The Mechanism Of Omp Catalyzed By Orotidine 5'-monophosphate Decarboxylase

Orotidine 5'-monophosphate decarboxylase (ODCase, E. C. 4.1.1.23) catalyzes the decarboxylation of OMP with one of the largest rate enhancements by any enzyme, and it performs its task without the assistance of metals or small molecule cofactors. The decarboxylation reaction catalyst assists in the delocalization of negative charge that accompanies the release of CO2 from the substrate molecule. However, the substrate of ODCase lacks a p-orbital into which electrons can be delocalized. For this, the decarboxylation of OMP remains a special mechanistic challenge to the enzyme after years'extensive experimental and theoretical studies. Additionally,analyzing the mechanism of ODCase can therefore be an important step in understanding enzyme catalysis on a more general level.Despite extensive experimental and theoretical studies, the detailed catalytic mechanism of ODCase remains controversial. Several catalytic mechanisms have been proposed and examined in detail. Prevalent among them are the direct decarboxylation, the ylide mechanism, and the carbene mechanism.Different theoretical and experimental methods used by different groups'studies will attribute for conclusions they drawn conflicted with each other. For example,如,Beck and Siegel conducted experimental studies on 1,3-dimethylorotate and suggested O2 protonation mechanism. Lee and Houk calculated gas phase proton affinities of orotate and deprotonated uracil and proposed proposed a carbene-based mechanism. Although, all the mechanisms are supported by some results respectively, we believe that there is essentially difference between enzyme-catalyzed and uncatalyzed reactions. Is it suitable that enzyme-catalyzed system is modeled by general chemical rection? Additionally, at present, systematic and comprehensive studies on ODCase using the same theoretical method is not performed. In this papers, first, several uncatalyzed reaction models are designed. The role of hydrogen bonding between water molecules and carbonyl oxygen and desolvention effect on the mechansim of OMP decarboxylation is discussed in detail. Second, the three prevalent mechansims(O2, O4 and C6 protonation mechansim) are fully discusssed in gas phase and solvent, including the further study on anti-solvent effect and the effect of proton on decarboxylation reaction. Additionally, the effect of bassis set is also discussed . At last, on the base of the studies on the uncatalyzed and general catalyzed models, we design a possible enzyme-catalyzed model in which two important factors, dielectric constant and acid catalysis, are considered. Then, the possibility and rationality of this mechansim are calculated. The model design and following results analyzing aim to encover the essence of decarboxylation reaction catalyzed by enzyme.This paper consists of five parts.The first part of the paper is preface,it describes the worth of the study about the mechanism of decarboxylation of orotidine 5`-phosphate (OMP) catalyzed by the orotidine 5`-phosphate decarboxylase (ODCase) and the status quo of the study about this mechanism.The second part of the paper makes a introduction of the background and the content of the basic theory that will be used in the paper.In the third part, several uncatalyzed reaction models are designed and calculated at HF/6-31+G(d) level. The role of hydrogen bonding between water molecules and carbonyl oxygen and desolvention effect on the mechansim of OMP decarboxylation is discussed in detail. Mechsims of two derivatives of OMP is also studies and compared with exiprimental results. The results showed that (1) hydrogen bonding between water molecules and O2/O4 helps to delocalize the negative charge of CO2- which leads to lowering reaction barrier and increased reactivity. And hydrogen bonding is more effective on O4. (2) nopolar solvents will lower reaction barrier and increase the reactivity compared with water.In the forth part, the three prevalent mechansims(O2, O4 and C6 protonation mechansim) are fully discusssed in gas phase and solvent at B3LYP/6-31+G(d,p) level, including the further study on anti-solvent effect and the effect of proton on decarboxylation reaction. Additionally, the effect of bassis set is also discussed .the results indicated tha(t1)protonation will reduce the reaction barrier furthur compared with hydrogen bonding. And it is more effective on O4 than O2 just the same with results concluded from uncatalyzed reactions. (2) nopolar solvents will lower reaction barrier and increase the reactivity compared with water. And in the solvent withε=4.0, the calculated reaction barrier agrees well with the experiment. (3) Dispersion function play an important role in OMP negative charge-rich system.In the fifth part, on the base of the studies on the uncatalyzed and general catalyzed models, we design a possible enzyme-catalyzed model in which two important factors, dielectric constant and aci d catalysis, are considered. Then, the possibility and rationality of this mechansim are calculated. The results shown (1) protonated residues of ODCase is the possible proton donor bridged by water molecules for protonation mechanisms. (2) O4 mechanism might be the most likely mechanism for OMP decarboxylation. And protonation processes play an important role in the OMP decarboxylation reactions.