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Crystal structure and site-directed mutagenesis analyses of haloalkane dehalogenase LinB from Sphingobium sp. strain MI1205. J Bacteriol 2013; 195:2642-51. [PMID: 23564170 DOI: 10.1128/jb.02020-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzymes LinB(UT) and LinB(MI) (LinB from Sphingobium japonicum UT26 and Sphingobium sp. MI1205, respectively) catalyze the hydrolytic dechlorination of β-hexachlorocyclohexane (β-HCH) and yield different products, 2,3,4,5,6-pentachlorocyclohexanol (PCHL) and 2,3,5,6-tetrachlorocyclohexane-1,4-diol (TCDL), respectively, despite their 98% identity in amino acid sequence. To reveal the structural basis of their different enzymatic properties, we performed site-directed mutagenesis and X-ray crystallographic studies of LinB(MI) and its seven point mutants. The mutation analysis revealed that the seven amino acid residues uniquely found in LinB(MI) were categorized into three groups based on the efficiency of the first-step (from β-HCH to PCHL) and second-step (from PCHL to TCDL) conversions. Crystal structure analyses of wild-type LinB(MI) and its seven point mutants indicated how each mutated residue contributed to the first- and second-step conversions by LinB(MI). The dynamics simulation analyses of wild-type LinB(MI) and LinB(UT) revealed that the entrance of the substrate access tunnel of LinB(UT) was more flexible than that of LinB(MI), which could lead to the different efficiencies of dehalogenation activity between these dehalogenases.
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Degtjarik O, Chaloupkova R, Rezacova P, Kuty M, Damborsky J, Kuta Smatanova I. Differences in crystallization of two LinB variants from Sphingobium japonicum UT26. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:284-7. [PMID: 23519805 PMCID: PMC3606575 DOI: 10.1107/s1744309113002467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/24/2013] [Indexed: 11/11/2022]
Abstract
Haloalkane dehalogenases are microbial enzymes that convert a broad range of halogenated aliphatic compounds to their corresponding alcohols by the hydrolytic mechanism. These enzymes play an important role in the biodegradation of various environmental pollutants. Haloalkane dehalogenase LinB isolated from a soil bacterium Sphingobium japonicum UT26 has a relatively broad substrate specificity and can be applied in bioremediation and biosensing of environmental pollutants. The LinB variants presented here, LinB32 and LinB70, were constructed with the goal of studying the effect of mutations on enzyme functionality. In the case of LinB32 (L117W), the introduced mutation leads to blocking of the main tunnel connecting the deeply buried active site with the surrounding solvent. The other variant, LinB70 (L44I, H107Q), has the second halide-binding site in a position analogous to that in the related haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94. Both LinB variants were successfully crystallized and full data sets were collected for native enzymes as well as their complexes with the substrates 1,2-dibromoethane (LinB32) and 1-bromobutane (LinB70) to resolutions ranging from 1.6 to 2.8 Å. The two mutants crystallize differently from each other, which suggests that the mutations, although deep inside the molecule, can still affect the protein crystallizability.
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Affiliation(s)
- Oksana Degtjarik
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and Institute of Complex Systems, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, 37333 Ceske Budejovice, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Pavlina Rezacova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 108, 14220 Prague, Czech Republic
| | - Michal Kuty
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and Institute of Complex Systems, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Ivana Kuta Smatanova
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and Institute of Complex Systems, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic
- Institute of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 37333 Nove Hrady, Czech Republic
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Sato Y, Natsume R, Tsuda M, Damborsky J, Nagata Y, Senda T. Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:294-6. [PMID: 17401198 PMCID: PMC2330215 DOI: 10.1107/s1744309107008652] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 02/21/2007] [Indexed: 11/10/2022]
Abstract
Haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. The haloalkane dehalogenase DbjA constitutes a novel substrate-specificity class with high catalytic activity for beta-methylated haloalkanes. In order to reveal the mechanism of its substrate specificity, DbjA has been crystallized using the hanging-drop vapour-diffusion method. The best crystals were obtained using the microseeding technique with a reservoir solution consisting of 17-19.5%(w/v) PEG 4000, 0.2 M calcium acetate and 0.1 M Tris-HCl pH 7.7-8.0. The space group of the DbjA crystal is P2(1)2(1)2, with unit-cell parameters a = 212.9, b = 117.8, c = 55.8 A. The crystal diffracts to 1.75 A resolution.
