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Mandal N, Surpeta B, Brezovsky J. Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. J Chem Inf Model 2024; 64:6623-6635. [PMID: 39143923 DOI: 10.1021/acs.jcim.4c00966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Tunnels are structural conduits in biomolecules responsible for transporting chemical compounds and solvent molecules from the active site. They have been shown to be present in a wide variety of enzymes across all functional and structural classes. However, the study of such pathways is experimentally challenging, because they are typically transient. Computational methods, such as molecular dynamics (MD) simulations, have been successfully proposed to explore tunnels. Conventional MD (cMD) provides structural details to characterize tunnels but suffers from sampling limitations to capture rare tunnel openings on longer time scales. Therefore, in this study, we explored the potential of Gaussian accelerated MD (GaMD) simulations to improve the exploration of complex tunnel networks in enzymes. We used the haloalkane dehalogenase LinB and its two variants with engineered transport pathways, which are not only well-known for their application potential but have also been extensively studied experimentally and computationally regarding their tunnel networks and their importance in multistep catalytic reactions. Our study demonstrates that GaMD efficiently improves tunnel sampling and allows the identification of all known tunnels for LinB and its two mutants. Furthermore, the improved sampling provided insight into a previously unknown transient side tunnel (ST). The extensive conformational landscape explored by GaMD simulations allowed us to investigate in detail the mechanism of ST opening. We determined variant-specific dynamic properties of ST opening, which were previously inaccessible due to limited sampling of cMD. Our comprehensive analysis supports multiple indicators of the functional relevance of the ST, emphasizing its potential significance beyond structural considerations. In conclusion, our research proves that the GaMD method can overcome the sampling limitations of cMD for the effective study of tunnels in enzymes, providing further means for identifying rare tunnels in enzymes with the potential for drug development, precision medicine, and rational protein engineering.
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Affiliation(s)
- Nishita Mandal
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
| | - Bartlomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
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2
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Khusnutdinova AN, Batyrova KA, Brown G, Fedorchuk T, Chai YS, Skarina T, Flick R, Petit AP, Savchenko A, Stogios P, Yakunin AF. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J 2023; 290:4966-4983. [PMID: 37437000 DOI: 10.1111/febs.16903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
Fluorine forms the strongest single bond to carbon with the highest bond dissociation energy among natural products. However, fluoroacetate dehalogenases (FADs) have been shown to hydrolyze this bond in fluoroacetate under mild reaction conditions. Furthermore, two recent studies demonstrated that the FAD RPA1163 from Rhodopseudomonas palustris can also accept bulkier substrates. In this study, we explored the substrate promiscuity of microbial FADs and their ability to defluorinate polyfluorinated organic acids. Enzymatic screening of eight purified dehalogenases with reported fluoroacetate defluorination activity revealed significant hydrolytic activity against difluoroacetate in three proteins. Product analysis using liquid chromatography-mass spectrometry identified glyoxylic acid as the final product of enzymatic DFA defluorination. The crystal structures of DAR3835 from Dechloromonas aromatica and NOS0089 from Nostoc sp. were determined in the apo-state along with the DAR3835 H274N glycolyl intermediate. Structure-based site-directed mutagenesis of DAR3835 demonstrated a key role for the catalytic triad and other active site residues in the defluorination of both fluoroacetate and difluoroacetate. Computational analysis of the dimer structures of DAR3835, NOS0089, and RPA1163 indicated the presence of one substrate access tunnel in each protomer. Moreover, protein-ligand docking simulations suggested similar catalytic mechanisms for the defluorination of both fluoroacetate and difluoroacetate, with difluoroacetate being defluorinated via two consecutive defluorination reactions producing glyoxylate as the final product. Thus, our findings provide molecular insights into substrate promiscuity and catalytic mechanism of FADs, which are promising biocatalysts for applications in synthetic chemistry and bioremediation of fluorochemicals.
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Affiliation(s)
- Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Khorcheska A Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Fedorchuk
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Yao Sheng Chai
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Health Research Innovation Centre, University of Calgary, AB, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, UK
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3
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Improvement in the Environmental Stability of Haloalkane Dehalogenase with Self-Assembly Directed Nano-Hybrid with Iron Phosphate. Catalysts 2022. [DOI: 10.3390/catal12080825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Haloalkane dehalogenase (DhaA) catalyzes the hydrolysis of halogenated compounds through the cleavage of carbon halogen bonds. However, the low activity, poor environmental stability, and difficult recycling of free DhaA greatly increases the economic cost of practical application. Inspired by the organic–inorganic hybrid system, an iron-based hybrid nanocomposite biocatalyst FeHN@DhaA is successfully constructed to enhance its environmental tolerability. A series of characterization methods demonstrate that the synthesized enzyme–metal iron complexes exhibit granular nanostructures with good crystallinity. Under optimized conditions, the activity recovery and the effective encapsulation yield of FeHN@DhaA are 138.54% and 87.21%, respectively. Moreover, it not only exhibits excellent immobilized enzymatic properties but also reveals better tolerance to extreme acid, and is alkali compared with the free DhaA. In addition, the immobilized enzyme FeHN@DhaA can be easily recovered and has a satisfactory reusability, retaining 57.8% of relative activity after five reaction cycles. The results of this study might present an alternative immobilized DhaA-based clean biotechnology for the decontamination of organochlorine pollutants.
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Chan PWY, Chakrabarti N, Ing C, Halgas O, To TKW, Wälti M, Petit AP, Tran C, Savchenko A, Yakunin AF, Edwards EA, Pomès R, Pai EF. Defluorination Capability of l-2-Haloacid Dehalogenases in the HAD-Like Hydrolase Superfamily Correlates with Active Site Compactness. Chembiochem 2022; 23:e202100414. [PMID: 34643018 PMCID: PMC10281000 DOI: 10.1002/cbic.202100414] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Indexed: 11/11/2022]
Abstract
l-2-Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon-halogen bond in S-2-halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. A screen for novel dehalogenase activities revealed four l-2-haloacid dehalogenases capable of defluorination. We now report crystal structures for two of these enzymes, Bpro0530 and Rha0230, as well as for the related proteins PA0810 and RSc1362, which hydrolyse chloroacetate but not fluoroacetate, all at ∼2.2 Å resolution. Overall structure and active sites of these enzymes are highly similar. In molecular dynamics (MD) calculations, only the defluorinating enzymes sample more compact conformations, which in turn allow more effective interactions with the small fluorine atom. Structural constraints, based on X-ray structures and MD calculations, correctly predict the defluorination activity of the homologous enzyme ST2570.
