Catalytic mechanisms and metal ion specificity of class II fructose-1,6-bisphosphatases: A QM/MM study

Abstract

Class II Fructose-1,6-bisphosphatases (FBPaseII) play an essential role in gluconeogenesis of bacteria and exhibit conserved catalytic ability with their crucial threonine residue. The activity of FBPaseII is affected when the native metal ion cofactor is replaced. In this study, we developed the FBPaseII catalytic complex models for different species Francisella tularensis and Mycobacterium tuberculosis, with different divalent metal cation Mn²⁺ and Mg²⁺. We simulated the two-step reaction using the Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) method. The results suggest that the Mg²⁺ in FtFBPase and Mn²⁺ in MtFBPase significantly increase the reaction barrier of FBPaseII, especially in the first step of the reaction. Additionally, we analyzed the stability of the metal ion and the behavior of the water molecules in the active site during the reaction. We propose that the metal ion in the active site plays a role in recruiting water molecules to the reaction center.