A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations.
Decarboxylation of orotidine 5'-monophosphate (Omp) to uridine 5'-monophosphate by orotidine 5'-monophosphate decarboxylase (ODCase) is currently the object of vivid debate. Here, we clarify its enzymatic activity with long time scale classical molecular dynamics and hybrid ab initio Car-Parrinello/molecular mechanics simulations. The lack of structural (experimental) information on the ground state of ODCase/Omp complex is overcome by a careful construction of the model and the analysis of three different strains of the enzyme. We find that the ODCase/substrate complex is characterized by a very stable charged network Omp-Lys-Asp-Lys-Asp, which is incompatible with the previously proposed direct decarboxylation driven by a ground-state destabilization. A direct decarboxylation induced by a transition-state electrostatic stabilization is consistent with our findings. The calculated activation free energy for the direct decarboxylation with the formation of a C6 carboanionic intermediate yields an overall rate enhancement by the enzyme (k(cat)/k(wat) = 3.5 x 10(16)) in agreement with experiments (k(cat)/k(wat) = 1.7 x 10(17)). The decarboxylation is accompanied by the movement of a fully conserved lysine residue toward the developing negative charge at the C6 position.
Raugei
Simone
S
International School for Advanced Studies (SISSA/ISAS) and INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, Via Beirut 2-4, 34014-Trieste, Italy. raugei@sissa.it
Cascella
Michele
M
Carloni
Paolo
P
D003198:Computer Simulation; D004795:Enzyme Stability; D004926:Escherichia coli / Q000201:enzymology; D008958:Models, Molecular; D009964:Orotidine-5'-Phosphate Decarboxylase / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D011789:Quantum Theory; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D013816:Thermodynamics; D014542:Uridine Monophosphate / Q000031:analogs & derivatives* / Q000378:metabolism*
C005417:orotidylic acid; D014542:Uridine Monophosphate; D009964:Orotidine-5'-Phosphate Decarboxylase