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Affiliation(s)
- Peter W Y Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Present address: Zymeworks, Inc., 1385 West 8th Avenue Suite 540, Vancouver, British Columbia, V6H 3 V9, Canada
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Chris Ing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Present address: ProteinQure, Inc., 119 Spadina Avenue suite 304, Toronto, Ontario, M5V 2L1, Canada
| | - Ondrej Halgas
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Terence K W To
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Present address: International Point of Care, Inc., 135 The West Mall, Unit 9, Toronto, Ontario, M9C 1C2, Canada
| | - Marielle Wälti
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Present address: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0510, USA
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Present address: Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Christopher Tran
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Present address: Ramboll Environment & Health, 2400 Meadowpine Boulevard, Suite 100, Mississauga, Ontario, L5N 6S2, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Present address: Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Health Research Innovation Centre, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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Mazur A, Prudnikova T, Grinkevich P, Mesters JR, Mrazova D, Chaloupkova R, Damborsky J, Kuty M, Kolenko P, Kuta Smatanova I. The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:347-356. [PMID: 33645538 DOI: 10.1107/s2059798321000486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/13/2021] [Indexed: 11/10/2022]
Abstract
Haloalkane dehalogenases (EC 3.8.1.5) are microbial enzymes that catalyse the hydrolytic conversion of halogenated compounds, resulting in a halide ion, a proton and an alcohol. These enzymes are used in industrial biocatalysis, bioremediation and biosensing of environmental pollutants or for molecular tagging in cell biology. The novel haloalkane dehalogenase DpaA described here was isolated from the psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2, which was found in marine sediment collected from the East Sea near Korea. Gel-filtration experiments and size-exclusion chromatography provided information about the dimeric composition of the enzyme in solution. The DpaA enzyme was crystallized using the sitting-drop vapour-diffusion method, yielding rod-like crystals that diffracted X-rays to 2.0 Å resolution. Diffraction data analysis revealed a case of merohedral twinning, and subsequent structure modelling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to haloalkane dehalogenase subfamily I.
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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
| | - Tatyana Prudnikova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Pavel Grinkevich
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Jeroen R Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Daria Mrazova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Kuty
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Petr Kolenko
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague, Czech Republic
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
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Lee SY, Yun SH, Lee H, Seo G, Kim SI. Multi-omics analysis of aniline-degrading bacterium, Delftia sp. K82. J Anal Sci Technol 2021. [DOI: 10.1186/s40543-021-00258-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractDelftia sp. K82 is a soil bacterium capable of utilizing monocyclic aromatic hydrocarbons, including aniline, as its sole carbon and nitrogen source. In this study, the genome analysis of Delftia sp. K82 was completed and the genome data (6117 protein-coding genes and 62 RNA genes) were utilized for proteomic and transcriptomic analysis of Delftia sp. K82 cultured in aniline culture medium. Using these multi-omics approaches (genomics, transcriptomics, and proteomics), complete gene clusters for aniline biodegradation pathways were identified and transcriptomic or proteomic sets specifically induced in aniline culture conditions were elucidated. These data provide multi-layered information on the metabolic characteristics of Delftia sp. K82. The findings suggest that multi-omics approaches are useful analytical tools for the elucidation of the metabolic diversity of soil bacteria and for the identification of novel metabolic enzymes.
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Structure-guided protein design of fluoroacetate dehalogenase for kinetic resolution of rac-2-bromobutyric acid. GREEN SYNTHESIS AND CATALYSIS 2020. [DOI: 10.1016/j.gresc.2020.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Aslan‐Üzel AS, Beier A, Kovář D, Cziegler C, Padhi SK, Schuiten ED, Dörr M, Böttcher D, Hollmann F, Rudroff F, Mihovilovic MD, Buryška T, Damborský J, Prokop Z, Badenhorst CPS, Bornscheuer UT. An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 2020; 12:2032-2039. [PMID: 32362951 PMCID: PMC7188320 DOI: 10.1002/cctc.201901891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/16/2019] [Indexed: 12/31/2022]
Abstract
Halide assays are important for the study of enzymatic dehalogenation, a topic of great industrial and scientific importance. Here we describe the development of a very sensitive halide assay that can detect less than a picomole of bromide ions, making it very useful for quantifying enzymatic dehalogenation products. Halides are oxidised under mild conditions using the vanadium-dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein. The assay is up to three orders of magnitude more sensitive than currently available alternatives, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. We demonstrate that the assay can be used to determine specific activities of dehalogenases and validate this by comparison to a well-established GC-MS method. This new assay will facilitate the identification and characterisation of novel dehalogenases and may also be of interest to those studying other halide-producing enzymes.
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Affiliation(s)
- Aşkın S. Aslan‐Üzel
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Andy Beier
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - David Kovář
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Clemens Cziegler
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | - Santosh K. Padhi
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life SciencesUniversity of HyderabadGachibowli500046India
| | - Eva D. Schuiten
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Mark Dörr
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Dominique Böttcher
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyDelft2629 HZ (TheNetherlands
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | | | - Tomáš Buryška
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Zbyněk Prokop
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
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Janssen DB, Stucki G. Perspectives of genetically engineered microbes for groundwater bioremediation. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:487-499. [PMID: 32095798 DOI: 10.1039/c9em00601j] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Biodegradation is the main process for the removal of organic compounds from the environment, but proceeds slowly for many synthetic chemicals of environmental concern. Research on microbial biodegradation pathways revealed that recalcitrance is - among other factors - caused by biochemical blockages resulting in dysfunctional catabolic routes. This has raised interest in the possibility to construct microorganisms with improved catabolic activities by genetic engineering. Although this goal has been pursued for decades, no full-scale applications have emerged. This perspective explores the lagging implementation of genetically engineered microorganisms in practical bioremediation. The major technical and scientific issues are illustrated by comparing two examples, that of 1,2-dichloroethane where successful full-scale application of pump-and-treat biotreatment processes has been achieved, and 1,2,3-trichloropropane, for which protein and genetic engineering yielded effective bacterial cultures that still await application.
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Affiliation(s)
- Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands.