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Affiliation(s)
- Yukari Sato
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
- Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ryo Natsume
- Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masataka Tsuda
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Jiri Damborsky
- Loschmidt Laboratories, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic
| | - Yuji Nagata
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Toshiya Senda
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
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Wu J, Hong Q, Han P, He J, Li S. A gene linB2 responsible for the conversion of β-HCH and 2,3,4,5,6-pentachlorocyclohexanol in Sphingomonas sp. BHC-A. Appl Microbiol Biotechnol 2007; 73:1097-105. [PMID: 16977465 DOI: 10.1007/s00253-006-0579-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 07/09/2006] [Accepted: 07/10/2006] [Indexed: 10/24/2022]
Abstract
Commercial formulations of hexachlorocyclohexane (HCH) consist of a mixture of four isomers: alpha, beta, gamma, and delta. All four isomers are toxic and recalcitrant pollutants. beta-HCH is more problematic due to its longer persistence in the environment. Sphingomonas sp. BHC-A was able to degrade not only alpha-, gamma-, and delta-HCH but also beta-HCH. To clone a gene responsible for the degradation of beta-HCH, a Tn5 mutation was introduced into BHC-A, and one mutant BHC-A45 defective in beta-HCH degradation was selected. Sequencing analysis showed this mutant had a Tn5 insertion at the site of one haloalkane dehalogenase gene, designated linB2. linB2 was overexpressed in Escherichia coli and the 32-kDa product LinB2 showed the conversion activity of not only beta-HCH to beta-2,3,4,5,6-pentachlorocyclohexanol (beta-PCHL) but also beta-PCHL to beta-2,3,5,6-tetrachloro-1,4-cyclohexanediol.
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Affiliation(s)
- Jun Wu
- Department of Microbiology, Nanjing Agricultural University, 6 Tongwei Rd, Nanjing, Jiangsu Province, 210095, People's Republic of China
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Oakley AJ, Klvana M, Otyepka M, Nagata Y, Wilce MCJ, Damborský J. Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Biochemistry 2004; 43:870-8. [PMID: 14744129 DOI: 10.1021/bi034748g] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the structure of LinB, a 33-kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in two conformations, one similar to that observed previously (conformation A) and one strained (conformation B) that approached the catalytic base (His272). The strain in conformation B was mainly in the C(alpha)-C(beta)-C(gamma) angle (126 degrees ) that deviated by 13.4 degrees from the "ideal" bond angle of 112.6 degrees. On the basis of these observations, we propose a role for the charge state of the catalytic histidine in determining the geometry of the catalytic residues. We hypothesized that double-protonation of the catalytic base (His272) reduces the distance between the side-chain of this residue and that of the Asp108. The results of molecular dynamics simulations were consistent with the structural data showing that protonation of the His272 side-chain nitrogen atoms does indeed reduce the distance between the side-chains of the residues in question, although the simulations failed to demonstrate the same degree of strain in the Asp108 C(alpha)-C(beta)-C(gamma) angle. Instead, the changes in the molecular dynamics structures were distributed over several bond and dihedral angles. Quantum mechanics calculations on LinB with 1-chloro-2,2-dimethylpropane as a substrate were performed to determine which active site conformations and protonation states were most likely to result in catalysis. It was shown that His272 singly protonated at N(delta)(1) and Asp108 in conformation A gave the most exothermic reaction (DeltaH = -22 kcal/mol). With His272 doubly protonated at N(delta)(1) and N(epsilon)(2), the reactions were only slightly exothermic or were endothermic. In all calculations starting with Asp108 in conformation B, the Asp108 C(alpha)-C(beta)-C(gamma) angle changed during the reaction and the Asp108 moved to conformation A. The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB.
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Affiliation(s)
- Aaron J Oakley
- Crystallography Centre, School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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Marek J, Vévodová J, Smatanová IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborský J. Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 2000; 39:14082-6. [PMID: 11087355 DOI: 10.1021/bi001539c] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. Here, we present the 1.58 A crystal structure of LinB and the 2.0 A structure of LinB with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. The enzyme belongs to the alpha/beta hydrolase family and contains a catalytic triad (Asp108, His272, and Glu132) in the lipase-like topological arrangement previously proposed from mutagenesis experiments. The LinB structure was compared with the structures of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 and from Rhodococcus sp. and the structural features involved in the adaptation toward xenobiotic substrates were identified. The arrangement and composition of the alpha-helices in the cap domain results in the differences in the size and shape of the active-site cavity and the entrance tunnel. This is the major determinant of the substrate specificity of this haloalkane dehalogenase.
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Affiliation(s)
- J Marek
- Laboratory of Biomolecular Structure and Dynamics, and Department of Inorganic Chemistry, Faculty of Science, Masaryk University, Kotlárská 2, CZ 611 37 Brno, Czech Republic.
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Abstract
There is an ever increasing flood of structural information and over 1,000 protein structures have been deposited in the Protein Data Base between January 1999 and January 2000. Major advances in the past year in the field of redox enzymes have included the structures of nitric oxide synthases in ligand-free and ligand-bound complexes, and the determination of the multi-subunit mitochondrial bc1 complex. The first,structures of flavocytochrome have also appeared providing insight into novel electron and proton pathways.
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Affiliation(s)
- A W Munro
- Department of Pure and Applied Chemistry, University of Strathclyde, The Royal College, Glasgow, UK
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