Structure-Specificity Relationships for Haloalkane Dehalogenases


Damborsky, J., Rorije, E., Jesenska, A., Nagata, Y., Klopman, G., Peijnenburg, W.J.G.M.




A structural analysis of the substrate specificity of hydrolytic dehalogenases originating from three different bacterial isolates has been performed using the multiple computer automated structure evaluation methodology. This methodology identifies structural fragments in substrate molecules which either activate or deactivate biological processes. The analysis presented in this contribution is based on newly measured dehalogenation data combined with data from the literature (91 substrates). The enzymes under study represent different specificity classes of haloalkane dehalogenases, i.e. haloalkane dehalogenase from Xanthobacter autotrophicus GJ10, Rhodococcus erythropolis Y2 and Sphingomonas paucimobilis UT26. Three sets of structural rules have been identified to explain their substrate specificity, and to predict activity for untested substrates. Predictions of activity and inactivity based on the structural rules from this analysis were provided for those compounds that were not yet tested experimentally. The predictions were also conducted for the compounds with available experimental data not used for the model construction, i.e. the external validation set. Correct predictions were obtained for 28 out of 30 compounds in the validation set. Incorrect predictions were noted for two substrates that lie outside the chemical domain of the set of compounds for which the structural rules were generated. A mechanistic interpretation of the structural rules generated, provided a fundamental understanding of the structure-specificity relationships for the family of haloalkane dehalogenases.

Full text


Damborsky, J., Rorije, E., Jesenska, A., Nagata, Y., Klopman, G., Peijnenburg, W.J.G.M., 2001: Structure-Specificity Relationships for Haloalkane Dehalogenases. Environmental Toxicology and Chemistry 20: 2681-2689.

Ondrej Vavra celebrating success with his presentation on CaverDock
Lecture by Dr. Stavrakis from ETH Zurich
High evaluation of the team’s research performance
Klaudia Chmelova and Veronika Liskova passed doctoral state exam
ELIXIR CZ annual conference 15 – 16 Nov, 2017
New video explaining the goals of Rafts4Biotech EU project
Invitation to a presentation by Synthetic Genomics