Structure-functional analysis of the α/β-hydrolase fold superfamily member

Katsiaryna Tratsiak* 1, Lukas Chrast 2 , Tatyana Prudnikova 1,  Jiri Damborsky 2, Oksana Degtjarik 1, Pavlina Rezacova 3,4, Radka Chaloupkova 2, Michal Kuty 1,5and Ivana Kuta Smatanova 1,5.

1 University of South Bohemia in Ceske Budejovice, Faculty of Science, Branisovska 31, 370 05 České Budějovice, Czech Republic, *E-mail:

2 Masaryk University, Faculty of Science, Brno, Czech Republic

3 Academy of Sciences of the Czech Republic v.v.i., Institute of Molecular Genetics, Prague, Czech Republic

4Academy of Sciences of the Czech Republic v.v.i., Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic

5Academy of Sciences of the Czech Republic, Institute of Nanobiology and Structural Biology GCRC, Nove Hrady, Czech Republic


The enzyme DmxA, belonging to the family of haloalkane dehalogenases (EC; HLDs), catalyzing the hydrolytic conversion of halogenated aliphatic compounds to their corresponding alcohols was isolated from Marinobacter sp. ELB 17. DmxA is one of the α/β-hydrolases which can be practical useful for such applications as biodegradation, biosensing, protein tagging for cell imaging and protein analysis, decontamination of warfare agents, production of optically active hydrocarbons and alcohols.

DmxA is an extremozyme, exhibiting high enantioselectivity, reveals the highest activity at high temperatures (the maximal activity towards 1,3-diiodopropane was detected at 55 °C and pH 9.0), what highlights it among the other HLDs.

Diffracted crystals of DmxA were refined up to the resolutions 1.45 Å. Diffraction data for DmxA were collected using Pilatus 6M-F detector at the wavelengths of 0.972 Å on the beamline ID29, at the European Synchrotron Radiation Facility (ESRF) in Grenoble (France).

Crystal of DmxA belonged to P212121 space group (a = 43.371, b = 78.343, c = 150.51; α = γ = β = 90.0) and contained 2 molecules in the asymmetric unit. The structure was solved by molecular replacement with MOLREP from the CCP4 software suite by using the coordinates of Rhodococcus rhodochrous (PDB entry 4E46; 48% sequence identity for 142 residues and 63% sequence similarity).

Structurally DmxA is represented by the two domains: a highly conserved α/β - hydrolase main domain, composed of eight β - strands, within antiparallel (β2) and are flanked by α - helices: four are on the one side and two are on the other side of the β – sheet; and the second - is smaller helical cap domain, composed of α - helices, covering the active site, which has revealed the catalytic pentad essential for the SN2 reaction mechanism: D105, H273, E129, W106 and uniquely Q40 halide-stabilizing residue among of the other HLDII subfamily members.

This work is supported by the Grant Agency of the Czech Republic (P207/12/0775).Also was supported by the Ministry of Education of the Czech Republic (CZ.1.05/2.1.00/01.0024 and CZ.1.05/2.1.00/01.0001). The support of the Academy of Sciences of the Czech Republic is acknowledged as well.