5-phosphoribosyl 1-diphosphate

In a sequence of complex reactions, which will not be considered in detail, the indole ring system is formed by incorporating two carbons from phosphoribosyl diphosphate, with loss of the original anthranilate carboxyl. The remaining ribosyl carbons are then removed by a reverse aldol reaction, to be replaced on a bound form of indole by those from L-serine, which then becomes the... 

From a study of the P n.m.r. spectra of phosphoribosyl diphosphate in the presence of magnesium ions, it has been deduced that the mono- and pyrophosphate residues act as independent binding sites for these ions. The anomeric composition and mutarotation rate of fructose 1,6-bisphosphate has been determined by P n.m.r., and it has also been observed that magnesium and zinc ions bind preferentially to the 1-phosphoryl group when it is in the a-ano-meric position. ... 

Arnvig, K, Hove-Jensen, B., and Switzer, R.L, (1990) Purification and properties of phosphoribosyl-diphosphate synthetase from Bacillus subtilis. Eur. J. Biochent, 192 (1), 195-200,... 

Phosphoribosyl-diphosphate synthetase catalyzes the phosphorylation of ribose 5-phosphate during the biosynthesis of pyrimidine nucleotides. 

The hypE proteins are 302-376 residues long and appear to consist of three domains. Domain 1 shows sequence identity to a domain from phosphoribosyl-aminoimida-zole synthetase which is involved in the fifth step in de novo purine biosynthesis and to a domain in thiamine phosphate kinase which is involved in the synthesis of the cofactor thiamine diphosphate (TDP). TDP is required by enzymes which cleave the bond adjacent to carbonyl groups, e.g. phosphoketolase, transketolase or pyruvate decarboxylase. Domain 2 also shows identity to a domain found in thiamine phosphate kinase. Domain 3 appears to be unique to the HypF proteins. 

Fig. 13.1 Pathways of thiopurine metabolism. The positions of two polymorphically expressed enzymes, TPMT (thiopurine methyl transferase) and ITPA (inosine triphosphate pyrophosphatase), are shown. HGPRT, hypoxanthine guanine phosphoribosyl transferase 6-TIDP, 6-thioi-nosine diphosphate 6-TIMP, 6-thioinosine monophosphate 6-TITP, 6-thio inosine trinophosphate...

A common intermediate for all the nucleotides is 5-phosphoribosyl-l-diphosphate (PRPP), produced by successive ATP-dependent phosphorylations of ribose. This has an a-diphosphate leaving group that can be displaced in Sn2 reactions. Similar Sn2 reactions have been seen in glycoside synthesis (see Section 12.4) and biosynthesis (see Box 12.4), and for the synthesis of aminosugars (see Section 12.9). For pyrimidine nucleotide biosynthesis, the nucleophile is the 1-nitrogen of uracil-6-carboxylic acid, usually called orotic acid. The product is the nucleotide orotidylic acid, which is subsequently decarboxylated to the now recognizable uridylic acid (UMP). 

This enzyme [EC 2.4.2.14], also known as glutamine phosphoribosyl-pyrophosphate amidotransferase, catalyzes the reaction of glutamine with S-phospho-a-D-ri-bose 1-diphosphate and water to produce 5-phospho-)3-D-ribosylamine, diphosphate (or, pyrophosphate), and glutamate. 

This enzyme [EC 3.6.1.31] catalyzes the hydrolysis of 5-phosphoribosyl-ATP to produce 5-phosphoribosyl-AMP and pyrophosphate (or, diphosphate). The Neurospora crassa enzyme also catalyzes the reactions of histidinol dehydrogenase and phosphoribosyl-AMP cyclohydrolase. 

This enzyme [EC 2.7.6.1], also known as phosphoribosyl pyrophosphate synthetase, catalyzes the reaction of ATP with D-ribose 5-phosphate to produce AMP and 5-phospho-a-D-ribose 1-diphosphate. dATP can also function as a substrate. 