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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13
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Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L, Dvorak P, Stepankova V, Chaloupkova R, Brezovsky J, Prokop Z, Damborsky J. Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03523] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Pavel Vanacek
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Eva Sebestova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Petra Babkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sarka Bidmanova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Pavel Dvorak
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Veronika Stepankova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
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14
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Wang Y, Feng Y, Cao X, Liu Y, Xue S. Insights into the molecular mechanism of dehalogenation catalyzed by D-2-haloacid dehalogenase from crystal structures. Sci Rep 2018; 8:1454. [PMID: 29362453 PMCID: PMC5780510 DOI: 10.1038/s41598-017-19050-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/17/2017] [Indexed: 11/09/2022] Open
Abstract
D-2-haloacid dehalogenases (D-DEXs) catalyse the hydrolytic dehalogenation of D-2-haloacids, releasing halide ions and producing the corresponding 2-hydroxyacids. A structure-guided elucidation of the catalytic mechanism of this dehalogenation reaction has not been reported yet. Here, we report the catalytic mechanism of a D-DEX, HadD AJ1 from Pseudomonas putida AJ1/23, which was elucidated by X-ray crystallographic analysis and the H218O incorporation experiment. HadD AJ1 is an α-helical hydrolase that forms a homotetramer with its monomer including two structurally axisymmetric repeats. The product-bound complex structure was trapped with L-lactic acid in the active site, which is framed by the structurally related helices between two repeats. Site-directed mutagenesis confirmed the importance of the residues lining the binding pocket in stabilizing the enzyme-substrate complex. Asp205 acts as a key catalytic residue and is responsible for activating a water molecule along with Asn131. Then, the hydroxyl group of the water molecule directly attacks the C2 atom of the substrate to release the halogen ion instead of forming an enzyme-substrate ester intermediate as observed in L-2-haloacid dehalogenases. The newly revealed structural and mechanistic information on D-DEX may inspire structure-based mutagenesis to engineer highly efficient haloacid dehalogenases.
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Affiliation(s)
- Yayue Wang
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xupeng Cao
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yinghui Liu
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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15
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Abstract
Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.
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16
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Li X, Luo YD, Pan DR, Shi XD, Tan YL, Li ZH. Effect of Zn 2+ on halohydrin dehalogenase expression and accumulation through multi-parameter correlation research with Escherichia coli P84A/MC1061. Bioengineered 2017; 8:585-593. [PMID: 28282255 DOI: 10.1080/21655979.2017.1285985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Using 5 Zn2+ supplementation strategies in a 50 L batch bioreactor named FUS-50L(A), possible correlations among Zn2+ content and addition timing, physiologic activity (PA), halohydrin dehalogenase (HheC) accumulation of Escherichia coli P84A/MC1061 were systematically investigated. First, Zn2+ was confirmed as the significant factor, and its optimal concentration for HheC expression was 3.87 mg/L through fermentation experiments in shaking flasks. Second, based on experimental results from the different strategies, it was found that PA, nutrient consumption rate (NCR) and specific growth rate (μ) for E. coli P84A/MC1061 were promoted in the log phase (4-8 h) under appropriate Zn2+ concentrations in the lag phase and late log phase. Furthermore cell biomass was also increased to a higher level and the maximum HheC activity (i.e. HheCmax) was increased by 9.80%, and the time to reach HheCmax was reduced from 16 to 12 hours. Furthermore, appropriate supplementation of Zn2+ caused higher μ for E. coli P84A/MC1061, which resulted in more rapid accumulation of increased acetic acid concentrations, leading to higher acetic acid consumption avoiding any negative effects on producing HheC because of carbon source being exhausted prematurely and acetic acid being consumed rapidly.
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Affiliation(s)
- Xiao Li
- a College of Biological and Pharmaceutica Engineering, China Three Gorges University , Yichang , P. R. China.,b Angel Yeast Co., Ltd. Yichang , P. R. China
| | - Yu-Di Luo
- a College of Biological and Pharmaceutica Engineering, China Three Gorges University , Yichang , P. R. China.,b Angel Yeast Co., Ltd. Yichang , P. R. China
| | - Dong-Rui Pan
- a College of Biological and Pharmaceutica Engineering, China Three Gorges University , Yichang , P. R. China
| | - Xiao-Dan Shi
- a College of Biological and Pharmaceutica Engineering, China Three Gorges University , Yichang , P. R. China
| | - Ya-Li Tan
- b Angel Yeast Co., Ltd. Yichang , P. R. China
| | - Zhi-Hong Li
- b Angel Yeast Co., Ltd. Yichang , P. R. China
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17
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Marques SM, Dunajova Z, Prokop Z, Chaloupkova R, Brezovsky J, Damborsky J. Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. J Chem Inf Model 2017; 57:1970-1989. [PMID: 28696117 DOI: 10.1021/acs.jcim.7b00070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements. Using molecular dynamics and quantum mechanics approaches we have surveyed (i) the substrate binding, (ii) the formation of the reactive complex, (iii) the chemical step, and (iv) the release of the products. We showed that the binding of the substrate and its transport through the molecular tunnel to the active site is a relatively fast process. The cleavage of the carbon-halogen bond was previously identified as the rate-limiting step in the wild-type. Here we demonstrate that this step was enhanced in DhaA31 due to a significantly higher number of reactive configurations of the substrate and a decrease of the energy barrier to the SN2 reaction. C176Y and V245F were identified as the key mutations responsible for most of those improvements. The release of the alcohol product was found to be the rate-limiting step in DhaA31 primarily due to the C176Y mutation. Mutational dissection of DhaA31 and kinetic analysis of the intermediate mutants confirmed the theoretical observations. Overall, our comprehensive computational approach has unveiled mechanistic details of the catalytic cycle which will enable a balanced design of more efficient enzymes. This approach is applicable to deepen the biochemical knowledge of a large number of other systems and may contribute to robust strategies in the development of new biocatalysts.
