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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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2
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Wang Y, Xiang Q, Zhou Q, Xu J, Pei D. Mini Review: Advances in 2-Haloacid Dehalogenases. Front Microbiol 2021; 12:758886. [PMID: 34721367 PMCID: PMC8554231 DOI: 10.3389/fmicb.2021.758886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The 2-haloacid dehalogenases (EC 3.8.1.X) are industrially important enzymes that catalyze the cleavage of carbon-halogen bonds in 2-haloalkanoic acids, releasing halogen ions and producing corresponding 2-hydroxyl acids. These enzymes are of particular interest in environmental remediation and environmentally friendly synthesis of optically pure chiral compounds due to their ability to degrade a wide range of halogenated compounds with astonishing efficiency for enantiomer resolution. The 2-haloacid dehalogenases have been extensively studied with regard to their biochemical characterization, protein crystal structures, and catalytic mechanisms. This paper comprehensively reviews the source of isolation, classification, protein structures, reaction mechanisms, biochemical properties, and application of 2-haloacid dehalogenases; current trends and avenues for further development have also been included.
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Affiliation(s)
- Yayue Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Qiao Xiang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, China
- Zhengzhou Tuoyang Industrial Co., Ltd., Zhengzhou, China
| | - Dongli Pei
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
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Che S, Jin B, Liu Z, Yu Y, Liu J, Men Y. Structure-Specific Aerobic Defluorination of Short-Chain Fluorinated Carboxylic Acids by Activated Sludge Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2021; 8:668-674. [PMID: 35316934 PMCID: PMC8936751 DOI: 10.1021/acs.estlett.1c00511] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a large group of manmade chemicals that impose emerging environmental concerns. Among them, short-chain per- and polyfluorinated carboxylic acids represent an important subgroup used as building blocks of biologically active chemicals and functional materials. Some are also considered PFAS alternatives, and some could be byproducts of the physicochemical treatment of PFAS. However, little is known about the environmental fate of short-chain fluorinated carboxylic acids (FCAs) and their defluorination/transformation by microorganisms. To fill the knowledge gap, we investigated the structure-reactivity relationships in the aerobic defluorination of C3-C5 FCAs by activated sludge communities. Four structures exhibited greater than 20% defluorination, with 3,3,3-trifluoropropionic acid being almost completely defluorinated. We further analyzed the defluorination/transformation pathways and inferred the structures susceptible to aerobic microbial defluorination. We also demonstrated that the defluorination was via cometabolism. The findings advance the fundamental understanding of aerobic microbial defluorination and help assess the environmental fate of PFAS. Since some short-chain PFAS, such as 3,3,3-trifluoropropionic acid, are the incomplete defluorination byproducts of advanced reduction processes, their defluorination by activated sludge communities sheds light on the development of cost-effective chemical-biological PFAS treatment train systems.
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Affiliation(s)
- Shun Che
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Bosen Jin
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Zekun Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Yaochun Yu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jinyong Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Molecular Cloning and Expression of Haloacid Dehalogenase Gene from a Local Pseudomonas aeruginosa ITB1 Strain and Tertiary Structure Prediction of the Produced Enzyme. JURNAL KIMIA SAINS DAN APLIKASI 2021. [DOI: 10.14710/jksa.24.5.161-169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Organohalogens are widely utilized as pesticides, herbicides, solvents, and for many other industrial purposes. However, the use of these compounds caused some negative impacts to the environment due to their toxicity and persistency. In the light of this, some microbes have been identified and employed to perform dehalogenation, converting halogenated organic compounds to non-toxic materials. In this research, we successfully cloned and sequenced the haloacid dehalogenase gene from a local Pseudomonas aeruginosa ITB1 strain, which is involved in the degradation of monochloroacetate. First, the haloacid dehalogenase gene was amplified by PCR using a pair of primers designed from the same gene sequences of other P. aeruginosa strains available in the GenBank. The cloned gene in pGEM-T in E. coli TOP10 was sequenced, analyzed, and then sub-cloned into pET-30a(+) for expression in E. coli BL21 (DE3). To facilitate direct sub-cloning, restriction sequences of EcoRI (G/AATTC) and HindIII (A/AGCTT) were added to the forward and reversed primers, respectively. The expressed protein in E. coli BL21 (DE3) appeared as a 26-kDa protein in SDS-PAGE analysis, which is in good agreement with the size predicted by ExPASy Protparam. We obtained that the best expression in LB liquid medium was achieved with 0.01 mM IPTG induction at 30°C incubation for 3 hours. We also found that the enzyme is more concentrated in the pellet cells as inclusion bodies. Furthermore, the in-silico analysis revealed that this enzyme consists of 233 amino acid residues. This enzyme’s predicted tertiary structure shows six β-sheets flanked by α-helixes and thus belongs to Group II haloacid dehalogenase. Based on the structural prediction, amino acid residues of Asp7, Ser121, and Asn122 are present in the active site and might play essential roles in catalysis. The presented study laid the foundation for recombinant haloacid dehalogenase production from P. aeruginosa local strains. It provided an insight into the utilization of recombinant local strains to remediate environmental problems caused by organohalogens.
