Orotidinate 5’-monophosphate OMP

The biosynthetic pathway to pyrimidine nucleotides is simpler than that for purine nucleotides, reflecting the simpler structure of the base. In contrast to the biosynthetic pathway for purine nucleotides, in the pyrimidine pathway the pyrimidine ring is constructed before ribose-5-phosphate is incorporated into the nucleotide. The first pyrimidine mononucleotide to be synthesized is orotidine-5 -monophosphate (OMP), and from this compound, pathways lead to nucleotides of uracil, cytosine, and thymine. OMP thus occupies a central role in pyrimidine nucleotide biosynthesis, somewhat analogous to the position of IMP in purine nucleotide biosynthesis. Like IMP, OMP is found only in low concentrations in cells and is not a constituent of RNA. 

Orotidine S -monophosphate decarboxylase (ODCase) is a key enzyme in the biosynthesis of nucleic acids, effecting the decarboxylation of orotidine 5 -monophosphate (OMP, 1) to form uridine S -monophosphate (UMP, 2, Scheme l).1,2 The conversion of OMP to UMP is biomechanistically intriguing, because the decarboxylation appears to result, uniquely, in a carbanion (3, mechanism i, Scheme 2) that cannot delocalize into a it orbital.3,4 The uncatalyzed reaction in solution is therefore extremely unfavorable, with a AG of... 

Reaction of aspartic acid (14) with carbamoyl phosphoric acid (17) in the presence of the allosteric enzyme aspartate carbamoyltransferase (aspartate transcar-bamoylase) gives N-carbamoyl aspartic acid (18), which is cyclised to L-dihy-droorotic acid (19) by dihydroorotase. Oxidation of L-dihydroorotic acid by flavoprotein, orotate reductase gives orotic acid (20), which reacts with 5-phosphori-bosy 1-1-pyrophosphate (PRPP) in the presence of orotate phosphoribosyl transferase to form orotidine 5 -monophosphate (OMP, 21). Decarboxylation of OMP by orotid-ine 5 -phosphate decarboxylase yields uridine 5 -monophosphate (UMP, 22), which acts as precursor for the cytidine nucleotides (CTP) (Chart 6). 

Menz, R. I., Cinquin, O., and Christopherson, R. I. (2002). The identification, cloning and functional expression of the gene encoding orotidine 5 -monophosphate (OMP) decarboxylase from Plasmodium falciparum. Ann. Trop. Med. Parasitol. 96,469 176. 

The reaction of carbamoyl phosphate with aspartate to produce W-carbamo-ylaspartate is the committed step in pyrimidine biosynthesis. The compounds involved in reactions up to this point in the pathway can play other roles in metabolism after this point, A -carbamoylaspartate can be used only to produce pyrimidines—thus the term committed step. This reaction is catalyzed by aspartate transcarbamoylase, which we discussed in detail in Ghapter 7 as a prime example of an allosteric enzyme subject to feedback regulation. The next step, the conversion of A-carbamoylaspartate to dihydroorotate, takes place in a reaction that involves an intramolecular dehydration (loss of water) as well as cyclization. This reaction is catalyzed by dihydroorotase. Dihydroorotate is converted to orotate by dihydroorotate dehydrogenase, with the concomitant conversion of NAD to NADH. A pyrimidine nucleotide is now formed by the reaction of orotate with PRPP to give orotidine-5 -monophosphate (OMP), which is a reaction similar to the one that takes place in purine salvage (Section 23.8). Orotate phosphoribosyltransferase catalyzes this reaction. Finally, orotidine-5 -phosphate decarboxylase catalyzes the conversion of OMP to UMP... 

