Quantum chemical modeling of the reaction path of chorismate mutase based on the experimental substrate/product complex

Abstract

Chorismate mutase is a well-known model enzyme, catalyzing the Claisen rearrangement of chorismate to prephenate. Recent high-resolution crystal structures along the reaction coordinate of this enzyme enabled computational analyses at unprecedented detail. Using quantum chemical simulations, we investigated how the catalytic reaction mechanism is affected by electrostatic and hydrogen-bond interactions. Our calculations showed that the transition state (TS) was mainly stabilized electrostatically, with Arg90 playing the leading role. The effect was augmented by selective hydrogen-bond formation to the TS in the wild-type enzyme, facilitated by a small-scale local induced fit. We further identified a previously underappreciated water molecule, which separates the negative charges during the reaction. The analysis includes the wild-type enzyme and a non-natural enzyme variant, where the catalytic arginine was replaced with an isosteric citrulline residue.

Keywords: Claisen rearrangement; chorismate mutase; enzyme catalysis; pericyclic reaction; transition state stabilization.

Figure 1

Claisen rearrangement from chorismate (1) to prephenate (2) via a chair‐like TS (1→2).

Figure 2

Schematic representation of the active site model of BsCM containing the TS (1→2) that was used for geometry optimization. X = O for Cit90 and X = ${\text{NH}}_2^{+}$ for Arg90. Asterisks indicate atomic coordinates that were frozen during all optimization steps. Hydrogen bonds to the TS are indicated with dashed lines.

Figure 3

Stereo view of the transition state model of wild‐type BsCM. Asterisks denote the atomic coordinates that were frozen during optimization. The TS is depicted with black carbons, enzyme side chain carbons are shown in green, with light green denoting side chains from another subunit. Hydrogen bonds to the TS are shown in yellow.

Figure 4

The energy barrier ∆G ^† of the chorismate‐to‐prephenate reaction, calculated at different dielectric constants ε for wild‐type BsCM (○) and BsCM Arg90Cit (▲). Convergence is reached from ε = 10. The corresponding energies are listed in Table S1).

Figure 5

Close‐up view of the active site model after energy optimization. BsCM Arg90Cit with chorismate (A) and the TS (B) in the active site is contrasted with wild‐type BsCM, bound to chorismate (C) and the TS (D). The coloring is equivalent to Fig. 3, except for the hydrogen bond between residue 90 and the substrate/TS, which is colored in magenta and marked with an arrow.