A definitive mechanism for chorismate mutase.

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• The chorismate --> prephenate reaction is crucial in biological pathways.
• Previous studies utilized molecular dynamics (MD) and thermodynamic integration.
• Understanding the enzymatic mechanism requires detailed computational analysis.

Purpose of the Study:

• To elucidate the reaction mechanism of chorismate mutase in E. coli.
• To determine activation energies and transition state structures in enzyme and water.
• To identify the source of kinetic advantage provided by the enzyme.

Main Methods:

• Employed Quantum Mechanics/Molecular Mechanics (QM/MM) procedures.
• Utilized SCCDFTB/MM for reaction coordinates and transition state identification.
• Performed B3LYP/6-31+G* single-point computations for activation energies.

Main Results:

• Computed activation energies closely match experimental values (11.3 kcal/mol in enzyme vs. 12.7 kcal/mol experimental; 20.3 kcal/mol in water vs. 20.7 kcal/mol experimental).
• Transition state structures are similar across gas, water, and enzyme phases, indicating a concerted pericyclic rearrangement.
• Enzyme stabilizes the transition state and favors chorismate formation by 8.5 kcal/mol, providing the major kinetic advantage.

Conclusions:

• The chorismate mutase enzyme provides a significant kinetic advantage through preferential stabilization of the transition state and favorable chorismate formation.
• The computational findings align with previous experimental and computational observations.
• A definitive mechanism for chorismate mutase enzymes has been established.