Didanosine is a synthetic purine nucleoside analog that inhibits the activity of reverse transcriptase in HIV-1, HIV-2, other retroviruses and zidovudine-resistant strains. A nucleobase carrier helps transport it into the cell where it needs to be phosphorylated by 5 -nucleoiidase and inosine 5 -monophosphate phosphotransferase to didanosine S -monophosphate. Adenylosuccinate synthetase and adenylosuccinate lyase then convert didanosine 5 -monophosphate to dideoxyadenosine S -monophosphate, followed by its conversion to diphosphate by adenylate kinase and phosphoribosyl pyrophosphate synthetase, which is then phosphorylated by creatine kinase and phosphoribosyl pyrophosphate synthetase to dideoxyadenosine S -triphosphate, the active reverse transcriptase inhibitor. Dideoxyadenosine triphosphate inhibits the activity of HIV reverse transcriptase by competing with the natural substrate, deoxyadenosine triphosphate, and its incorporation into viral DNA causes termination of viral DNA chain elongation. It is 10-100-fold less potent than zidovudine in its antiviral activity, but is more active than zidovudine in nondividing and quiescent cells. At clinically relevant doses, it is not toxic to hematopoietic precursor cells or lymphocytes, and the resistance to the drug results from site-directed mutagenesis at codons 65 and 74 of viral reverse transcriptase. 

The biosynthesis of uracil proceeds via decarboxylation of orotidin-5 -phosphate, which is formed from carbamoyl phosphate and aspartate via orotate after nucleosidation with 5-phosphoribosyl-l-diphosphate. Uracil can also be generated from cytosine by oxidative deamination using sodium hydrogensulfite. 

Purine salvage usually involves phosphoribosyltransferase reactions, which generate ribonucleoside monophosphates (rNMPs) from the purine bases and 5-phosphoribosyl-l-pyrophosphate (PRPP). These are phosphorylated to diphosphates (rNDPs) and then reduced to deoxyribonucleotides (dNDPs) with ribonucleotide reductase. 

FIGURE 48-2 Action of flucytosine in fungi. 5-Flucytosine is transported by cytosine permease into the fungal cell, where it is deaminated to 5-fluorouracil (5-FU). The 5-FU is then converted to 5-fluorouracil-ribose monophosphate (5-FUMP) and then is either converted to 5-fluorouridine triphosphate (5-FUTP) and incorporated into RNA or converted by ribonucleotide reductase to 5-fluoro-2 -deoxyuridine-5 -monophosphate (5-FdUMP), which is a potent inhibitor of thymidylate synthase. 5-FUDP, 5-fluorouridine-5 -diphosphate dUMP, deoxyuridine-5 -monophosphate dTMP, deoxyuridine-5 -monophosphate UPRTase, uracil phosphoribosyl transferase. 

FIGURE 50-3 Intracellular activation of nucleoside analog reverse transcriptase inhibitors. Drugs and phosphory-lated anabolites are abbreviated the enzymes responsible for each conversion are spelled out. The active antiretroviral anabolite for each drug is shown in the blue box. Key ZDV, zidovudine d4T, stavudine ddC, dideoxycytidine FTC, emtricitabine 3TC, lamivudine ABC, abacavir ddl, didanosine DF, disoproxil fumarate MP, monophosphate DP, diphosphate TP, triphosphate AMP, adenosine monophosphate CMP, cytosine monophosphate dCMP, deoxycytosine monophosphate IMP, inosine 5 -monophosphate PRPP, phosphoribosyl pyrophosphate NDR, nucleoside diphosphate. 

FIGURE 51-5 Activation pathways for 5 fluorouracil (5-FU) and 5-floxuridine (FUR). FUDP, floxuridine diphosphate FUMP, floxuridine monophosphate FUTP, floxuridine triphosphate FUdR, fluorodeoxyuridine FdUDP fluorodeoxyuridine diphosphate FdUMP fluorodeoxyuridine monophosphate FdUTP fluorodeoxyuridine triphosphate PRPP 5-phosphoribosyl-1 -pyrophosphate. 

Shima T, Hasegawa S, Fujimura S, Matsubara H, Sugimura T (1969) Studies on poly(adenosine diphosphate-ribose). VII. Methods of separation and identification of 2 -(5"-phosphoribosyl)-5 -adenosine monophosphate. J Biol Chem 244 6632-6635... 

