Pyrimidine, biosynthesis

The pathways for thiamine biosynthesis have been elucidated only partiy. Thiamine pyrophosphate is made universally from the precursors 4-amino-5-hydroxymethyl-2-methylpytimidinepyrophosphate [841-01-0] (47) and 4-methyl-5-(2-hydroxyethyl)thiazolephosphate [3269-79-2] (48), but there appear to be different pathways ia the eadier steps. In bacteria, the early steps of the pyrimidine biosynthesis are same as those of purine nucleotide biosynthesis, 5-Aminoimidazole ribotide [41535-66-4] (AIR) (49) appears to be the sole and last common iatermediate ultimately the elements are suppHed by glycine, formate, and ribose. AIR is rearranged in a complex manner to the pyrimidine by an as-yet undetermined mechanism. In yeasts, the pathway to the pyrimidine is less well understood and maybe different (74—83) (Fig. 9). 

Aspartate transcarbamoylase (ATCase), the catalyst for the first reaction unique to pyrimidine biosynthesis (Figure 34-7), is feedback-inhibited by cytidine tri-... 

Condensation of CO2, ammonia, and ATP to form carbamoyl phosphate is catalyzed by mitochondrial carbamoyl phosphate synthase I (reaction 1, Figure 29-9). A cytosolic form of this enzyme, carbamoyl phosphate synthase II, uses glutamine rather than ammonia as the nitrogen donor and functions in pyrimidine biosynthesis (see Chapter 34). Carbamoyl phosphate synthase I, the rate-hmiting enzyme of the urea cycle, is active only in the presence of its allosteric activator JV-acetylglutamate, which enhances the affinity of the synthase for ATP. Formation of carbamoyl phosphate requires 2 mol of ATP, one of which serves as a phosphate donor. Conversion of the second ATP to AMP and pyrophosphate, coupled to the hydrolysis of pyrophosphate to orthophosphate, provides the driving... 

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.

Multifunctional Proteins Catalyze the Early Reactions of Pyrimidine Biosynthesis... 

Five of the first six enzyme activities of pyrimidine biosynthesis reside on multifunctional polypeptides. One such polypeptide catalyzes the first three reactions of Figure 34-2 and ensures efficient channeling of carbamoyl phosphate to pyrimidine biosynthesis. A second bifunctional enzyme catalyzes reactions 5 and 6. 

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. 

Since pyrimidine catabolites are water-soluble, their overproduction does not result in clinical abnormalities. Excretion of pyrimidine precursors can, however, result from a deficiency of ornithine transcar-bamoylase because excess carbamoyl phosphate is available for pyrimidine biosynthesis. 

Lee, L., Kelly, R.E., Pastra-Landis, S.C., and Evans, D.R. (1985) Oligomeric structure of the multifunctional protein CAP that initiates pyrimidine biosynthesis in mammalian cells. Proc. Natl. Acad. Sci. USA 82, 6802-6806. 

Function To donate methyl groups to phospholipid, biogenic amines, thymidine, and amino acid biosynthesis To provide one-carbon fragments at the level of formaldehyde and formic acid for purine and pyrimidine biosynthesis Location Most everywhere... 

In the U.S.A. various pyridazine analogues of naturally occurring pyrimidine nucleosides have been prepared [299, 300] for a review on this subject see [13]. Within this series, 3-deaza-6-azauridine (86) has been found to inhibit the growth of L-1210 mouse leukaemic cells with an ID50 value of a 7 X 10 5 M [299, 301], The inhibitory effect of this uridine isoster might be due to interference in pyrimidine biosynthesis [302],... 

Under normal conditions, many of the enzymes involved in the pathway for pyrimidine biosynthesis de novo may not operate at maximum efficiency but rather exist in an inhibited state. This inhibition is released during the course of regeneration (for example after partial hepatectomy [133] or castration... 

Folic acid derivatives are essential for DNA synthesis, in that they are cofactors for certain reactions in purine and pyrimidine biosynthesis, including the uracil-thymine methylation just described. They are also cofactors for several reactions relating to amino acid metabolism. The folic acid system thus offers considerable scope for drug action. 

