Density functional models of the mechanism for decarboxylation in orotidine decarboxylase.
The mechanism of orotidine 5-monophosphate decarboxylase (ODCase) has been modeled using hybrid Density Functional Theory (B3LYP functional). The main goal of the present study was to investigate if much larger quantum chemical models of the active site than previously used could shed new light on the mechanism. The models used include the five conserved amino acids expected to be the most important ones for catalysis. One result of this model is that a mechanism involving a direct cleavage of the C-C bond followed by a protonation of C6 by Lys93 appears unlikely, with a barrier for decarboxylation 20 kcal mol(-1) too high. Additional effects like electrostatic stress and ground-state destabilization have been estimated to have only a minor influence on the reaction barrier. The conclusion from the calculations is that the negative charge developing on the substrate during decarboxylation must be stabilized by a protonation of the carbonyl O2 of the substrate. For this mechanism, the addition of the catalytic amino acids decreases the reaction barrier by 25 kcal mol(-1), but full agreement with experimental results has still not been reached. Further modifications of this mechanism are discussed.
Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, Sweden. marc@physto.se
Marcus
M
Lundberg
Margareta R A
MR
Blomberg
Per E M
PE
Siegbahn
D002262:Carboxy-Lyases / Q000378:metabolism*; D003653:Decarboxylation; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D009964:Orotidine-5'-Phosphate Decarboxylase / Q000737:chemistry* / Q000378:metabolism*; D014542:Uridine Monophosphate / Q000031:analogs & derivatives* / Q000737:chemistry*; D014961:X-Ray Diffraction
C005417:orotidylic acid; D014542:Uridine Monophosphate; D002262:Carboxy-Lyases; D009964:Orotidine-5'-Phosphate Decarboxylase