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Affiliation(s)
- Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
| | - Zuzana Dunajova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
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18
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Kotik M, Vanacek P, Kunka A, Prokop Z, Damborsky J. Metagenome-derived haloalkane dehalogenases with novel catalytic properties. Appl Microbiol Biotechnol 2017; 101:6385-6397. [PMID: 28674849 DOI: 10.1007/s00253-017-8393-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 06/11/2017] [Accepted: 06/13/2017] [Indexed: 01/30/2023]
Abstract
Haloalkane dehalogenases (HLDs) are environmentally relevant enzymes cleaving a carbon-halogen bond in a wide range of halogenated pollutants. PCR with degenerate primers and genome-walking was used for the retrieval of four HLD-encoding genes from groundwater-derived environmental DNA. Using specific primers and the environmental DNA as a template, we succeeded in generating additional amplicons, resulting altogether in three clusters of sequences with each cluster comprising 8-13 closely related putative HLD-encoding genes. A phylogenetic analysis of the translated genes revealed that three HLDs are members of the HLD-I subfamily, whereas one gene encodes an enzyme from the subfamily HLD-II. Two metagenome-derived HLDs, eHLD-B and eHLD-C, each from a different subfamily, were heterologously produced in active form, purified and characterized in terms of their thermostability, pH and temperature optimum, quaternary structure, substrate specificity towards 30 halogenated compounds, and enantioselectivity. eHLD-B and eHLD-C showed striking differences in their activities, substrate preferences, and tolerance to temperature. Profound differences were also determined in the enantiopreference and enantioselectivity of these enzymes towards selected substrates. Comparing our data with those of known HLDs revealed that eHLD-C exhibits a unique combination of high thermostability, high activity, and an unusually broad pH optimum, which covers the entire range of pH 5.5-8.9. Moreover, a so far unreported high thermostability for HLDs was determined for this enzyme at pH values lower than 6.0. Thus, eHLD-C represents an attractive and novel biocatalyst for biotechnological applications.
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Affiliation(s)
- Michael Kotik
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Pavel Vanacek
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic.
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19
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Enzyme-catalyzed cationic epoxide rearrangements in quinolone alkaloid biosynthesis. Nat Chem Biol 2017; 13:325-332. [PMID: 28114276 PMCID: PMC5310975 DOI: 10.1038/nchembio.2283] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/28/2016] [Indexed: 11/08/2022]
Abstract
Epoxides are highly useful synthons and biosynthons for the construction of complex natural products during total synthesis and biosynthesis, respectively. Among enzyme-catalyzed epoxide transformations, a reaction that is notably missing, in regard to the synthetic toolbox, is cationic rearrangement that takes place under strong acid. This is a challenging transformation for enzyme catalysis, as stabilization of the carbocation intermediate upon epoxide cleavage is required. Here, we discovered two Brønsted acid enzymes that can catalyze two unprecedented epoxide transformations in biology. PenF from the penigequinolone pathway catalyzes a cationic epoxide rearrangement under physiological conditions to generate a quaternary carbon center, while AsqO from the aspoquinolone pathway catalyzes a 3-exo-tet cyclization to forge a cyclopropane-tetrahydrofuran ring system. The discovery of these new epoxide-modifying enzymes further highlights the versatility of epoxides in complexity generation during natural product biosynthesis.
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20
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Vatsal A, Potdar C, Zinjarde SS, Ravi Kumar V, Kulkarni BD, RaviKumar A. Role of aliasing and interacting factors in the enhanced production of dehalogenase from Yarrowia lipolytica for degradation of brominated compounds. J IND ENG CHEM 2016. [DOI: 10.1016/j.jiec.2016.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Manna RN, Zinovjev K, Tuñón I, Dybala-Defratyka A. Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study. J Phys Chem B 2015; 119:15100-9. [DOI: 10.1021/acs.jpcb.5b07538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rabindra Nath Manna
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
| | - Kirill Zinovjev
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Agnieszka Dybala-Defratyka
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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22
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Wang Y, Cao X, Feng Y, Xue S. Environment-induced conformational and functional changes of L-2-haloacid dehalogenase. J Biosci Bioeng 2015; 121:491-6. [PMID: 26508534 DOI: 10.1016/j.jbiosc.2015.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/11/2015] [Accepted: 09/11/2015] [Indexed: 11/29/2022]
Abstract
2-Haloacid dehalogenases have been highly studied due to their potential applications in chemical industries and bioremediation. Although biochemical and structural characterizations of the enzyme have been detailed, no information was available regarding environmental effects on the structure-function relationship. Here, circular dichroism spectroscopy (CD) was used to investigate the correlation between changes on the conformation and the function of l-2-haloacid dehalogenase (HadL AJ1) from the Pseudomonas putida induced by the environmental factors. Decreased α-helix and increased β-sheet contents were observed in the structure of HadL AJ1 along with activity losses caused by pH, temperature and inhibitors. Regardless of which factor above-mentioned existed, more than 65.0% of HadL AJ1 activity could be remained if its α-helix content was over 12.0%. The maintenance of α-helical structure in HadL AJ1 was indispensable to its catalysis, while β-sheet increase restricts its activity. This study revealed the variation of enzymatic activity due to environmental conditions resulting in structural changes monitored by CD, which contributed to rational modification and was instructive for predicting changes of the enzymatic activity during application.
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Affiliation(s)
- Yayue Wang
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xupeng Cao
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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23
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Properties and biotechnological applications of natural and engineered haloalkane dehalogenases. Appl Microbiol Biotechnol 2015; 99:9865-81. [DOI: 10.1007/s00253-015-6954-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/19/2015] [Accepted: 08/22/2015] [Indexed: 01/01/2023]
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24
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25
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Yarrowia lipolytica NCIM 3589, a tropical marine yeast, degrades bromoalkanes by an initial hydrolytic dehalogenation step. Biodegradation 2015; 26:127-38. [DOI: 10.1007/s10532-015-9721-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/10/2015] [Indexed: 10/24/2022]
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26
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Li A, Shao Z. Biochemical characterization of a haloalkane dehalogenase DadB from Alcanivorax dieselolei B-5. PLoS One 2014; 9:e89144. [PMID: 24586552 PMCID: PMC3938430 DOI: 10.1371/journal.pone.0089144] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/14/2014] [Indexed: 11/18/2022] Open
Abstract
Recently, we found that Alcanivorax bacteria from various marine environments were capable of degrading halogenated alkanes. Genome sequencing of A. dieselolei B-5 revealed two putative haloalkane dehalogenase (HLD) genes, which were supposed to be involved in degradation of halogenated compounds. In this report, we confirm for the first time that the Alcanivorax bacterium encodes a truly functional HLD named DadB. An activity assay with 46 halogenated substrates indicated that DadB possesses broad substrate range and has the highest overall activity among the identified HLDs. DadB prefers brominated substrates; chlorinated alkenes; and the C2-C3 substrates, including the persistent pollutants of 1,2-dichloroethane, 1,2-dichloropropane and 1,2,3-trichloropropane. As DadB displays no detectable activity toward long-chain haloalkanes such as 1-chlorohexadecane and 1-chlorooctadecane, the degradation of them in A. dieselolei B-5 might be attributed to other enzymes. Kinetic constants were determined with 6 substrates. DadB has highest affinity and largest kcat/Km value toward 1,3-dibromopropane (Km = 0.82 mM, kcat/Km = 16.43 mM−1·s−1). DadB aggregates fast in the buffers with pH≤7.0, while keeps stable in monomer form when pH≥7.5. According to homology modeling, DadB has an open active cavity with a large access tunnel, which is supposed important for larger molecules as opposed to C2-C3 substrates. Combined with the results for other HLDs, we deduce that residue I247 plays an important role in substrate selection. These results suggest that DadB and its host, A. dieselolei B-5, are of potential use for biocatalysis and bioremediation applications.
