Crystallographic Analysis of 1,2,3–Trichloropropane Biodegradation by Haloalkane Dehalogenase DhaA31
Lahoda, M., Mesters, J. R., Stsiapanava, A., Chaloupkova, R., Kuty, M., Damborsky, J., Kuta Smatanova, I.
ACTA CRYSTALLOGRAPHICA D70: 209-217 (2014)
Haloalkane dehalogenases catalyze the hydrolytic cleavage of carbon-halogen bonds, which is a key step in aerobic mineralization of many environmental pollutants. One important pollutant is the toxic and anthropogenic compound 1,2,3-trichloropropane (TCP). Rational design was combined with saturation mutagenesis to obtain the haloalkane dehalogenase variant DhaA31, which displays an increased catalytic activity towards TCP. Here we report the 1.31 Å crystal structure of substrate-free DhaA31, the 1.26 Å structure of DhaA31 in a complex with TCP, and the 1.85 Å wild-type DhaA structure. Crystals of the enzyme-substrate complex were successfully obtained by adding volatile TCP to the reservoir at crystallization at room temperature and pH 6.4. Comparison of the substrate-free structure with the DhaA31 enzyme-substrate complex reveals that the nucleophilic Asp106 changes its conformation from an inactive to an active state during the catalytic cycle. The positions of three chloride ions found inside the enzyme’s active site indicate a possible pathway for halide release from the active site through the main tunnel. Comparison of the mutant DhaA31 with wild-type DhaA revealed that introduced substitutions reduced volume and solvent accessibility of the active site pocket.