Protoporphyrinogen oxidase (PPO), an important target for herbicides, is distributed widely throughout nature. The PPO enzymes from various species exhibit low sequence identity, different substrate adaptability and different susceptibility to inhibition by some herbicides, such as acifluorfen, a commercial herbicide. Interpretation of the specificity of the target enzyme will facilitate the rational design of herbicides with high affinity and species selectivity (safety to non-target organisms). Therefore we determined a series of crystal structures of wild-type and mutant PPO enzyme in complex with inhibitors, and clarified the structural basis for bacillus subtilis PPO-resistance to acifluorfen. We quantitatively deciphered the relationship between the catalytic activity with the probability of the privileged conformations of human PPO mutants through combined use of molecular dynamics simulation and statistical analysis, which provided a new insight into the structure-function relationship of enzyme. Based on this result, we established an approach for predicting catalytic efficiency of enzyme, called Prenzyme. Recently, we successfully predicted the catalytic efficiency of PPO enzymes from various species using Prenzyme.

Mutation dependent enzymatic activities of a herbicide target: Protoporphyrinogen oxidase

248th National Meeting (2014)

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