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Mazur A, Grinkevich P, Chaloupkova R, Havlickova P, Kascakova B, Kuty M, Damborsky J, Kuta Smatanova I, Prudnikova T. Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA. Int J Mol Sci 2021; 22:ijms222111992. [PMID: 34769421 PMCID: PMC8584953 DOI: 10.3390/ijms222111992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Haloalkane dehalogenases (EC 3.8.1.5) play an important role in hydrolytic degradation of halogenated compounds, resulting in a halide ion, a proton, and an alcohol. They are used in biocatalysis, bioremediation, and biosensing of environmental pollutants and also for molecular tagging in cell biology. The method of ancestral sequence reconstruction leads to prediction of sequences of ancestral enzymes allowing their experimental characterization. Based on the sequences of modern haloalkane dehalogenases from the subfamily II, the most common ancestor of thoroughly characterized enzymes LinB from Sphingobium japonicum UT26 and DmbA from Mycobacterium bovis 5033/66 was in silico predicted, recombinantly produced and structurally characterized. The ancestral enzyme AncLinB-DmbA was crystallized using the sitting-drop vapor-diffusion method, yielding rod-like crystals that diffracted X-rays to 1.5 Å resolution. Structural comparison of AncLinB-DmbA with their closely related descendants LinB and DmbA revealed some differences in overall structure and tunnel architecture. Newly prepared AncLinB-DmbA has the highest active site cavity volume and the biggest entrance radius on the main tunnel in comparison to descendant enzymes. Ancestral sequence reconstruction is a powerful technique to study molecular evolution and design robust proteins for enzyme technologies.
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Affiliation(s)
- Andrii Mazur
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Pavel Grinkevich
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (R.C.); (J.D.)
- Enantis Ltd., Kamenice 771/34, 625 00 Brno, Czech Republic
| | - Petra Havlickova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Barbora Kascakova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Michal Kuty
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (R.C.); (J.D.)
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
- Correspondence: (I.K.S.); (T.P.)
| | - Tatyana Prudnikova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
- Correspondence: (I.K.S.); (T.P.)
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