Pyrimidine-3 -phosphate

As an example of an enzyme reaction which has been studied with fast-reaction techniques, we consider the mechanism of action of pancreatic ribonuclease A. Ribonuclease catalyzes the breakdown of ribonucleic acid in two distinct steps as shown in Fig. 9-6. First the diester linkage is broken, and a pyrimidine 2 3 -cyclic phosphate is formed then the cyclic phosphate is hydrolyzed to give the pyrimidine 3 -monophosphate and purine oligonucleotides with a terminal pyrimidine 3 -phosphate. Ribonuclease has been extensively studied with a variety of chemical and physical techniques, and its three-dimensional structure is known (cf. Richards and Wyckoff [12] for a comprehensive review). 

The interaction of dinucleosides, pyrimidine 2 3 -cyclic phosphates, or pyrimidine 3 -phosphates with the enzyme is characterized by two relaxation processes, in addition to the process associated with the unliganded enzyme. In all cases the results can be described by a two-step mechanism a bimolec-ular combination of enzyme and substrate followed by an isomerization or conformational change of the enzyme-substrate complex ... 

Ribonuclease has a very pronounced specificity. It cleaves only those phospho-diester bonds that leave the pyrimidine 3 -phosphates. The first step of enzymic catalysis is transphosphorylation ... 

Biosynthesis of pyrophosphate (5) from pyrimidine phosphate (47) and thia2ole phosphate (48) depends on the activity of five en2ymes, four of them kinases (87). In yeasts and many other organisms, including humans, pyrophosphate (5) can be obtained from exogenous thiamine in a single step cataly2ed by thiamine pyrophosphokinase (88). 

Figure 4 Biosynthesis of thiamine (vitamin ). 37, aminoimidazole ribotide 38, 2-methyl-4-amino-5-hydroxymethyl-pyrimidine phosphate 39, pyridoxal 5 -phosphate 40, histidine 41, 2-methyl-4-amino-5-hydroxymethyl-pyrimidine pyrophosphate 42, 4-methyl-5-p-hydroxyethylthiazole phosphate 43,1 -deoxy-D-xylulose 5-phosphate 44, 5-ADP-D-ribulose 45, thiamine phosphate 46, thiamine pyrophosphate.

Pyrimidine-5 -nucleotidases are a group of enzymes dephos-phorylating pyrimidine nucleotides to the corresponding nucleosides. The pyrimidine bases diffuse out of the erythrocyte and the phosphates are retained. Pyrimidine phosphates are present on ribosomes of erythroblasts and reticulocytes, but there are normally no pyrimidines in mature RBCs. Two cytoplasmic forms of the enzyme were identified in the erythrocyte, P5 N-1 and P5 N-2. These enzymes are encoded by different genes and have different molecular properties and substrate specificities. Since there are no known disorders associated with deficiency of P5 N-2, this enzyme will not be further discussed here. 

The biosynthetic pathway is outlined in Figure 1. The thiazole 4 is formed by an oxidative condensation of glycine (1), deoxy-D-xylulose-5-phosphate (DXP, 2), and a sulfide carrier protein with a thiocarboxylate at its carboxy terminus (ThiS-COSH, 3). The pyrimidine phosphate 8 is formed by a deep-seated rearrangement of aminoimidazole ribotide (AIR, 7). It is then pyrophosphorylated and used to alkylate the thiazole to give 10. A final phosphorylation completes the biosynthesis. The entire pathway from glycine, DXP, cysteine, AIR, and ATP has now been reconstituted using purified enzymes. 

Tyrocidine was found to produce a rapid decrease of respiration of staphylococci . Its action is directed towards the osmotic barriers resulting in a massive leakage of amino acids, purines, pyrimidines, phosphates-and phosphate esters from the cell into the medium . The resulting dilution of essential metabolites practically stops any biosynthetic process. This action is independent of growth. 

Methylpirimiphos Pirimifosmethyl Pyrimidine phosphate Pyrimiphos methyl Empirical C11H20N3O3PS Properties M.w. 305.37 Toxicology LD50 (oral, rat) 1250 mg/kg, (oral, mouse) 1180 mg/kg mod. toxic by ing. mutagen... 

H,3H)-Pyrimidinedione, 5-chloro-3-(1,1-dimethylethyl)-6-methyl-. See Terbacil 5-Pyrimidinemethanol, a-(2-chlorophenyl)-a-(4-chlorophenyl)-. See Fenarimol Pyrimidine phosphate. See Pirimiphos-methyl, Pyrimidinetetrone hydrate 2,4,5,6(1H,3H)-Pyrimidinetetrone hydrate. See Alloxan monohydrate... 

Nucleic acids are acidic substances present m the nuclei of cells and were known long before anyone suspected they were the primary substances involved m the storage transmission and processing of genetic information There are two kinds of nucleic acids ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) Both are complicated biopolymers based on three structural units a carbohydrate a phosphate ester linkage between carbohydrates and a heterocyclic aromatic compound The heterocyclic aro matic compounds are referred to as purine and pyrimidine bases We 11 begin with them and follow the structural thread... 

