Pyrimidine de novo pathway

Dihydroorotate dehydrogenase, the enzyme catalyzing the dehydrogenation of dihydroorotate to orotate (reaction 4 of the pathway Fig. 15-15), is located on the outer side of the inner mitochondrial membrane. This enzyme has FAD as a prosthetic group and in mammals electrons are passed to ubiquinone. The de novo pyrimidine pathway is thus compartmentalized dihydroorotate synthesized by trifunctional DHO synthetase in the cytosol must pass across the outer mitochondrial membrane to be oxidized to orotate, which in turn passes back to the cytosol to be a substrate for bifunctional UMP synthase. Mammalian cells contain two carbamoyl phosphate synthetases the glutamine-dependent enzyme (CPSase II) which is part of CAD, and an ammonia-dependent enzyme (CPSase /) which is found in the mitochondrial matrix, and which is used for urea and arginine biosynthesis. Under certain conditions (e.g., hyperammonemia), carbamoyl phosphate synthesized in the matrix by CPSase I may enter pyrimidine biosynthesis in the cytosol. 

Our finding of two pyrimidine biosynthetic enzymes (OMPDC and TS) in P. lophurae suggested that, unlike the duckling host, malaria parasites synthesized pyrimidines de novo from precursors such as C02, glutamine and aspartic acid (Walsh and Sherman, 1968b). Since that time, the enzymatic reactions of the de novo pyrimidine pathway and TS have been demonstrated in a variety of Plasmodium spp. and for P. falciparum (available online at http //sites.huji.ac.il/malaria/maps/pyrimidinemetpath. html last accessed 16 July 2008). 

The de novo pyrimidine pathway is thus compartmentalized dihydroorotate synthesized by trifunctional DHO synthetase in the cytosol passes across the outer mitochondrial membrane to be oxidized to orotate, which in turn passes back to the cytosol where it is a substrate of the bifimctional UMP synthase. 

EXAMPLE 14.9 In bacteria, such as E. coli, the first six reactions of the de novo pyrimidine pathway (Fig. 14-7) are catalyzed by six distinct and separable enzymes but in higher animals, reactions 1, 2, and 3 are catalyzed by a trifunctional enzyme, and reactions 5 and 6 by a bifunctional enzyme. What advantages might there be in the spatial proximity of these active sites ... 

Utilizes pre-formed purine or pyrimidine De novo synthesis pathway... 

Figure 20.9 The positions in the pathway for de novo pyrimidine nucleotide synthesis where GLUCOSE provides the ribose molecule and GLUTAMINE provides nitrogen atoms. Glucose forms ribose 5-phosphate, via the pentose phosphate pathway (see chapter 6), which enters the pathway, after phosphorylation, as 5-phospho-ribosyl 1-pyrophosphate. Glutamine provides the nitrogen atom to synthesise carbamoylphos-phate (with formation of glutamate), and also to form cytidine triphosphate (CTP) from uridine triphosphate (UTP), catalysed by the enzyme CTP synthetase. It is the amide nitrogen of glutamine that is the nitrogen atom that is provided in these reactions.

The answer is E. Methotrexate is an analog of folic acid that binds with very high affinity to the substrate-binding site of dihydrofolate reductase, the enzyme that catalyzes conversion of DHF to THE, which is used in various forms by enzymes of both the purine and pyrimidine de novo synthetic pathways. Thus, synthesis of dTMP from dUMP catalyzed by thymidylate synthetase and several steps in purine synthesis catalyzed by formyltransferase are indirectly blocked by the action of methotrexate because both those enzymes require THE coenzymes. 

The following sections explore nature s use of domain swapping to evolve new function. These include the formation of multifunctional proteins, tandem duplication, domain recruitment, and cicular permutation (Fig. 1). The evolution of several enzymes in the purine (Fig. 2) and pyrimidine (Fig. 3) de novo biosynthetic pathways, as well as other enzymes, are discussed as illustrative examples. 

