Evolution of phosphotriesterase activities of the metallo-β-lactamase family: A theoretical study

Metallo-beta-lactamase (M beta L) is a eubacterial zinc metallo-hydrolase superfamily. Despite their well-known lactamase activities, M beta L family members also have the ability to catalyze phosphotriester hydrolysis with different phosphotriesterase activities. In the present study, based on crystal structure comparisons of the related MIlL members, a series of models was constructed and calculated using the density functional theory (DFT) method to explore the relationship between active-site changes and phosphotriesterase activities. These calculations show that the energetic barriers for phosphotriesterase activity are considerably reduced due to active-site differences, which describes an evolutionary trend for the development of phosphotriesterase activity in the M beta L super-family. The key event is the appearance of a specialized and negatively charged residue bridging both zinc ions, which plays the two important roles of maintaining charge balance and stabilizing the binuclear active-site structure. This pathway is also consistent with the evolutionary relationships determined by phylogenetic tree analysis using complete residue sequences. Our studies provide the first methodology to explore the development of a new enzyme activity within a superfamily, and to shed new light on understanding the catalytic mechanism from an evolutionary perspective.