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Affiliation(s)
- Anzhang Li
- School of Life Sciences, Xiamen University, Xiamen, China ; Key Laboratory of Marine Biogenetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center of Deep Sea Biology; Key Laboratory of Marine Biogenetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources-State Key Laboratory Breeding Base, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center of Deep Sea Biology; Key Laboratory of Marine Biogenetic Resources of Fujian Province, Xiamen, China
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27
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Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications. Appl Microbiol Biotechnol 2014; 98:2917-35. [PMID: 24562178 DOI: 10.1007/s00253-014-5557-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/17/2014] [Accepted: 01/20/2014] [Indexed: 01/02/2023]
Abstract
Marine microorganisms play key roles in every marine ecological process, hence the growing interest in studying their populations and functions. Microbial communities on algae remain underexplored, however, despite their huge biodiversity and the fact that they differ markedly from those living freely in seawater. The study of this microbiota and of its relationships with algal hosts should provide crucial information for ecological investigations on algae and aquatic ecosystems. Furthermore, because these microorganisms interact with algae in multiple, complex ways, they constitute an interesting source of novel bioactive compounds with biotechnological potential, such as dehalogenases, antimicrobials, and alga-specific polysaccharidases (e.g., agarases, carrageenases, and alginate lyases). Here, to demonstrate the huge potential of alga-associated organisms and their metabolites in developing future biotechnological applications, we first describe the immense diversity and density of these microbial biofilms. We further describe their complex interactions with algae, leading to the production of specific bioactive compounds and hydrolytic enzymes of biotechnological interest. We end with a glance at their potential use in medical and industrial applications.
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28
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Skopelitou K, Georgakis N, Efrose R, Flemetakis E, Labrou NE. Sol–gel immobilization of haloalkane dehalogenase from Bradyrhizobium japonicum for the remediation 1,2-dibromoethane. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Influence of the nutritional conditions on haloalcohol dehalogenase HheC production by recombinant Escherichia coli P84A/MC1061. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0582-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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30
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Hasan K, Gora A, Brezovsky J, Chaloupkova R, Moskalikova H, Fortova A, Nagata Y, Damborsky J, Prokop Z. The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58. FEBS J 2013; 280:3149-59. [PMID: 23490078 DOI: 10.1111/febs.12238] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/05/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
Abstract
Haloalkane dehalogenases catalyze the hydrolysis of carbon-halogen bonds in various chlorinated, brominated and iodinated compounds. These enzymes have a conserved pair of halide-stabilizing residues that are important in substrate binding and stabilization of the transition state and the halide ion product via hydrogen bonding. In all previously known haloalkane dehalogenases, these residues are either a pair of tryptophans or a tryptophan-asparagine pair. The newly-isolated haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 (EC 3.8.1.5) possesses a unique halide-stabilizing tyrosine residue, Y109, in place of the conventional tryptophan. A variant of DatA with the Y109W mutation was created and the effects of this mutation on the structure and catalytic properties of the enzyme were studied using spectroscopy and pre-steady-state kinetic experiments. Quantum mechanical and molecular dynamics calculations were used to obtain a detailed analysis of the hydrogen-bonding patterns within the active sites of the wild-type and the mutant, as well as of the stabilization of the ligands as the reaction proceeds. Fluorescence quenching experiments suggested that replacing the tyrosine with tryptophan improves halide binding by 3.7-fold, presumably as a result of the introduction of an additional hydrogen bond. Kinetic analysis revealed that the mutation affected the substrate specificity of the enzyme and reduced its K(0.5) for selected halogenated substrates by a factor of 2-4, without impacting the rate-determining hydrolytic step. We conclude that DatA is the first natural haloalkane dehalogenase that stabilizes its substrate in the active site using only a single hydrogen bond, which is a new paradigm in catalysis by this enzyme family.
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Affiliation(s)
- Khomaini Hasan
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
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Stepankova V, Khabiri M, Brezovsky J, Pavelka A, Sykora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Chaloupkova R, Damborsky J. Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. Chembiochem 2013; 14:890-7. [DOI: 10.1002/cbic.201200733] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Indexed: 11/11/2022]
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Zhang J, Cao X, Xin Y, Xue S, Zhang W. Purification and characterization of a dehalogenase from Pseudomonas stutzeri DEH130 isolated from the marine sponge Hymeniacidon perlevis. World J Microbiol Biotechnol 2013; 29:1791-9. [PMID: 23543208 DOI: 10.1007/s11274-013-1340-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/25/2013] [Indexed: 11/24/2022]
Abstract
2-haloacid dehalogenases are enzymes that are capable of degrading 2-haloacid compounds. These enzymes are produced by bacteria, but so far they have only been purified and characterized from terrestrial bacteria. The present study describes the purification and characterization of 2-haloacid dehalogenase from the marine bacterium Pseudomonas stutzeri DEH130. P. Stutzeri DEH130 contained two kinds of 2-haloacid dehalogenase (designated as Dehalogenase I and Dehalogenase II) as detected in the crude cell extract after ammonium sulfate fractionation. Both enzymes appeared to exhibit stereo-specificity with respect to substrate. Dehalogenase I was a 109.9-kDa enzyme that preferentially utilized D-2-chloropropropionate and had optimum activity at pH 7.5. Dehalogenase II, which preferentially utilized L-2-chloropropionate, was further purified by ion-exchange chromatography and gel filtration. Purified Dehalogenase II appeared to be a dimeric enzyme with a subunit of 26.0-kDa. It had maximum activity at pH 10.0 and a temperature of 40 °C. Its activity was not inhibited by DTT and EDTA, but strongly inhibited by Cu²⁺, Zn²⁺, and Co²⁺. The K(m) and V(max) for L-2-chloropropionate were 0.3 mM and 23.8 μmol/min/mg, respectively. Its substrate specificity was limited to short chain mono-substituted 2-halocarboxylic acids, with no activity detected toward fluoropropionate and monoiodoacetate. This is the first report on the purification and characterization of 2-haloacid dehalogenase from a marine bacterium.
