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.