D-ribose-1-diphosphate xanthine phosphoribosyl-transferase] (2.4.2.22) is produced. 

Phosphoribosyl 1-pyrophosphate. S-phos-phoribosa 1-diphosphate, PftPP an energy-rich sugar phosphate, M, 390.1, formed by transfer of a pyro-phosphoryl residue from ATP to ribose 5-phosphate. PRPP is concerned in various biosynthetic reactions, e.g. biosynthesis of purines, pyrimidines and histidine. 

PRPP = 5-phosphoribosyl 1-pyrophosphate, or 5-phospho-a-D-ribose 1- diphosphate. 

Aspartate carbamyltransferase 2 dihydroorotase 3 orotate reductase 4 orotate phosphoribosyl-transferase 5 orotidine-5 -phosphate decarboxylase 6 cytidylate kinase, nucleotide diphosphate kinase 7 cytidine triphosphate synthetase 8 nucleoside monophosphate kinase, ribonucleoside diphosphate reductase, phosphatase 9 thymidylate synthase... 

The final amino acid to be considered here is histidine (His, H). As shown in Scheme 12.26, the initial steps begin with the reaction of ribose-1,5-diphosphate with ATP in the presence of ATP-phosphoribosyl transferase (EC 2.4.2.17) then, after phosphate is lost (phosphoribosyl-ATP diphosphatase [EC 3.6.1.31]), the pyrimidine ring is hydrolytically cleaved (phosphoribosyl-adenosine 5 -phosphate [AMP] cyclohydrolase [EC 3.5.4.19]), a process that is followed by the opening of... 

Both the pyrimidines and the purines are built up from small precursor molecules which are readily available in the metabolic pool (page 185). The free bases are not synthesized as such but, while being assembled, the partially constructed ring structure reacts with a special phosphorylated pentose known as PRPP (5-phosphoribosyl-l-pyrophosphate) and forms a ribonucleotide. The deoxyribonucleotides, with the exception of TMP which is formed by methylation of deoxyuridylate, are formed by reduction of the corresponding ribonucleoside diphosphate. The conversion is precisely controlled by allosteric effects which ensure that all four deoxyribonucleotides are available in amounts appropriate for nucleic acid synthesis. 

Nucleotide biosynthesis, like nucleotide catabolism, is relatively complex. Thus, we ll again look at only one example, adenosine monophosphate. Purine nucleotides are formed by initial attachment of an -NH2 group to ribose, followed by multistep buildup of the heterocyclic base. The attachment of -NH2 takes place by a nucleophilic suhstitution reaction of ammonia with 5-phosphoribosyl a-diphosphate to give /3-5-phosphorihosylamine and probably involves an SNl-like loss of diphosphate ion with formation of an 0x0-nium-ion intermediate. Although we ll not cover the details of its formation, inosine monophosphate (IMP) is the first fully formed purine ribonucleotide, with adenosine monophosphate (AMP) derived fi-om it. 

FIG, 1. Proposed mechanism of action of pyrazofurin (PF) converted into the 5 -monophosphate (PFMP) in cells, the drug inhibits the conversion of orotidine 5 -monophosphate (OMP) to uridine 5 -monophosphate (UMP). Other abbreviations are CA-carbamylaspartase, DHOA-dihydroorotic acid, OA-orotic acid, PRPP-5 -phosphoribosyl pyrophosphate, PP-pyrophosphoric acid, UDP--uridine diphosphate, CTP-cytidine triphosphate, RNA-ribonucleate, DNA-deoxyribonucleate,... 

Anthranilate phosphoribosyl transferase (EC 2.4.2.18) (AnPRT) belongs to the class of transferase enzyme, which enacts the transfer of specific functional group (e.g., methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor). It transfer a ribose group between the basic functional group of anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP). AnPRT has four domains and its quaternary structure consists of two identical protein structures [13]. Each domain of AnPRT contains a magnesium ion and a pyrophosphate molecule as the active site. The secondary structure of AnPRT consists mainly of alpha helices with a beta sheet within each domain (Fig. 14.6). 

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