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Affiliation(s)
- Jinyou Zhang
- Marine Bioproducts Engineering Group, Dalian Institution of chemical physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, People's Republic of China
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Sudi IY, Wong EL, Joyce-Tan KH, Shamsir MS, Jamaluddin H, Huyop F. Structure prediction, molecular dynamics simulation and docking studies of D-specific dehalogenase from Rhizobium sp. RC1. Int J Mol Sci 2012; 13:15724-54. [PMID: 23443090 PMCID: PMC3546658 DOI: 10.3390/ijms131215724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 10/16/2012] [Accepted: 11/07/2012] [Indexed: 11/16/2022] Open
Abstract
Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD) in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD) simulation and docking of D-2-chloropropionate (D-2CP), D-2-bromopropionate (D-2BP), monochloroacetate (MCA), monobromoacetate (MBA), 2,2-dichloropropionate (2,2-DCP), d,l-2,3-dichloropropionate (d,l-2,3-DCP), and 3-chloropropionate (3-CP) into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD) from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25-30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials.
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Affiliation(s)
- Ismaila Yada Sudi
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor Bahru, Malaysia; E-Mails: (I.Y.S.); (E.L.W.); (M.S.S.); (H.J.)
| | - Ee Lin Wong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor Bahru, Malaysia; E-Mails: (I.Y.S.); (E.L.W.); (M.S.S.); (H.J.)
| | - Kwee Hong Joyce-Tan
- School of Bioscience and Technology, Faculty Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia; E-Mail:
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor Bahru, Malaysia; E-Mails: (I.Y.S.); (E.L.W.); (M.S.S.); (H.J.)
| | - Haryati Jamaluddin
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor Bahru, Malaysia; E-Mails: (I.Y.S.); (E.L.W.); (M.S.S.); (H.J.)
| | - Fahrul Huyop
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor Bahru, Malaysia; E-Mails: (I.Y.S.); (E.L.W.); (M.S.S.); (H.J.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +607-5558452; Fax: +607-5531112
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Properties and biotechnological applications of halohydrin dehalogenases: current state and future perspectives. Appl Microbiol Biotechnol 2012; 97:9-21. [DOI: 10.1007/s00253-012-4523-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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Koudelakova T, Bidmanova S, Dvorak P, Pavelka A, Chaloupkova R, Prokop Z, Damborsky J. Haloalkane dehalogenases: Biotechnological applications. Biotechnol J 2012; 8:32-45. [DOI: 10.1002/biot.201100486] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 06/30/2012] [Accepted: 07/20/2012] [Indexed: 12/21/2022]
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Gehret JJ, Gu L, Geders TW, Brown WC, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Structure and activity of DmmA, a marine haloalkane dehalogenase. Protein Sci 2012; 21:239-48. [PMID: 22124946 DOI: 10.1002/pro.2009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/16/2011] [Accepted: 11/23/2011] [Indexed: 11/07/2022]
Abstract
DmmA is a haloalkane dehalogenase (HLD) identified and characterized from the metagenomic DNA of a marine microbial consortium. Dehalogenase activity was detected with 1,3-dibromopropane as substrate, with steady-state kinetic parameters typical of HLDs (K(m) = 0.24 ± 0.05 mM, k(cat) = 2.4 ± 0.1 s(-1) ). The 2.2-Å crystal structure of DmmA revealed a fold and active site similar to other HLDs, but with a substantially larger active site binding pocket, suggestive of an ability to act on bulky substrates. This enhanced cavity was shown to accept a range of linear and cyclic substrates, suggesting that DmmA will contribute to the expanding industrial applications of HLDs.
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Affiliation(s)
- Jennifer J Gehret
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
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Sequence diversity in haloalkane dehalogenases, as revealed by PCR using family-specific primers. J Microbiol Methods 2011; 88:212-7. [PMID: 22155739 DOI: 10.1016/j.mimet.2011.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/21/2011] [Accepted: 11/21/2011] [Indexed: 11/24/2022]
Abstract
Haloalkane dehalogenases (HLDs) are hydrolytic enzymes that cleave carbon-halogen bonds in various halogenated compounds. Interest initially grew in HLDs as biocatalysts for bioremediation and later for biotransformation applications; each specific HLD within the HLD family has its own substrate specificity, enantioselectivity and product inhibition characteristics. We developed degenerate oligonucleotide primers for HLD-encoding genes and used these to PCR-amplify large hld gene fragments using genomic DNA from the microbial community of a chlorinated-solvent-contaminated aquifer as a template. An analysis of small subunit ribosomal RNA genes revealed a high complexity in the eubacterial population, dominated by α-, β- and γ-Proteobacteria, and Acidobacteria. Using HLD-family-specific primers, we also retrieved transcribed hld homologues from the microbial consortium of this contaminated site. The DNA-derived hld sequences were phylogenetically broadly distributed over both HLD subclasses I and II. Most hld sequences of the environmental RNA data set clustered in three groups within both HLD subclasses, indicating that a considerable proportion of the microbial consortium carrying hld genes was actively involved in haloalkane dehalogenation. The small sequence variation in hld genes and transcripts within each HLD cluster inferred the presence of a substantial pool of highly related HLD genes. The sequence variability appeared to be unevenly distributed over the HLD genes, however, with no apparent preference for a particular protein segment or domain.
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Abstract
An enzyme's substrate specificity is one of its most important characteristics. The quantitative comparison of broad-specificity enzymes requires the selection of a homogenous set of substrates for experimental testing, determination of substrate-specificity data and analysis using multivariate statistics. We describe a systematic analysis of the substrate specificities of nine wild-type and four engineered haloalkane dehalogenases. The enzymes were characterized experimentally using a set of 30 substrates selected using statistical experimental design from a set of nearly 200 halogenated compounds. Analysis of the activity data showed that the most universally useful substrates in the assessment of haloalkane dehalogenase activity are 1-bromobutane, 1-iodopropane, 1-iodobutane, 1,2-dibromoethane and 4-bromobutanenitrile. Functional relationships among the enzymes were explored using principal component analysis. Analysis of the untransformed specific activity data revealed that the overall activity of wild-type haloalkane dehalogenases decreases in the following order: LinB~DbjA>DhlA~DhaA~DbeA~DmbA>DatA~DmbC~DrbA. After transforming the data, we were able to classify haloalkane dehalogenases into four SSGs (substrate-specificity groups). These functional groups are clearly distinct from the evolutionary subfamilies, suggesting that phylogenetic analysis cannot be used to predict the substrate specificity of individual haloalkane dehalogenases. Structural and functional comparisons of wild-type and mutant enzymes revealed that the architecture of the active site and the main access tunnel significantly influences the substrate specificity of these enzymes, but is not its only determinant. The identification of other structural determinants of the substrate specificity remains a challenge for further research on haloalkane dehalogenases.
