Orotidine 5’-monophosphate decarboxylase

Miller and Wolfenden6 compared the rates of decarboxylation of the substrate of orotidine-5 -monophosphate decarboxylase (OMPDC) in quantitative detail, on and off the enzyme. They showed that the apparent unimolecular rate constant of decarboxylation of the substrate when bound to the enzyme is about 1015 times greater than the decarboxylation process in the absence of the enzyme. Further studies confirm that the enzyme-promoted reaction does not involve additional intermediates or covalent alterations of the substrate. The reaction consists of carbon dioxide being formed and the resulting carbanion becoming protonated. Since thermodynamic barriers are not altered by catalysis, the energy of the carbanion must be a component that reflects the energy of the environment in which it is created, one in which the carbanion that is formed is selectively stabilized. 

Wise, E. Y., Yew, W. S., Babbitt, P. C., Gerlt, J. A., and Rayment, I. (2002) Homologous (p/a)8-barrcl enzymes that catalyze unrelated reactions orotidine 5 -monophosphate decarboxylase and 3-keto-l-gulonate 6-phosphate decarboxylase. Biochemistry 41, 3861-3869. 

T.P. Begley, T.C. Appleby, and S.E. Ealick. 2000. The structural basis for the remarkable proficiency of orotidine 5 -monophosphate decarboxylase Curr. Opin. Struct. Biol. 10 711-718. (PubMed)... 

T.W. Traut and B.R. Temple. 2000. The chemistry of the reaction determines the invariant amino acids during the evolution and divergence of orotidine 5 -monophosphate decarboxylase T. Biol. Chem. 275 28675-28681. (PubMed)... 

Warshel, A., et al. (2000). Remarkable rate enhancement of orotidine 5 -monophosphate decarboxylase is due to transition state stabilization rather than ground state de-stabilization. Biochemistry 39, 14728-14738... 

Figure 27-27), aspartate transcarbamoylase, and dihydroorotase activity. Each subunit of Pyr 1-3 has a molecular weight of 200,000-220,000, and the native enzyme exists as multiples of three subunits. The second gene codes for dihydroorotate dehydrogenase which is located on the outer side of the inner mitochondrial membrane. Dihydroorotate, the product of Pyr 1-3, passes freely through the outer mitochondrial membrane and converted to orotate. Orotate readily diffuses to the cytosol for conversion to UMP. The third gene codes for another multifunctional polypeptide known as UMP synthase (Pyr 5,6). Pyr 5,6 (M.W. 55,000) contains orotate phosphoribosyltransferase and orotidylate (orotidine-5 -monophosphate) decarboxylase activity. Use of multifunctional polypeptides is very efficient, since the intermediates neither accumulate nor become consumed in side reactions. They are... 

De novo pathway of uridine-5 -monophosphate (UMP) synthesis. Enzymes (1) carbamoyl phosphate synthetase II (2) aspartate transcarbamoylase (3) dihydroorotase (4) dihydroorotate dehydrogenase (5) orotate phosphoribosyltransferase (6) orotidine-5 -monophosphate decarboxylase (orotidylate decarboxyla.se). 

Schematic representation of the intracellular location of the six enzymes of UMP biosynthesis in animals. Pyr 1-3 = 1, Carbamoyl phosphate synthetase II 2, aspartate transcarbamoylase 3, dihydroorotase 4, dihydroorotate dehydrogenase Pyr 5,6 = 5, orotate phosphoribosyltransferase 6, orotidine-5 -monophosphate decarboxylase.

Krungkrai, S. R., DelFraino, B. J., Smiley, J. A., Prapunwattana, P., Mitamura, T., Horii, T., and Krungkrai, J. (2005). A novel enzyme complex of orotate phosphoribosyltransferase and orotidine 5 -monophosphate decarboxylase in human malaria parasite Plasmodium falciparum Physical association, kinetics, and inhibition characterization. Biochemistry 44, 1643-1652. 

Collett MA, Bradshaw RE, Scott DB. A mutualistic fungal symbiont of perennial ryegrass contains two different pyr4 genes, both expressing orotidine-5 -monophosphate decarboxylase. Gene 158 31-39, 1995. 