The final steps of pyrimidine biosynthesis novo which are catalyzed by two sequential enzymes, orotate phosphoribosyltransfer-ase (OPRT) and orotidylic decarboxylase (ODC), involve the PP-ribose P dependent conversion of orotic acid to orotidine-5 -monophosphate (OMP) followed by decarboxylation at the 7 position to form uridine 5 -monophosphate (UMP) (Fig. 1). UMP is then utilized further in the synthesis of nucleic acids and co-enzymes. Defects at this site in this metabolic pathway are important for they can result in "pyrimidine starvation" from depletion of the intracellular pool of pyrimidine nucleotides. In man the rare genetic disease, orotic aciduria, involves a deficiency of both OPRT and ODC (Type 1) (Smith, Sullivan and Huguley, 1961) or, less commonly, only ODC (Type II) (Fox, 0 Sullivan and Firken, 1969). 

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,... 

In Figure 8 (top, left) the structure of orotidine, the nucleoside of the above nucleotide, is shown a stability ccmstant of its Cd complex has been measured [93], Orotidinate 5 -monophosphate (OMP is involved in the biosynthesis of pyrimidine-nucleotides OMP is decarboxylated to UMP (cf. Figures 1 and 8), which is then further transformed, e.g., to UTP or CTP (Figure 10). OMP itself exists predominately in the syn conformation, which is depictured for H(Or) in Figure 8 (top, left) (i.e., the (C2)0 group being above the ribose ring). 

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.

This article summarizes the mechanistic, crystallographic, and computational evidence for the mechanism of decarboxylation of OMP by the family of orotidine 5 -monophosphate decarboxylase enzymes, and offers a critical evaluation of the various mechanisms based upon this evidence. 

With in vivo experiments, Hurlbert and Potter ) first showed that in rat liver, uridine nucleotides were intermediates in the conversion of orotate to nucleic acid pyrimidines the first of the three uridine phosphates to become labeled in this process was the monophosphate, uridylate (UMP) IS). The synthesis of uridylate from orotate takes place in two steps (a) the condensation of orotate with PP-ribose-P to form orotidylate (orotidine 5 -monophosphate, or OMP), and (b) decarboxylation of orotidylate. 

While mammahan cells reutilize few free pyrimidines, salvage reactions convert the ribonucleosides uridine and cytidine and the deoxyribonucleosides thymidine and deoxycytidine to their respective nucleotides. ATP-dependent phosphoryltransferases (kinases) catalyze the phosphorylation of the nucleoside diphosphates 2 "-de-oxycytidine, 2 -deoxyguanosine, and 2 -deoxyadenosine to their corresponding nucleoside triphosphates. In addition, orotate phosphoribosyltransferase (reaction 5, Figure 34-7), an enzyme of pyrimidine nucleotide synthesis, salvages orotic acid by converting it to orotidine monophosphate (OMP). 

The mechanism of the enzymatic decarboxylation of orotidine 5 -mono-phosphate (OMP) to uridine 5 -monophosphate (UMP) (see Fig. 1) is an intriguing problem for which many solutions have been offered. Even before 1995 when Wolfenden and Radzicka declared OMP decarboxylase (ODCase) to be the most proficient enzyme [1], several different mechanisms had been proposed. Since that time, other mechanisms have been advocated. Curiously, the appearance of crystal structures for various wild-type and mutant ODCases has led not to a definitive picture of catalysis, but to even more conjecture and controversy concerning the mechanism. 

Orotidine S -monophosphate, OMPi a nucleotide of orotic acid. M, 368.2. OMP is an intermediate in Pyrimidine biosynthesis (see). Orotidine 5 -phos-phate pyrophosphorylase catalyses the synthesis of OMP from orotic add and S-phosphoribosyl 1-pyro-phosphate. 

The first step of the biosynthesis of pyrimidine nucleotides is the irreversible carbamylation of L-aspartate by carbamyl-phosphate to form carbamylaspartate (catalyzed by the enzyme aspartate transcarbamylase). Next, carbamylaspartate is converted, by ring closure, to dihydro-orotic acid which, in turn, is reduced to orotic acid, catalyzed by the enzyme orotic acid dehydrogenase (OAD). Orotic acid (6-carboxyuracil) reacts with 5 -phosphoribosyl--1-pyrophosphate (PRPP) to form orotidine monophosphate (OMP). 

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