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Hesseler M, Bogdanović X, Hidalgo A, Berenguer J, Palm GJ, Hinrichs W, Bornscheuer UT. Cloning, functional expression, biochemical characterization, and structural analysis of a haloalkane dehalogenase from Plesiocystis pacifica SIR-1. Appl Microbiol Biotechnol 2011; 91:1049-60. [DOI: 10.1007/s00253-011-3328-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Revised: 03/30/2011] [Accepted: 04/09/2011] [Indexed: 10/18/2022]
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Huang J, Xin Y, Zhang W. Isolation, characterization and identification of a Paracoccus sp. 2-haloacid-degrading bacterium from the marine sponge Hymeniacidon perlevis. J Basic Microbiol 2011; 51:318-24. [PMID: 21298680 DOI: 10.1002/jobm.201000205] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 10/12/2010] [Indexed: 11/10/2022]
Abstract
A 2-haloacid dehalogenase-producing bacterium, designated DEH99, was isolated from the marine sponge Hymeniacidon perlevis using a modified enrichment medium and a pH indicator method. DEH99 could degrade only half of the racemic mixture 2-chloropropionic acid (2-CPA) in the medium. The dehalogenase of DEH99 was further determined to be a (S)-2-haloacid dehalogenase, which can degrade 2-CPA, 2-bromopropionic acid (2-BPA), and iodoacetic acid. The gene encoding the (S)-2-haloacid dehalogenase was partially sequenced and classified into the Group II family. The 2-haloacid dehalogenase showed the highest sequence similarity (77% with 21% query coverage) to the haloacid dehalogenase (dhlB) gene of Xanthobacter autotrophicus. A phylogenetic analysis of the 16S rDNA sequence demonstrated that the isolate DEH99 is a member of the genus Paracoccus. To our knowledge, this is the first report detailing the isolation of a strain of genus Paracoccus having 2-haloacid dehalogenase activity from marine sponges.
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Affiliation(s)
- Jianyu Huang
- Marine Bioproducts Engineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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41
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Huang J, Xin Y, Cao X, Zhang W. Phylogenetic diversity and characterization of 2-haloacid degrading bacteria from the marine sponge Hymeniacidon perlevis. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-010-0636-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Stsiapanava A, Dohnalek J, Gavira JA, Kuty M, Koudelakova T, Damborsky J, Kuta Smatanova I. Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:962-9. [PMID: 20823547 DOI: 10.1107/s0907444910027101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 07/08/2010] [Indexed: 11/10/2022]
Abstract
The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 is a bacterial enzyme that shows catalytic activity for the hydrolytic degradation of the highly toxic industrial pollutant 1,2,3-trichloropropane (TCP). Mutagenesis focused on the access tunnels of DhaA produced protein variants with significantly improved activity towards TCP. Three mutants of DhaA named DhaA04 (C176Y), DhaA14 (I135F) and DhaA15 (C176Y + I135F) were constructed in order to study the functional relevance of the tunnels connecting the buried active site of the protein with the surrounding solvent. All three protein variants were crystallized using the sitting-drop vapour-diffusion technique. The crystals of DhaA04 belonged to the orthorhombic space group P2(1)2(1)2(1), while the crystals of DhaA14 and DhaA15 had triclinic symmetry in space group P1. The crystal structures of DhaA04, DhaA14 and DhaA15 with ligands present in the active site were solved and refined using diffraction data to 1.23, 0.95 and 1.22 A, resolution, respectively. Structural comparisons of the wild type and the three mutants suggest that the tunnels play a key role in the processes of ligand exchange between the buried active site and the surrounding solvent.
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Affiliation(s)
- A Stsiapanava
- Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
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2-haloacrylate hydratase, a new class of flavoenzyme that catalyzes the addition of water to the substrate for dehalogenation. Appl Environ Microbiol 2010; 76:6032-7. [PMID: 20656877 DOI: 10.1128/aem.00334-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enzymes catalyzing the conversion of organohalogen compounds are useful in the chemical industry and environmental technology. Here we report the occurrence of a new reduced flavin adenine dinucleotide (FAD) (FADH(2))-dependent enzyme that catalyzes the removal of a halogen atom from an unsaturated aliphatic organohalogen compound by the addition of a water molecule to the substrate. A soil bacterium, Pseudomonas sp. strain YL, inducibly produced a protein named Caa67(YL) when the cells were grown on 2-chloroacrylate (2-CAA). The caa67(YL) gene encoded a protein of 547 amino acid residues (M(r) of 59,301), which shared weak but significant sequence similarity with various flavoenzymes and contained a nucleotide-binding motif. We found that 2-CAA is converted into pyruvate when the reaction was carried out with purified Caa67(YL) in the presence of FAD and a reducing agent [NAD(P)H or sodium dithionite] under anaerobic conditions. The reducing agent was not stoichiometrically consumed during this reaction, suggesting that FADH(2) is conserved by regeneration in the catalytic cycle. When the reaction was carried out in the presence of H(2)(18)O, [(18)O]pyruvate was produced. These results indicate that Caa67(YL) catalyzes the hydration of 2-CAA to form 2-chloro-2-hydroxypropionate, which is chemically unstable and probably spontaneously dechlorinated to form pyruvate. 2-Bromoacrylate, but not other 2-CAA analogs such as acrylate and methacrylate, served as the substrate of Caa67(YL). Thus, we named this new enzyme 2-haloacrylate hydratase. The enzyme is very unusual in that it requires the reduced form of FAD for hydration, which involves no net change in the redox state of the coenzyme or substrate.
