The reaction path for the rearrangement of chorismate to prephenate in B.subtilis has been determined in a QM/MM study including the entire protein environment while treating the reaction with ab initio quantum chemistry. In addition to the reactant, chorismate, the side-chains of glu78 and arg90 are included in the quantum region to explore whether the strong ionic hydrogen bonding of the side chains to the substrate has a catalytic effect. The hydrogen bonds from glu78 and arg90 induce electronic effects that activate the substrate. The energetic residue analysis finds that the binding from arg7, arg63, and arg90 are all catalytic due to a differential stabilization along the reaction path of the transition state with respect to the reactant by the local environment. A global QM/MM optimization including the entire protein environment shows only slight changes in the protein environment around the active site along the reaction path. The rearrangement reaction occurs with almost a complete break in the C-O ether bond in chorismate before the C-C bond forms to create prephenate. In this study, the reacting complex forms a hydrogen bond to arg63 that stabilizes the region near the protein surface where the substrate may enter the active site.