Dynamics of 1,2-dichloroethane in the active site of haloalkane dehalogenase LinB: Effect of solvent and halide ion on productive binding.

Michal Otyepka1 and Jiří Damborský2

1Department of Physical Chemistry, Faculty of Science, Palacký University, tř. Svobody 26, 771 46 Olomouc, Czech Republic

2National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic


1,2-dichloroethane (DCE) is a toxic and carcinogenic chlorinated compound that is not known to be formed naturally. As many other synthetic halogenated aliphatic compounds, DCE is rather resistant to biodegradation and persists in the environment. Nevertheless, several bacterial cultures that are able to use DCE as the only carbon and halogen source have been isolated. The most efficient catalysis of DCE has been observed with haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Even lower activity with DCE was observed for haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Crystallographic analysis of LinB-DCE complex showed non-productive binding of DCE to the enzyme active site, while molecular docking suggested that DCE molecule can possibly bind to the active site but is prevented by chloride ion and/or water molecules [1].

Two nanoseconds-long trajectories of LinB with different number of ligands bound to the active site were carried out and compared. The results show that productive binding of DCE (i.e., binding to the Michaelis-Menten complex) is blocked by the presence of chloride ion or water molecule in the halide-stabilization pocket of the active site. In case of empty halide-stabilization pocket, the productive binding of DCE occurs very rapidly (in less then 20 ps). On the other hand, DCE locks the chloride ion in the halide-stabilization pocket as was confirmed by steered molecular dynamics simulations and by fact that chloride ion can easy leave LinB active site in the system without DCE.


 [1] Oakley AJ, Prokop Z, Bohac M, Kmunicek J, Jedlicka T, Monincova M, Kuta-Smatanova I, Nagata Y, Damborsky J, Wilce MCJ BIOCHEMISTRY-US, 41 (2002) 4847-4855.