Orotidine 5’-phosphate decarboxylase

Michalski J, Dabkowski W (2003) State of the Art. Chemical Synthesis of Biophosphates and Their Analogues via P Derivatives. 232 93-144 Miller BG (2004) Insight into the Catalytic Mechanism of Orotidine 5 -Phosphate Decarboxylase fi"om Crystallography and Mutagenesis. 238 43-62 Mikolajezyk M, Balczewski P (2003) Phosphonate Chemistry and Reagents in the Synthesis of Biologically Active and Natural Products. 223 161-214 Mikolajezyk M, see Drabowicz J (2000) 208 143-176... 

Wu N, Pai EP (2004) Crystallographic Studies of Native and Mutant Orotidine 5 -Phosphate Decarboxylases. 238 23-42... 

In the case of orotic acid, nonenzymatic decarboxylation proceeds with a half-time (ti/2) of about 2.45 X 10 s near pH 7 at room temperature, as indicated by reactions in quartz tubes at elevated temperatures Orotidine 5 -phosphate decarboxylase thus appears to be an extremely proficient enzyme which enhances the reaction rate by a factor of 10 . They estimate the transition state form of the substrate has a dissociation constant that is less than 5 x 10 M. 

This enzyme [EC 4.1.1.23], also known as orotidine-5 -phosphate decarboxylase, catalyzes the conversion of orotidine 5 -phosphate to UMP and carbon dioxide. 

OROTIDYLATE DECARBOXYLASE Orotidine-5 -phosphate decarboxylase, OROTIDYLATE DECARBOXYLASE Orotidine-5 -phosphate pyrophosphorylase,... 

The catalytic power of enzymes is awesome (Table 2.1). A most spectacular example is that of the decarboxylation of orotic acid. It spontaneously decarboxy-lates with tm of 78 million years at room temperature in neutral aqueous solution. Orotidine 5 -phosphate decarboxylase enhances the rate of decarboxylation enzyme-bound substrate by 1017 fold. The classical challenge is to explain the magnitude of the rate enhancements in Table 2.1. We will not ask why enzymatic reactions are so fast but instead examine why the uncatalyzed reactions are so slow, and how they can be speeded up. 

Figure 2.5 Logarithmic scale comparison of k,d and kuncat (= (rnon) for some representative reactions at 25 °C. The length of each vertical bar represents the rate enhancement. (Wolfenden, 2001). ADC arginine decarboxylase ODC orotidine 5 -phosphate decarboxylase STN staphylococcal nuclease GLU sweet potato /3-amylase FUM fumarase MAN mandelate racemase PEP carboxypeptodase B CDA E. coli cytidine deaminase KSI ketosteroid isomerase CMU chorismate mutase CAN carbonic anhydrase.

PFACRI N -[(5 -phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide isomerase ImGPS imidazole 3-glycerol phosphate synthase OMPDC orotidine 5 -phosphate decarboxylase R5PE ribulose 5-phosphate epimerase HUMPS hex-3-ulose monophosphate... 

In hereditary orotic aciduria, orotic acid is excreted in the urine because the enzymes that convert it to uridine monophosphate, orotate phosphoribosyl transferase and orotidine 5 -phosphate decarboxylase, are defective (see Figure 7-20). Pyrimidines cannot be synthesized, and therefore, normal growth does not occur. Oral administration of uridine bypasses the metabolic block and provides the body with a source of pyrimidines. 

Hereditary orotic aciduria is a rare autosomal recessive trait. In this disorder, both orotate phosphoribosyltrans-ferase and orotidine-5 -phosphate decarboxylase activities (reactions 5 and 6 in Figure 27-26) are markedly deficient. Recall that these activities occur on the polypeptide Pyr 5,6. 

Deficiency of folate or vitamin Bn can cause hematological changes similar to hereditary orotic aciduria. Folate is directly involved in thymidylic acid synthesis and indirectly involved in vitamin Bn synthesis. Orotic aciduria without the characteristic hematological abnormalities occurs in disorders of the urea cycle that lead to accumulation of carbamoyl phosphate in mitochondria (e.g., ornithine transcarbamoylase deficiency see Chapter 17). The carbamoyl phosphate exits from the mitochondria and augments cytosolic pyrimidine biosynthesis. Treatment with allopurinol or 6-azauridine also produces orotic aciduria as a result of inhibition of orotidine-5 phosphate decarboxylase by their metabolic products. 

FIG. 6.12 Pyrimidine de novo synthesis pathway. Enzymes are as follows (1) carbamoyl-phosphate synthetase II (2) asparate carbamoyl-transferase (3) dihydro-orotase (4) dihydro-orotate oxidase (5) orotate phosphoribosyltransferase (6) orotidine-5 -phosphate decarboxylase (7) nucleoside monophosphate kinase (8) nucleotide diphospho kinase (9) CTP synthetase. 

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... 

Insight into the Catalytic Mechanism of Orotidine 5 -Phosphate Decarboxylase from Crystallography and Mutagenesis... 

Orotidine 5 -phosphate decarboxylase (ODCase, E. C. 4.1.1.23) catalyzes the decarboxylation of orotidine 5 -phosphate (OMP) to form uridine 5 -phos-phate in the sixth and final step of pyrimidine biosynthesis (Fig. 1) [1]. The discovery of ODCase in 1954 followed the identification, three years earlier, of orotic acid as the metabolic precursor of nucleic acids [2, 3]. ODCase is a distinct, monofunctional polypeptide in bacteria and fungi, whereas in mammals it combines with orotate phosphoribosyltransferase (OPRTase) to form the bifunctional enzyme UMP synthase. Human deficiencies in either OPRTase or ODCase activity result in an autosomal recessive disorder called hereditary orotic aciduria [4]. The disease is characterized by depleted levels of pyrimidine nucleotides in the blood and by the appearance of crystalline... 

Wong MW (2003) Quantum-Chemical Calculations of Sulfur-Rich Compounds. 231 1-29 Wrodnigg TM, Eder B (2001) The Amadori and Heyns Rearrangements Landmarks in the History of Carbohydrate Chemistry or Unrecognized Synthetic Opportunities 215 115-175 Wu N, Pai EP (2004) Crystallographic Studies of Native and Mutant Orotidine 5 phosphate Decarboxylases. 238 23-42... 

Crystallographic Studies of Native and Mutant Orotidine 5 -Phosphate Decarboxylases... 

Carboxymethyl-agarose has been treated with 5-(2-carboxyethyl)-6-azauridine 5 -phosphate using a carbodi-imide mediator, to provide an efficient affinity column for purification of orotidine-5 -phosphate decarboxylase from yeast. ... 

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