Posttranslational modification is a critical process in the cellular regulation, an example of which is the carboxylation of lysine. Pyruvate carboxylase is an enzyme, in which a carboxylated lysine has been found in the metal coordination shell of the active center. In our previous study, the reaction mechanism of the carboxyl transferase domain of the pyruvate carboxylase from Staphylococcus aureus has been investigated by using QM/MM calculations. The suggested mechanism supports the previous proposal, and most of the results are consistent with the experimental data. However, the calculated overall barrier is too high for an enzymatic reaction, which may be the result of the used model failing to take into account the modification of the metal-coordinated lysine. Here, we present a successive study to investigate the importance of lysine carboxylation in the reaction and also to examine if the Zn-coordinated water molecule is required for the catalysis. The reaction mechanism from the new models is consistent with the previous suggestion. More importantly, the energy barriers of all elementary steps are calculated to be much lower than those in our previous work. Notably, the calculated barrier of the overall reaction is ~ 14 kcal/mol, which is in good agreement with the experimental value. Therefore, this study supplies a theoretical evidence for the importance of the modification of Zn-coordinated lysine in the pyruvate carboxylase-catalyzed reaction. In addition, the water molecule in the zinc coordination shell is suggested to contribute to the catalysis.