Biochemical and Structural Characterization of New Haloalkane Dehalogenase DbeA from Bradyrhizobium elkani USDA94

Tatyana Prudnikova^a, Tomas Mozga^c, Pavlina Rezacova^e,f, Radka Chaloupkova^c, Yukari Sato^g, Michal Kuty^a,b, Tana Koudelakova^c, Yuji Nagata^g, Jiri Damborsky^c,d, and Ivana Kuta Smatanova^a,b

^aInstitute of Physical Biology University of South Bohemia Ceske Budejovice, Zamek 136, 373 33 Nove Hrady, Czech Republic

^bInstitute of Systems Biology and Ecology Academy of Science of the Czech Republic, Zamek 136, 373 33 Nove Hrady, Czech Republic

^cLoschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic

^dLoschmidt Laboratories, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech Republic

^eInstitute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 37 Prague, Czech Republic

^fInstitute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 37 Prague, Czech Republic

^gDepartment of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan

A novel enzyme belonging to the family of haloalkane dehalogenases (EC 3.8.1.5) was isolated from Bradyrhizobium elkani USDA94. Haloalkane dehalogenases are important class of microbial enzymes with catalytic activity for detoxification of halogenated aliphatic compounds. DbeA protein is closely related to DbjA enzyme from Bradyrhizobium japonicum USDA110 (71% identity), but has different biochemical properties. DbeA is generally less active than DbjA and has a higher specificity towards brominated and iodinated compounds. Crystal structure of novel haloalkane dehalogenase DbeA of Bradyrhizobium elkani USDA94 has been solved and refined using diffraction data to 2.2 Å resolution. Overall fold and topology of DbeA is very similar to related enzymes with known structure. Structural comparison discovered differences in active site tunnel which can explain differential substrate specificities and inhibitor affinities.