The crystal structure of the first haloalkane dehalogenase tetramer

Andrii Mazur^a, Tatyana Prudnikova^a, Pavel Grinkevich^a, Jeroen R. Mesters^b, Radka Chaloupkova^c, Jiri Damborsky^c,e, Michal Kuty^a, Petr Kolenko^d and Ivana Kuta Smatanova^a,*

^aFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, Ceske Budejovice, 37005, Czech Republic
^bInstitute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, Lübeck, D-23538, Germany
^cLoschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
^dFaculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague, Czech Republic
^eInternational Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic

Haloalkane dehalogenases (EC 3.8.1.5) are microbial enzymes that catalyze the breakdown of halogenated compounds resulting in a halide ion, proton and alcohol. These enzymes are applied in industrial catalysis, bioremediation and biosensing of environmental pollutants. Novel haloalkane dehalogenase DpaA that belongs to the superfamily of α/β hydrolases was isolated from a psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2 found in marine sediment collected from the East Sea, Korea. Here, we report its crystallization and X-ray diffraction data analysis. DpaA was crystallized using the sitting drop vapor diffusion method. Two independent crystallization and data collection experiments resulted in several data sets with the resolution ranging from 2.2 to 3.0 Å and from 2.5 to 3.17 Å, respectively. During structure solution DpaA shows interesting structural properties of its tetramer conformation and its interactions between individual chains. The difficulties during initial data processing and the right space group determination reveal the presence of pseudotranslation at every collected data set, which required further investigation and improvements of the existing model. Finally, merohedral twinning and subsequent structure modeling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to the HLD-I subfamily.

This research is supported by the Grant Agency of the Czech Republic (grant No. 17-24321S); DAAD mobility grant (grant No. DAAD-16-09); European Regional Development Fund-Project (grant No. CZ.02.1.01/0.0/0.0/15_003/0000441; grant No. CZ.02.1.01/0.0/0.0/16_019/0000778; grant No. LM2015047; grant No. LM2018121); GAJU (grant No. 017/2019/P); Czech Ministry of Education (grant No. CZ.02.1.01/0.0/0.0/16_026/0008451).