Biosynthesis of Deoxyribonucleotides

Tracer studies with isotopically labeled precursors have shown that both in mammalian tissues and in microorgan-isms, deoxyribonucleotides are formed from corresponding ribonucleotides by replacement of the 2 —OH group with hydrogen. 

Three types of ribonucleotide reductase catalyze this reduction of the ribose ring. The most widely distributed in nature occurs in mammalian and plant cells, in yeast, and in some prokaryotes. This type of reductase contains a tyrosyl radical closely associated with nonheme iron, as in the reductase from E. coli. The E. coli reductase is composed of two nonidentical subunits, both contributing to the active site it is specific for the reduction of diphosphates (ADP, GDP, CDP, and UDP). 

An unusual feature of ribonucleotide reductase is that the reaction it catalyzes involves a radical mechanism. The mammalian type of reductase initiates this reaction by the tyrosyl radical-nonheme iron. Hydroxyurea and related inhibit the majTrrrraiVarr retftrcCase 6y abolishing the radical state of the tyrosine residue. Inhibition of DNA synthesis by such compounds is secondary to this effect. 

The physiological reducing substrate is a low-molecular-weight (13,000) electron-transport protein, thioredoxin. Thioredoxin has two half-cystine residues that are separated in the polypeptide chain by two other residues. The oxidized form of thioredoxin, with a disulfide bridge between the 

Ribonucleotide reductase and the thioredoxin system. In some lactobacilli, vitamin B12 is involved in the reduction of ribonucleotide triphosphate to deoxyribonucleotide. 

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Understand the purine and pyrmidine de novo biosynthetic pathways, with special attention to enzymes controlling pathway rates and the properties of such enzymes the positive and negative effectors steps inhibited by the various antitumor agents and their mechanisms final products of the de novo pathways and how the various nucleotides are generated from them and the biosynthesis of deoxyribonucleotides and the attendant mechanisms. 

Which substance is not required for the biosynthesis of deoxyribonucleotides from ribonucleotides ... 

As we have seen, the biosynthesis of deoxyribonucleotides in E. coli has been studied in considerable depth discoveries made with that system greatly facilitated the exploration of this process in other cell types. Ribonucleotide reduction in several kinds of animal cells is evidently accomplished by a mechanism similar to that found in E. coli, whereas in Lactobacillus leichmannii and in certain Rhizobium and Clostridium species (2S), the process of ribonucleotide reduction differs distinctively from that in E. coli in that B12 cofactors are involved. 

Apart from that of E. coli, the only microbial system for deoxyribonu-cleotide synthesis which has been studied in detail is that of L. leichmannii. Prior to the definitive biochemical studies described below, nutritional experiments had demonstrated that the vitamin Bu requirement of L. leichmannii was involved in an essential way in the biosynthesis of deoxyribonucleotides. Blakley and Barker 24) showed that cell-free extracts of this microorganism catalyzed the reduction of cytidylate to deoxycyti-dylate and showed also that this reaction required a vitamin B12 derivative and NADP. 

Hydroxyurea interferes with the synthesis of both pyrimidine and purine nucleotides (see table 23.3). It interferes with the synthesis of deoxyribonucleotides by inhibiting ribonucleotide reductase of mammalian cells, an enzyme that is crucial and probably rate-limiting in the biosynthesis of DNA. It probably acts by disrupting the iron-tyrosyl radical structure at the active site of the reductase. Hydroxyurea is in clinical use as an anticancer agent. 

Chapter 23, Nucleotides, deals with the biosynthesis of ribonucleotides, deoxyribonucleotides, the roles of these biomolecules in metabolic processes, and the pathways for their degradation. Medically related topics such as nucleotide metabolism deficiencies or the use of nucleotide analogs in chemotherapy are also considered. 

The evolutionary transition from RNA to DNA is recapitulated in the biosynthesis of DNA in modem organisms. In all cases, the building blocks used in the synthesis of DNA are synthesized from the corresponding building blocks of RNA by the action of enzymes termed ribonucleotide reductases. These enzymes convert ribonucleotides (a base and phosphate groups linked to a ribose sugar) into deoxyribonucleotides (a base and phosphates linked to deoxyribose sugar). 

See also De Novo Biosynthesis of Purine Nucleotides, Purine Degradation, Excessive Uric Acid in Purine Degradation, Salvage Routes to Deoxyribonucleotide Synthesis, Nucleotide Analogs in Selection... 

See also De Novo Biosynthesis of Purine Nucleotides, Salvage Routes to Deoxyribonucleotide Synthesis... 

See also Figure 4.3, DNA, Deoxyuridine Nucleotide Metabolism, Biosynthesis of Thymine Deoxyribonucleotides... 

Regulation of Ribonucleotide Reductase Activity (Figure 22.13, Table 22.2) Biosynthesis of Thymine Deoxyribonucleotides (Figure 22.17, Figure 22.18)... 

Another important biological reaction shown to involve a radical intermediate is the conversion of a ribonucleotide into a deoxyribonucleotide. The biosynthesis of ribonucleic acid (RNA) requires ribonucleotides, whereas the biosynthesis of deoxyribonucleic acid (DNA) requires deoxyribonucleotides (Section 27.1). The first step in the conversion of a ribonucleotide to the deoxyribonucleotide needed for DNA biosynthesis involves abstraction of a hydrogen atom from the ribonucleotide to form... 

A dithiol protein, thioredoxin, functions in the transport of electrons from reduced nicotinamide adoiine dinucleotide phosphate (NADPH) to ribonucleotides in the biosynthesis of 2 -deoxyribonucleotides. A thioredoxin type carrier is involved in both vitamin dependent and independent type systems. Thioredoxin is frequently described as a polypeptide cofactor rather than an enzyme because its activity is not destroyed... 

An additional feature of thymidine kinase activity is that it is subject to allosteric regulation. Despite the implication in these facts that this enzyme activity is important in the deoxyribonucleotide economy of cells, thymidine is not an obligatory intermediate in the biosynthesis of the thymidine phosphates and the mutational loss of this enzyme is not lethal. 

The biosynthesis of many antibiotics is inhibited in vivo by phosphate (89,91). Antibiotics are synthesized only at concentrations of inorganic phosphate that are subc timal for growth (from I to 50 mM for different antibiotics). Phosphate in the range 0.3-500 mM supports excellent cell growth, whereas 10 mM phosphate often suppresses biosynthesis of antibiotics. The same inhibitory effect is exerted by deoxyribonucleotides, because they are cleaved during uptake by S. gn seus cells (97,98). 

Grimdy FJ, Lehman SC, HenMn TM (2003) The L box regtrlon lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci USA 100 12057-12062 Hartman JLIV (2007) Buffering of deoxyribonucleotide pool homeostasis by threonine metabolism. Proc Natl Acad Sci USA 104(10) 11700-11705 Henkin TM, Yanofsky C (2002) Regirlation by transcription attenuation in bacteria how RNA provides instructions for transcription termination/antitermination decisions. Bioessays 24 700-707... 

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