These are pyrimidine derivatives and are effective because of differences in susceptibility between the enzymes in humans and in the infective organism. Anticancer agents based on folic acid, e.g. methotrexate, inhibit dihydrofolate reductase, but they are less selective than the antimicrobial agents and rely on a stronger binding to the enzyme than the natural substrate has. They also block pyrimidine biosynthesis. Methotrexate treatment is potentially lethal to the patient, and is usually followed by rescue with folinic acid (A -formyl-tetrahydrofolic acid) to counteract the folate-antagonist action. The rationale is that folinic acid rescues normal cells more effectively than it does tumour cells. 

Atovaquone is a naphthoquinone whose mechanism of action involves inhibition of the mitochondrial electron transport system in the protozoa. Malaria parasites depend on de novo pyrimidine biosynthesis through dihy-droorotate dehydrogenase coupled to electron transport. Plasmodia are unable to salvage and recycle pyrimidines as do mammalian cells. 

Antimetabolite inhibitors of DNA synthesis act by the competitive or allosteric inhibition of a number of different enzymes participating in purine or pyrimidine biosynthesis. Actually, some such compounds interfere with as many as 10-12 different enzymes— although admittedly to a different degree. 

The phenoxyquinolines are a recent addition to crop fungicides and only one compound has been described. LY214352, an experimental fungicide, inhibits a novel target, dihydro-orotate dehydrogenase (DHO-DH) in the pyrimidine biosynthesis pathway that catalyses the conversion of dihydro-orotate into orotic acid9 (Figure 4.13). 

The liver also receives some ammonia via the portal vein from the intestine, from the bacterial oxidation of amino acids. Whatever its source, the Nib generated in liver mitochondria is immediately used, together with C02 (as HCO3) produced by mitochondrial respiration, to form carbamoyl phosphate in the matrix (Fig. 18-1 la see also Fig. 18-10). This ATP-dependent reaction is catalyzed by carbamoyl phosphate synthetase I, a regulatory enzyme (see below). The mitochondrial form of the enzyme is distinct from the cytosolic (II) form, which has a separate function in pyrimidine biosynthesis (Chapter 22). 

The de novo pathways for purine and pyrimidine biosynthesis appear to be nearly identical in all living organisms. Notably, the free bases guanine, adenine, thymine, cytidine, and uracil are not intermediates in these pathways that is, the bases are not synthesized and then attached to ribose, as might be expected. The purine ring structure is built up one or a few atoms at... 

Oligomeric structure of the multifunctional protein CAD that initiates pyrimidine biosynthesis in mammalian cells. Proc. Natl. Acad. Sci. USA 82, 6802-6806. 

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.]... 

Allosteric Enzymes Typically Exhibit a Sigmoidal Dependence on Substrate Concentration The Symmetry Model Provides a Useful Framework for Relating Conformational Transitions to Allosteric Activation or Inhibition Phosphofructokinase Allosteric Control of Glycolysis Is Consistent with the Symmetry Model Aspartate Carbamoyl Transferase Allosteric Control of Pyrimidine Biosynthesis Glycogen Phosphorylase Combined Control by Allosteric Effectors and Phosphorylation... 

A5-Methyltetrahydrofolate is the methyl-group donor substrate for methionine synthase, which catalyzes the transfer of the five-methyl group to the sulfhydryl group of homocysteine. This and selected reactions of the other folate derivatives are outlined in figure 10.15, which emphasizes the important role tetrahydrofolate plays in nucleic acid biosynthesis by serving as the immediate source of one-carbon units in purine and pyrimidine biosynthesis. 

Purine Biosynthesis Is Regulated at Two Levels Pyrimidine Biosynthesis Is Regulated at the Level of Carbamoyl Aspartate Formation Deoxyribonucleotide Synthesis Is Regulated by Both Activators and Inhibitors... 

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. 

Pyrimidine Biosynthesis Is Regulated at the Level of Carbamoyl Aspartate Formation... 

How do you explain the observation that pyrimidine biosynthesis in bacteria is regulated at the level of aspartate carbamoyltransferase, whereas most of the regulation in humans is at the level of carbamoyl phosphate synthase ... 

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