrimldo-blamic acid". During the study of biosynthesis, demethylpyrimi-doblamylhistidinylalanine was obtained and its copper complex was crystallized. Based on the x-ray analysis of this crystal (10), we proposed the strvxiturej gf bleomycin in Fig. 4. We also confirmed this structure by N-nmr (25). 

Several purine derivatives are found in nature, e.g. xanthine, hypoxanthine and uric acid. The pharmacologically important (CNS-stimulant) xanthine alkaloids, e.g. caffeine, theobromine and theophylline, are found in tea leaves, coffee beans and coco. The actual biosynthesis of purines involves construction of a pyrimidine ring onto a pre-formed imidazole system. 

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. 

The second step in pyrimidine synthesis is the formation of car-bamoylaspartate, catalyzed by aspartate transcarbamoylase. The pyrimidine ring is then closed hydrolytically by dihydroorotase. Thi resulting dihydroorotate is oxidized to produce orotic acid (onotate, Figure 22.21). The enzyme that produces orotate, dihydroorotate dehydrogenase, is located inside the mitochondria. All other reactions in pyrimidine biosynthesis are cytosolic. [Note The first three enzymes in this pathway (CPS II, aspartate transcarbamoylase, and dihydroorotase) are all domains of the same polypeptide chain. (See k p. 19 for a discussion of domains.) This is an example of a multifunctional or multicatalytic polypeptide that facilitates the ordered synthesis of an important compound.]... 

Figure 25-14 Assembly of the pyrimidine ring and biosynthesis of the pyrimidine nucleotide precursors of RNA and DNA.

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. 

Biosynthesis of UMP. The parts of the intermediates derived from aspartate are shown in red. Bold type indicates atoms derived from carbamoyl phosphate. In contrast to purine nucleotide synthesis, where ring formation starts on the sugar, in pyrimidine biosynthesis the pyrimidine ring is completed before being attached to the ribose. 

The actual biosynthesis of purines (illustrated below in abbreviated form for the nucleotide adenosine monophosphate AMP 10.9) involves construction of a pyrimidine ring onto a pre-formed imidazole. 

Although both purine and pyrimidine rings have one 6-mem-bered component with two nitrogens and four carbons, the purines and pyrimidnes are not related metabolically. Distinct pathways for purine biosynthesis and degradation and for pyrimidine biosynthesis and degradation, exist in all organisms. 

Unlike in purine biosynthesis, the pyrimidine ring is synthesized before it is conjugated to PRPP. The first reaction is the conjugation of carbamoyl phosphate and aspartate to make N-carbamoylaspartate. The carbamoyl phosphate synthetase used in pyrimidine biosynthesis is located in the cytoplasm, in contrast to the carbamoyl phosphate used in urea synthesis, which is made in the mitochondrion. The enzyme that carries out the reaction is aspartate transcarbamoylase, an enzyme that is closely regulated. 

The design for pyrimidine synthesis differs somewhat from that of purine biosynthesis in that the sugar is attached to the pyrimidine ring at the end of the pathway. In addition, pyrimidine biosynthesis occurs in part in the cytosol and in part in the mitochondria and involves the participation of two multifunctional enzymes. The pathway is summarized in Figure 10.9. One of the initial reactants is the compound carbamoyl phosphate (carbamoyl phosphoric acid). This compound is also formed in the urea biosynthetic pathway, but this takes place in the mitochondria and requires NH3 (Chapter 20). The cytosolic biosynthesis of carbamoyl phosphate for the purpose of pyrimidine biosynthesis requires glutamine as the nitrogen donor ... 

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.

The atoms of the pyrimidine ring are derived from carbamoyl phosphate and aspartate, as shown in Fig. 15-14. The de novo biosynthesis of pyrimidine nucleotides is shown in Fig. 15-15. The first completely formed pyrimidine ring is that of dihydroorotate. Only after oxidation to orotate is the ribose attached to produce orotidylate. The compound 5-phosphoribosyl 1-pyrophosphate (P-Rib-PP) provides the ribose phosphate. L-Glutamine is used as a substrate donating nitrogen atoms at reactions 1 and 9, catalyzed by carbamoyl phosphate synthetase II and CTP synthetase, respectively a second... 

FIGURE 9.7 Pyrimidine biosynthetic pathway. The pathway of pyrimidine biosynthesis involves sbc steps and results in the production of uridine 58-monophosphate. Folate is not used in this pathway The pathway commences with the transfer of the amide nitrogen of glutamine to bicarbonate to produce caibamy I phosphate. This molecule then reacts with aspartate to form the beginnings of the siK-membered pyrimidine ring. 

There is no experimental result to elucidate the biosynthesis of pyrimidobleonic acid moiety at the present time except for the methyl group of the pyrimidine ring, which comes from methionine. Compared with the biosynthesis of lycomarasmin39), the amine component II appears to be derived from aspartylasparagine via dehydrative cyclization, dehydrogenation, amination and methylation (Fig. 13). amino acid + acetate or acetate + C,... 

Figure 27-7). Free purines or purine nucleosides are not intermediates of this pathway. In pyrimidine biosynthesis, the pyrimidine ring is formed completely before addition of ribose 5-phosphate.

Sources of the pyrimidine ring atoms in de novo biosynthesis. 

Even though E. coli is a very well-studied bacterium, many interesting mechanistic problems in cofactor biosynthesis in this organism remain unsolved. The mechanisms for the formation of the nicotinamide ring of NAD, the pyridine ring of pyridoxal, the pterin system of molybdopterin, and the thiazole and pyrimidine rings of thiamin are unknown. The sulfur transfer chemistry involved in the biosynthesis of lipoic acid, biotin, thiamin and molybdopterin is not yet understood. The formation of the isopentenylpyrophosphate precursor to the prenyl side chain of ubiquinone and menaquinone does not occur by the mevalonate pathway. None of the enzymes involved in this alternative terpene biosynthetic pathway have been characterized. The aim of this review is to focus attention on these unsolved mechanistic problems. 

The answer is a. (Murray, pp 375-401. Scriver, pp 2513-2570. Sack, pp 121-138. Wilson, pp 287-320.) During purine ring biosynthesis, the amino acid glycine is completely incorporated to provide C4, C5, and N7. Glutamine contributes N3 and N9, aspartate provides Nl, and derivatives of tetrahydrofolate furnish C2 and C8. Carbon dioxide is the source of C6. In pyrimidine ring synthesis, C2 and N3 are derived from carbamoyl phosphate, while Nl, C4, C5, and C6 come from aspartate. 

Figure 22.10 illustrates the pathway for de novo pyrimidine biosynthesis. It differs from de novo purine synthesis in that the pyrimidine ring is synthesized separate from the ribose sugar (in purines, the ring is built upon the sugar - see Figure 22.4). In addition, de novo pyrimidine biosynthesis is not branched. Synthesis leads to UMP, from which CTP is ultimately made. By contrast, de novo purine biosynthesis branches after IMP is produced (Figure 22.6).

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