Structure-function analysis of DhmeA, a haloalkane dehalogenase of subfamily III from Haloferax mediterranei

K. Chmelova1,2, M. Marek1,2, T. Shaikh3, J. Novacek3, R. Chaloupkova1,2, J. Damborsky1,2

1 Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Bld. A13, 625 00 Brno, Czech Republic

2 International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic

3 CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, Bld. A35, 625 00 Brno, Czech Republic

klaudia.chmelova@gmail.com

 

Haloalkane dehalogenases (HLDs), which catalyse the cleavage of the carbon-halogen bond of organohalogen compounds, are recognized as the key tools in many industrial and biotechnological processes [1]. The HLDs are composed of two domains a main α/β domain containing catalytic residues and a cap domain. According to phylogenetic and structural analyses, HLDs can be divided into three subfamilies − HLD-I, HLD-II and HLD-III, which differ in the cap domain architecture and the composition of their catalytic pentads [2]. Unlike the HLD-I and HLD-II members, which structures have been studied by X-ray crystallography, the structural information on HLD-III enzymes is missing. A major problem with structural characterization of HLD-III members is the fact that these enzymes form polydisperse high-molecular weight oligomeric states [3, 4], which hampers their structural analysis. Here, we report an optimized method for recombinant production and purification of DhmeA from the halophilic archeon Haloferax mediterranei. The strategy employs a robust recombinant expression in Escherichia coli together with protein purification through a poly-histidine affinity tag and size-exclusion chromatography. Subsequent biophysical characterization by differential scanning fluorimetry and dynamic light scattering revealed that the newly developed purification method significantly improved monodispersity of DhmeA. Our findings pave a way for probing DhmeA structure by high-resolution techniques such as X-ray crystallography and single-particle cryo-electron microscopy analysis. Cryo-electron microscopy data was collected and initial 3D model of DhmeA was inferred. Future work will focus on 3D structure reconstruction, model building and experimental validation. 

           

1.         T. Koudelakova, S. Bidmanova, P. Dvorak, A. Pavelka, R. Chaloupkova, Z. Prokop, J. Damborsky, Biotechnol. J., 8, (2013), 32-45.

2.         E. Chovancova, J. Kosinski, M. J. Bujnicki, J. Damborsky, Proteins, 67, (2007), 305–316.

3.         A. Jesenska, M. Monincova, T. Koudelakova, K. Hasan, R. Chaloupkova, Z. Prokop, A. Geerlof, J. Damborsky, Appl. Environ. Microbiol., 75, (2009), 5157–5160.

4.         H. K. Fung, M. S. Gadd, T. A. Drury, S. Cheung, J. M. Guss, N. V.  Coleman, J. M. Matthews, Mol. Microbiol., 97, (2015), 439453.