Pyrimidine ribonucleotide synthesis

PYRIMIDINE RIBONUCLEOTIDE SYNTHESIS FROM BASES AND RIBONUCLEOSIDES... 

Enzymes of Pyrimidine Ribonucleotide Synthesis FROM Bases and Ribonucleobides ... 

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... 

IMP Is Converted into AMP and GMP Synthesis of Pyrimidine Ribonucleotides de Novo UMP Is a Precursor of Other Pyrimidine Nucleotides... 

How is the other major pyrimidine ribonucleotide, cytidine, formed It is synthesized from the uracil base of UMP, but UMP is converted into UTP before the synthesis can take place. Recall that the diphosphates and triphosphates are the active forms of nucleotides in biosynthesis and energy conversions. Nucleoside monophosphates are converted into nucleoside triphosphates in stages. First, nucleoside monophosphates are converted into diphosphates by specific nucleoside monophosphate kinases that utilize ATP as the phosphoryl-group donor (Section 9.4). For example, UMP is phosphorylated to UDP by UMP kinase. 

Figure 7-20. De novo synthesis of purines and pyrimidines. Ribonucleotide reductase (R.R.) catalyzes the reduction of the ribose moiety in ADP, GDP, and CDP to deoxyribose. The source of each of the atoms is indicated in the boxes at the bottom of the figure. In hereditary orotic aciduria, the enzymes converting orotate to UMP are defective ( ).

Pizzarello S, Weber AL (2010) Stereoselective syntheses of pentose sugars under realistic prebiotic conditions. Orig Life Evol Biosph 40 3-10 Powner MW, Garland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459 239-242 Scumlimbrene BR, Miller SJ (2001) Discovery of a catalytic asymmetric phosphorylation through selection of a minimal kinase mimic a concise total synthesis of D-myo-inositol-phosphate. J Am Chem Soc 123 10125-10126... 

Purine deoxyribonucleotides are derived primarily from the respective ribonucleotide (Fig. 6.2). Intracellular concentrations of deoxyribonucleotides are very low compared to ribonucleotides usually about 1% that of ribonucleotides. Synthesis of deoxyribonucleotides is by enzymatic reduction of ribonucleotide-diphosphates by ribonucleotide reductase. One enzyme catalyzes the conversion of both purine and pyrimidine ribonucleotides and is subject to a complex control mechanism in which an excess of one deoxyribonucleotide compound inhibits the reduction of other ribonucleotides. Whereas the levels of the other enzymes involved with purine and pyrimidine metabolism remain relatively constant through the cell cycle, ribonucleotide reductase level changes with the cell cycle. The concentration of ribonucleotide reductase is very low in the cell except during S-phase when DNA is synthesized. While enzymatic pathways, such as kinases, exist for the salvage of pre-existing deoxyribosyl compounds, nearly all cells depend on the reduction of ribonucleotides for their deoxyribonucleotide... 

The synthesis of deoxyuridine, cytidine, deoxycytidine and thymidine nucleotides from UMP (Fig. 6.13) involves three reactions CTP synthetase, ribonucleotide reductase, and thymidylate synthase (80). The first enzyme converts UTP into CTP and the second catalyzes the conversion of CDP, UDP, ADP and GDP into their respective deoxyribonucleotides. The last enzyme, thymidylate synthase, catalyzes the reductive methylation of deoxyUMP at the C-5 position giving deoxyTMP. The human enzyme has been extensively studied as it is a target enzyme in cancer chemotherapy. Besides these three enzymes, two other enzymes are involved in pyrimidine nucleotide synthesis and interconversion. DeoxyCMP deaminase converts deoxyCMP into deoxyUMP and deoxyUTP triphosphatase converts deoxyUTP into deoxyUMP. Giardia lamblia, and Trichomonas vaginalis lack both ribonucleotide reductase and thymidylate synthase and... 