Fig. 15-15 The de novo pyrimidine biosynthetic pathway. CAP, carbamoyl phosphate CA-asp, /V-carbamoyl-L-aspartate DHO, L-dihydroorotate Oro, orotate OMP, orotidine 5 -monophosphate. Enzymes (1) carbamoyl phosphate synthetase II (2) aspartate transcarbamoylase (3) dihydroorotase, (4) dihydroorotate dehydrogenase (5) orotate phosphoribosyltransferase (6) OMP decarboxylase (7) nucleoside monophosphate kinase (8) nucleoside diphosphate kinase (9) CTP synthetase.

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).

CMP is a pyrimidine nucleotide that is an intermediate in several metabolic pathways. It arises from synthesis of phosphatidic acid-containing compounds. In addition to being an intermediate in de novo pyrimidine biosynthesis, it participates in the reactions that follow ... 

The presence of a de novo synthesis pathway implies that pyrimidine sahmge may be functionally redundant and potentially less critical to the nutrition of the parasite than purine acquisition. Similar to purine salvage, pyrimidine salvage is initiated by the translocation of pyrimidine nucleosides or nucleobases across the parasite cell membrane via specific transporters. As described earlier, leishmanial NTl is responsible for the transport of pyrimidine nucleosides. The sole pyrimidine nucleobase transport activity in Leidrmania has been dtantctetized biochemically in L. major (LmUl) and shown to rect nize uracil exdusively and with hi affinity, but has not yet been doned. 

CAD catalyzes the initial steps (Figure 1) of the de novo pyrimidine biosynthetic pathway in mammalian cells, in which glutamine, ATP, bicarbonate and aspartate are converted to dihydroorotate (i). Dihydroorotate is subsequently oxidized by mitochondrial dihydroorotate dehydrogenase and then converted in two steps to UMP by a second multifunctional protein that has PRPP ttansferase and decarboxylase activities. 

Most rat tissues utilized primari y the de novo synthetic pathway for pyrimidine synthesis and did not use dietary uracil the intestine was an exception 455). On the other hand, uracil was utilized readily by many mouse tissues even thou the elementary precursors were also used to form pyrimidines 310). 

A number of chemical compoimds which inhibit purine and pyrimidine biosynthesis are not obviously related in structure to any of the intermediates of the de novo synthetic pathway. Urethane can inhibit the growth of certain tumours, cause the formation of abnormal mitoses, and damage chromosomes. It is also... 

In many cells, the capacity for de novo synthesis to supply purines and pyrimidines is insufficient, and the salvage pathway is essential for adequate nucleotide synthesis. In patients with Lesch-Nyhan disease, an enzyme for purine salvage (hypoxanthine guanine phosphoribosyl pyrophosphate transferase, HPRT) is absent. People with this genetic deficiency have CNS deterioration, mental retardation, and spastic cerebral palsy associated with compulsive self-mutilation, Cells in the basal ganglia of the brain (fine motor control) normally have very high HPRT activity. These patients also all have hyperuricemia because purines cannot be salvaged. 

Figure 20.8 Summary of pathways for de novo synthesis of purine and pyrimidine nucleotides. C represents transfer of a single carbon atom (a one-carbon transfer). Details are provided in Appendix 20.1. IMP - inosine monophosphate. For thymi-dylate synthesis, see Figure 20.12a.

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... 

De novo synthesis of purines and pyrimidines yields the monophosphates IMP and UMP, respectively (see p. 188). All other nucleotides and deoxynucleotides are synthesized from these two precursors. An overview of the pathways involved is presented here further details are given on p. 417. Nucleotide synthesis by recycling of bases (the salvage pathway) is discussed on p. 186. 

A. Salvage pathways allow synthesis of nucleotides from free purines or pyrimidines that arise from nucleic acid degradation or dietary sources, which is more economical for the cell than de novo synthesis. 

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... 

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