Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site
Haloalkane dehalogenases are a very important class of microbial enzymes for environmental detoxification of halogenated pollutants, for biocatalysis, biosensing and molecular tagging. The double mutant (Ile44Leu + Gln102His) of the haloalkane dehalogenase DbeA from <i>Bradyrhizobium elkanii&l...
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MDPI AG
2019-07-01
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| Series: | Crystals |
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| Online Access: | https://www.mdpi.com/2073-4352/9/7/375 |
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| author | Tatyana Prudnikova Barbora Kascakova Jeroen R. Mesters Pavel Grinkevich Petra Havlickova Andrii Mazur Anastasiia Shaposhnikova Radka Chaloupkova Jiri Damborsky Michal Kuty Ivana Kuta Smatanova |
| author_facet | Tatyana Prudnikova Barbora Kascakova Jeroen R. Mesters Pavel Grinkevich Petra Havlickova Andrii Mazur Anastasiia Shaposhnikova Radka Chaloupkova Jiri Damborsky Michal Kuty Ivana Kuta Smatanova |
| author_sort | Tatyana Prudnikova |
| collection | DOAJ |
| description | Haloalkane dehalogenases are a very important class of microbial enzymes for environmental detoxification of halogenated pollutants, for biocatalysis, biosensing and molecular tagging. The double mutant (Ile44Leu + Gln102His) of the haloalkane dehalogenase DbeA from <i>Bradyrhizobium elkanii</i> USDA94 (DbeAΔCl) was constructed to study the role of the second halide-binding site previously discovered in the wild-type structure. The variant is less active, less stable in the presence of chloride ions and exhibits significantly altered substrate specificity when compared with the DbeAwt. DbeAΔCl was crystallized using the sitting-drop vapour-diffusion procedure with further optimization by the random microseeding technique. The crystal structure of the DbeAΔCl has been determined and refined to the 1.4 Å resolution. The DbeAΔCl crystals belong to monoclinic space group <i>C</i>121. The DbeAΔCl molecular structure was characterized and compared with five known haloalkane dehalogenases selected from the Protein Data Bank. |
| first_indexed | 2024-04-14T00:49:44Z |
| format | Article |
| id | doaj.art-63b3adc37d684d7ebab94d1baec06b9e |
| institution | Directory Open Access Journal |
| issn | 2073-4352 |
| language | English |
| last_indexed | 2024-04-14T00:49:44Z |
| publishDate | 2019-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Crystals |
| spelling | doaj.art-63b3adc37d684d7ebab94d1baec06b9e2022-12-22T02:21:51ZengMDPI AGCrystals2073-43522019-07-019737510.3390/cryst9070375cryst9070375Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding SiteTatyana Prudnikova0Barbora Kascakova1Jeroen R. Mesters2Pavel Grinkevich3Petra Havlickova4Andrii Mazur5Anastasiia Shaposhnikova6Radka Chaloupkova7Jiri Damborsky8Michal Kuty9Ivana Kuta Smatanova10Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicInstitute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, GermanyFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicLoschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech RepublicLoschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A4, 62500 Brno, Czech RepublicFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicFaculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech RepublicHaloalkane dehalogenases are a very important class of microbial enzymes for environmental detoxification of halogenated pollutants, for biocatalysis, biosensing and molecular tagging. The double mutant (Ile44Leu + Gln102His) of the haloalkane dehalogenase DbeA from <i>Bradyrhizobium elkanii</i> USDA94 (DbeAΔCl) was constructed to study the role of the second halide-binding site previously discovered in the wild-type structure. The variant is less active, less stable in the presence of chloride ions and exhibits significantly altered substrate specificity when compared with the DbeAwt. DbeAΔCl was crystallized using the sitting-drop vapour-diffusion procedure with further optimization by the random microseeding technique. The crystal structure of the DbeAΔCl has been determined and refined to the 1.4 Å resolution. The DbeAΔCl crystals belong to monoclinic space group <i>C</i>121. The DbeAΔCl molecular structure was characterized and compared with five known haloalkane dehalogenases selected from the Protein Data Bank.https://www.mdpi.com/2073-4352/9/7/375Haloalkane dehalogenasehalide-binding siterandom microseeding |
| spellingShingle | Tatyana Prudnikova Barbora Kascakova Jeroen R. Mesters Pavel Grinkevich Petra Havlickova Andrii Mazur Anastasiia Shaposhnikova Radka Chaloupkova Jiri Damborsky Michal Kuty Ivana Kuta Smatanova Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site Crystals Haloalkane dehalogenase halide-binding site random microseeding |
| title | Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site |
| title_full | Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site |
| title_fullStr | Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site |
| title_full_unstemmed | Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site |
| title_short | Crystallization and Crystallographic Analysis of a <i>Bradyrhizobium Elkanii</i> USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site |
| title_sort | crystallization and crystallographic analysis of a i bradyrhizobium elkanii i usda94 haloalkane dehalogenase variant with an eliminated halide binding site |
| topic | Haloalkane dehalogenase halide-binding site random microseeding |
| url | https://www.mdpi.com/2073-4352/9/7/375 |
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