Sutherland and co-workers have obtained activated pyrimidine ribonucleotides from cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde, and inorganic phosphate in a reaction that bypassed free ribose. The synthesis yielded activated ribonucleotide P-ribocytidine-2 ,3 -cyclic phosphate as a major product and several co-products [17]. Prolonged irradiation of this mixture by 254 nm UV-light caused the destruction of various co-products and the partial conversion of P-ribocytidine-2 ,3 -cyclic phosphate into P-ribouridine-2 ,3 -cyclic phosphate. The authors concluded that there must be some (photo)protective mechanism functioning with the two natural nucleotides but not with other pyrimidine nucleosides and nucleotides [17]. 

Powner MW, Gerland B, Sutherland JD Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 2009,459(7244) 239— 242. 

In animal cells thymidine is specifically incorporated into DNA thy-midylate, contributing neither to DNA deoxycytidylate nor to the pyrimidine ribonucleotides (33). Since incorporation into DNA is the only major anabolic fate of labeled thymidine, DNA synthesis can be measured without isolation of DNA—only the removal of unused substrate and acid-soluble metabolites is necessary. Tritiated thymidine has been particularly valuable in autoradiographic studies of DNA synthesis and is available today in very high specific activities. 

In animal cells engaged in DNA synthesis, deoxyuridine can be incorporated without cleavage into DNA thymidylate, but phosphorolysis also occurs and the uracil so released will not have incorporation into DNA as a specific metabolic fate. Because of deamination, deoxycytidine may be converted to either of the pyrimidine nucleotides of DNA cleavage of the deamination product, deoxyuridine, liberates uracil which may enter the pathways of pyrimidine ribonucleotide metabolism. 

What works is not running three separate steps, but throwing the chemicals together. .. M. W. Powner et al. Synthesis of activated pyrimidine ribonucleotides in prebioticaUy plausible conditions. 2009. Nature 459, p. 239. DOI 10.1038/nature08013. 

Fig. 23.1. Pyrimidine pathways Pathways for the de novo synthesis, interconversion, and breakdown of pyrimidine ribonucleotides, indicating their metabolic importance as the essential precursors of the pyrimidine sugars and, with purines, of DNA and RNA. Note that in contrast to purines salvage takes place at the nucleoside not the base level in human cells and pyrimidine metabolism normally lacks any detectable end-product. The importance of this network is highlighted by the variety of clinical symptoms associated with the possible enzyme defects indicated. 23.10, Uridine monophosphate synthase (UMPS), 23.11a, uridine monophosphate hydrolase 1 (UMPHl), 23.12, thymidine phosphorylase (TP), 23.13, dihydropyrimidine dehydrogenase (DPD), 23.14, dihydropyrimidine amidohydrolase (DHP), 23.15, y -ureidopropionase (UP) (23.11b, UMPH superactivity specific to fibroblasts is not shown). CP, carbamoyl phosphate. The pathological metabolites used as specific markers in differential diagnosis are highlighted...

The atoms of the pyrimidine ring are derived from two amino acids, aspartate and glutamine, and carbon dioxide (Figure 16.6a). Biosynthesis does not produce free heterocyclic compounds but nucleotides. The synthetic pathway produces uridine ribonucleotides which also serve as the precursors of other pyrimidine ribonucleotides and deoxyribo-nucleotides. The cellular pool of free deoxyribo-nucleotides is normally held at an extremely low level but requires enhancement to support the synthesis of DNA when cells prepare for division. 

The two classes of nucleotide that must be synthesised are the pyrimidine and purine ribonucleotides for RNA synthesis and the deoxyribonucleotides for DNA synthesis. For the original sources of the nitrogen atoms in the bases of the pyrimidine and purine nucleotides, see Figure 20.7. The pathway for the synthesis of the pyrimidine nucleotides is... 

Pemetrexed is chemically similar to folic acid. It inhibits three enzymes used in purine and pyrimidine synthesis - thymidylate synthetase, dihydrofolate reductase, and glycinamide ribonucleotide formyl transferase. By inhibiting the formation of precursor purine and pyrimidine nucleotides, pemetrexed prevents the formation of DNA and RNA. In 2004 it was approved for treatment of malignant pleural mesothelioma and as a second-line agent for the treatment of non-small cell lung cancer. Adverse effects include gastrointestinal complaints, bone marrow suppression, alopecia, allergic and neurotoxic reactions. 

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