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. 

Abstract An energy decomposition scheme is presented to elucidate the importance of the change of protein conformation substates to the reduction of activation barrier in an enzyme-catalyzed reaction. The analysis is illustrated by the reaction of orotidine 5 -monophosphate decarboxylase (ODCase), in which the catalyzed reaction is at least 10 faster than the spontaneous reaction. Analysis reveals that the enzyme conformation is more distorted in the reactant state than in the transition state. The energy released from conformational relaxation of the protein is the main source of the rate enhancement. The proposed mechanism is consistent with results from site-directed mutagenesis where mutations remote from the reaction center affect kcat but not Kyi. 

K55 Krooth, R. S., Pan, Y.-L. and Pinsky, L. Orotidine 5 -monophosphate decarboxylase activity of crude extracts of human cells. Biochem. Genet., 8, 13 148 (1973)... 

K56 Krooth, R. S., Lam, G. F. M. and Chen Kiang, S. Y. Oxipurinol and orotic aciduria effect on the orotidine-5 -monophosphate decarboxylase activity of cultured human fibroblasts. Cell, 3, 55-57 (1974)... 

Wise EY, Yew WS, Babbitt PC, Gerlt JA, Rayment I (2002) Homologous (b/a)j-Barrel Enzymes That Catalyze Unrelated Reactions Orotidine 5 -Monophosphate Decarboxylase and 3-Keto-L-Gulonate 6-Phosphate Decarboxylase. Biochemistry 41 3861-3869... 

The number of inherited defects of the pyrimidine metabolism described so far is small, compared to that of the purine metabolism. Combined deficiency of orotate phosphoribosyltransferase (OPRT) (EC 2.4.2.10) and orotidine 5 -monophosphate decarboxylase (ODC) (EC 4.1.1.23), designated as type I hereditary orotic aciduria, presents with characteristic clinical features such as hypochromic anemia with a megaloblastic bone marrow and crystalluria. Only six patients have been described and, as far as we know, new cases have not been discovered recently. ODC deficiency with similar clinical phenomena and leading to increased urinary excretion of orotate and orotidine has been detected in only one patient (1). A third defect, a deficiency of pyrimidine 5 -nucleotidase (Py-5NX (EC 3.1.3.5.) in erythrocytes, is associated with chronic hemolytic anemia and prominent basophylic stippling of the erythrocytes due to accumulated pyrimidine nucleotides. An increasing number of patients have been reported, their detection being facilitated by the typical phenomena. We do not know whether the urinary pyrimidine profile in this condition is abnormal. 

Recently this transformation was applied for synthesis of orotidine-5 -monophosphate decarboxylase inhibitors [207]. Unexpected results was obtained during the methylation... 

Bello AM, Konforte D, Poduch E, Furlonger C, Wei L, Liu Y, Lewis M, Pai EF, Paige CJ, Kotra LP (2009) Structure-activity relationships of orotidine-5 -monophosphate decarboxylase inhibitors as anticancer agent. J Med Chem 52 1648-1658... 

Stanton CL et al (2007) QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5-monophosphate decarboxylase using two different QM regions acceleration too small to explain rate of enzyme catalysis. J Phys Chem B 111 12573-12581... 

The anticancer nucleoside Gemcitabine as its monophosphate derivative (3) has been modified by conjugation of squalene at the N4-position. Using a combination of cryo-EM and SAXS it was shown that the squalenoyl derivative exists as a unilamellar liposome, and that the nanoassembly exhibited enhanced activity compared with Gemcitabine in a resistant cell line." Various C6-modified 2 -deoxy-2 -fluoro-dUMP derivatives have been prepared as potential inhibitors of orotidine 5 -monophosphate decarboxylase (ODCase) of these, the most potent analogue was the 6-iodo-derivative which was found to covalently inhibit ODCase. Aminoacyl-tRNAs... 

Amyes TL, Wood BM, Chan K, Gerlt JA, Richard JP. Formation and stability of a vinyl carbanion at the active site of orotidine 5 -monophosphate decarboxylase pKa of the C-6 proton of enzyme-bound UMP. J Am Chem Soc. 2008 130 1574-1575. 

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