FIGURE 28 5 (a) Tube and (b) space filling models of a DNA double helix The carbohydrate-phosphate backbone is on the out side and can be roughly traced in (b) by the red oxygen atoms The blue atoms belong to the purine and pyrimidine bases and he on the inside The base pairing is more clearly seen in (a)... 

Section 28 8 The most common form of DNA is B DNA which exists as a right handed double helix The carbohydrate-phosphate backbone lies on the outside the punne and pyrimidine bases on the inside The double helix IS stabilized by complementary hydrogen bonding (base pairing) between adenine (A) and thymine (T) and guanine (G) and cytosine (C)... 

The primary stmcture of DNA is based on repeating nucleotide units, where each nucleotide is made up of the sugar, ie, 2 -deoxyribose, a phosphate, and a heterocycHc base, N. The most common DNA bases are the purines, adenine (A) and guanine (G), and the pyrimidines, thymine (T) and cytosine (C) (Fig. 1). The base, N, is bound at the I -position of the ribose unit through a heterocycHc nitrogen. 

Thiamine forms the expected derivatives of the thia zole alcohol function, such as carboxyUc and phosphate esters. Eew reactions at the pyrimidine 4-amino function have been reported. Most of the usual conditions used for formation of amides, for example, lead to destmction of the thiazolium ring. 

Basically, AZT is anabohcaHy phosphorylated to AZT mono-, di-, and tri-phosphates by various enzymes (kinases) of a target ceU (159). AZT-triphosphate competes with other phosphorylated pyrimidine nucleosides for incorporation into HIV DNA by the viral reverse transcriptase. Incorporation of the AZT-triphosphate into reverse transcriptase results in viral DNA chain termination. Reverse transcriptase is essential in the repHcative cycle of HIV. 

Consider carbamoyl phosphate, a precursor in the biosynthesis of pyrimidines ... 

RNA is relatively resistant to the effects of dilute acid, but gentle treatment of DNA with 1 mM HCl leads to hydrolysis of purine glycosidic bonds and the loss of purine bases from the DNA. The glycosidic bonds between pyrimidine bases and 2 -deoxyribose are not affected, and, in this case, the polynucleotide s sugar-phosphate backbone remains intact. The purine-free polynucleotide product is called apurinic acid. 

Just as proteins are biopolymers made of amino acids, nucleic acids are biopolv-mers made of nucleotides joined together to form a long chain. Each nucleotide is composed of a nucleoside bonded to a phosphate group, and each nucleoside is composed of an aldopentose sugar linked through its anomeric carbon to the nitrogen atom of a heterocyclic purine or pyrimidine base. 

The nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are biological polymers that act as chemical carriers of an organism s genetic information. Enzyme-catalyzed hydrolysis of nucleic acids yields nucleotides, the monomer units from which RNA and DNA are constructed. Further enzyme-catalyzed hydrolysis of the nucleotides yields nucleosides plus phosphate. Nucleosides, in turn, consist of a purine or pyrimidine base linked to Cl of an aldopentose sugar—ribose in RNA and 2-deoxyribose in DNA. The nucleotides are joined by phosphate links between the 5 phosphate of one nucleotide and the 3 hydroxyl on the sugar of another nucleotide. 

CpG stands for cytosine phosphate guanine dinucleotide in a particular sequence context. CpG motifs are responsible for proliferative effects of antisense oligonucleotides, particularly with respect to B-lymphocytes. Die optimal immune-stimulatory consensus sequence surrounding CpG is R1R2CGY1Y2, where R1 is a purine (mild preference for G), R2 is a purine or T (preference for A), and Y1 and Y2 are pyrimidines (preference for T). 

Thiamine can be considered to be the product of the quatemization of 4-methyl-5-(2-hydroxymethyl)thiazole (5) by an active derivative of 4-amino-5-(hydroxymethyl)-2-methyl pyrimidine (4) (Scheme 2). In living cells, pyramine can be activated by conversion into the diphosphate 7, via monophosphate 6, and the substrate of the enzyme responsible for the quatemization is not the thiamine thiazole, but its phosphate 8. The product of the condensation, thiamine phosphate (9), is finally converted into diphosphate 2—the biochemically active derivative—by hydrolysis to free thiamine, followed by diphosphorylation, or more directly, in some cases. Enzymes are known for all of the steps depicted in Scheme 2, and adenosine triphosphate (ATP) is, as usual, the phosphate donor. 

Because sugars are involved in most of the mechanisms established for the synthesis of these heterocycles, the development of carbohydrate chemistry has been most helpful in these researches—especially for the preparation of specifically labeled molecules. Conversely, the contribution of these efforts to carbohydrate chemistry and biochemistry has shown the involvement in biosynthesis of 1 -deoxy-D-f/rreo-pentulose—scarcely before recognized and considered a rare sugar—and of fully functionalized pentuloses of still unknown configuration (or their phosphates). Finally, evidence has been found in prokaryotes for a most extraordinary transformation of 5-amino-l-(P-D-ribofuranosyl)imidazole 5 -phos-phate into a pyrimidine. Surely, this transformation should be explained in terms... 

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