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Chan WY, Wong M, Guthrie J, Savchenko AV, Yakunin AF, Pai EF, Edwards EA. Sequence- and activity-based screening of microbial genomes for novel dehalogenases. Microb Biotechnol 2009; 3:107-20. [PMID: 21255311 PMCID: PMC3815952 DOI: 10.1111/j.1751-7915.2009.00155.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Dehalogenases are environmentally important enzymes that detoxify organohalogens by cleaving their carbon‐halogen bonds. Many microbial genomes harbour enzyme families containing dehalogenases, but a sequence‐based identification of genuine dehalogenases with high confidence is challenging because of the low sequence conservation among these enzymes. Furthermore, these protein families harbour a rich diversity of other enzymes including esterases and phosphatases. Reliable sequence determinants are necessary to harness genome sequencing‐efforts for accelerating the discovery of novel dehalogenases with improved or modified activities. In an attempt to extract dehalogenase sequence fingerprints, 103 uncharacterized potential dehalogenase candidates belonging to the α/β hydrolase (ABH) and haloacid dehalogenase‐like hydrolase (HAD) superfamilies were screened for dehalogenase, esterase and phosphatase activity. In this first biochemical screen, 1 haloalkane dehalogenase, 1 fluoroacetate dehalogenase and 5 l‐2‐haloacid dehalogenases were found (success rate 7%), as well as 19 esterases and 31 phosphatases. Using this functional data, we refined the sequence‐based dehalogenase selection criteria and applied them to a second functional screen, which identified novel dehalogenase activity in 13 out of only 24 proteins (54%), increasing the success rate eightfold. Four new l‐2‐haloacid dehalogenases from the HAD superfamily were found to hydrolyse fluoroacetate, an activity never previously ascribed to enzymes in this superfamily.
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Affiliation(s)
- Wing Yiu Chan
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
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Pavlova M, Klvana M, Prokop Z, Chaloupkova R, Banas P, Otyepka M, Wade RC, Tsuda M, Nagata Y, Damborsky J. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nat Chem Biol 2009; 5:727-33. [PMID: 19701186 DOI: 10.1038/nchembio.205] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 05/28/2009] [Indexed: 01/17/2023]
Abstract
Engineering enzymes to degrade anthropogenic compounds efficiently is challenging. We obtained Rhodococcus rhodochrous haloalkane dehalogenase mutants with up to 32-fold higher activity than wild type toward the toxic, recalcitrant anthropogenic compound 1,2,3-trichloropropane (TCP) using a new strategy. We identified key residues in access tunnels connecting the buried active site with bulk solvent by rational design and randomized them by directed evolution. The most active mutant has large aromatic residues at two out of three randomized positions and two positions modified by site-directed mutagenesis. These changes apparently enhance activity with TCP by decreasing accessibility of the active site for water molecules, thereby promoting activated complex formation. Kinetic analyses confirmed that the mutations improved carbon-halogen bond cleavage and shifted the rate-limiting step to the release of products. Engineering access tunnels by combining computer-assisted protein design with directed evolution may be a valuable strategy for refining catalytic properties of enzymes with buried active sites.
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Affiliation(s)
- Martina Pavlova
- Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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Jochens H, Stiba K, Savile C, Fujii R, Yu JG, Gerassenkov T, Kazlauskas R, Bornscheuer U. Umwandlung einer Esterase in eine Epoxidhydrolase. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Jochens H, Stiba K, Savile C, Fujii R, Yu JG, Gerassenkov T, Kazlauskas R, Bornscheuer U. Converting an Esterase into an Epoxide Hydrolase. Angew Chem Int Ed Engl 2009; 48:3532-5. [DOI: 10.1002/anie.200806276] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Leach LH, Zhang P, Lapara TM, Hozalski RM, Camper AK. Detection and enumeration of haloacetic acid-degrading bacteria in drinking water distribution systems using dehalogenase genes. J Appl Microbiol 2009; 107:978-88. [PMID: 19486431 DOI: 10.1111/j.1365-2672.2009.04277.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To develop a PCR-based tracking method for the detection of a subset of bacteria in drinking water distribution systems capable of degrading haloacetic acids (HAAs). METHODS AND RESULTS Published degenerate PCR primers were used to determine that 54% of tap water samples (7/13) were positive for a deh gene, indicating that drinking water distribution systems may harbour bacteria capable of HAA degradation. As the published primer sets were not sufficiently specific for quantitative PCR, new primers were designed to amplify dehII genes from selected indicator strains. The developed primer sets were effective in directly amplifying dehII genes from enriched consortia samples, and the DNA extracted from tap water provided that an additional nested PCR step for detection of the dehII gene was used. CONCLUSIONS This study demonstrates that drinking water distribution systems harbour microbes capable of degrading HAAs. In addition, a quantitative PCR method was developed to detect and quantify dehII genes in drinking water systems. SIGNIFICANCE AND IMPACT OF THE STUDY The development of a technique to rapidly screen for the presence of dehalogenase genes in drinking water distribution systems could help water utilities determine if HAA biodegradation is occurring in the distribution system.
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Affiliation(s)
- L H Leach
- Montana State University, Center for Biofilm Engineering, Bozeman, MT 59717 , USA
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Prudnikova T, Mozga T, Rezacova P, Chaloupkova R, Sato Y, Nagata Y, Brynda J, Kuty M, Damborsky J, Smatanova IK. Crystallization and preliminary X-ray analysis of a novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:353-6. [PMID: 19342778 DOI: 10.1107/s1744309109007039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 02/25/2009] [Indexed: 11/10/2022]
Abstract
A novel enzyme, DbeA, belonging to the haloalkane dehalogenase family (EC 3.8.1.5) was isolated from Bradyrhizobium elkani USDA94. This haloalkane dehalogenase is closely related to the DbjA enzyme from B. japonicum USDA110 (71% sequence identity), but has different biochemical properties. DbeA is generally less active and has a higher specificity towards brominated and iodinated compounds than DbjA. In order to understand the altered activity and specificity of DbeA, its mutant variant DbeA1, which carries the unique fragment of DbjA, was also constructed. Both wild-type DbeA and DbeA1 were crystallized using the sitting-drop vapour-diffusion method. The crystals of DbeA belonged to the primitive orthorhombic space group P2(1)2(1)2(1), while the crystals of DbeA1 belonged to the monoclinic space group C2. Diffraction data were collected to 2.2 A resolution for both DbeA and DbeA1 crystals.
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Affiliation(s)
- Tatyana Prudnikova
- Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
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Thasif S, Hamdan S, Huyop F. Degradation of D,L-2-chloropropionic Acid by Bacterial Dehalogenases that Shows Stereospecificity and its Partial Enzymatic Characteristics. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/biotech.2009.264.269] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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