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Sobrado P. Role of reduced flavin in dehalogenation reactions. Arch Biochem Biophys 2020; 697:108696. [PMID: 33245912 DOI: 10.1016/j.abb.2020.108696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022]
Abstract
Halogenated organic compounds are extensively used in the cosmetic, pharmaceutical, and chemical industries. Several naturally occurring halogen-containing natural products are also produced, mainly by marine organisms. These compounds accumulate in the environment due to their chemical stability and lack of biological pathways for their degradation. However, a few enzymes have been identified that perform dehalogenation reactions in specific biological pathways and others have been identified to have secondary activities toward halogenated compounds. Various mechanisms for dehalogenation of I, Cl, Br, and F containing compounds have been elucidated. These have been grouped into reductive, oxidative, and hydrolytic mechanisms. Flavin-dependent enzymes have been shown to catalyze oxidative dehalogenation reactions utilizing the C4a-hydroperoxyflavin intermediate. In addition, flavoenzymes perform reductive dehalogenation, forming transient flavin semiquinones. Recently, flavin-dependent enzymes have also been shown to perform dehalogenation reactions where the reduced form of the flavin produces a covalent intermediate. Here, recent studies on the reactions of flavoenzymes in dehalogenation reactions, with a focus on covalent catalytic dehalogenation mechanisms, are described.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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Johnson BM, Shu YZ, Zhuo X, Meanwell NA. Metabolic and Pharmaceutical Aspects of Fluorinated Compounds. J Med Chem 2020; 63:6315-6386. [PMID: 32182061 DOI: 10.1021/acs.jmedchem.9b01877] [Citation(s) in RCA: 310] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The applications of fluorine in drug design continue to expand, facilitated by an improved understanding of its effects on physicochemical properties and the development of synthetic methodologies that are providing access to new fluorinated motifs. In turn, studies of fluorinated molecules are providing deeper insights into the effects of fluorine on metabolic pathways, distribution, and disposition. Despite the high strength of the C-F bond, the departure of fluoride from metabolic intermediates can be facile. This reactivity has been leveraged in the design of mechanism-based enzyme inhibitors and has influenced the metabolic fate of fluorinated compounds. In this Perspective, we summarize the literature associated with the metabolism of fluorinated molecules, focusing on examples where the presence of fluorine influences the metabolic profile. These studies have revealed potentially problematic outcomes with some fluorinated motifs and are enhancing our understanding of how fluorine should be deployed.
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Affiliation(s)
- Benjamin M Johnson
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Yue-Zhong Shu
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Xiaoliang Zhuo
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A Meanwell
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Company, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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7
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The mechanistic role of active site residues in non-stereo haloacid dehalogenase E (DehE). J Mol Graph Model 2019; 90:219-225. [PMID: 31103914 DOI: 10.1016/j.jmgm.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/21/2019] [Accepted: 05/06/2019] [Indexed: 11/22/2022]
Abstract
Dehalogenase E (DehE) is a non-stereospecific enzyme produced by the soil bacterium, Rhizobium sp. RC1. Till now, the catalytic mechanism of DehE remains unclear although several literature concerning its structure and function are available. Since DehE is non-stereospecific, the enzyme was hypothesized to follow a 'direct attack mechanism' for the catalytic breakdown of a haloacid. For a molecular insight, the DehE modelled structure was docked in silico with the substrate 2-chloropropionic acid (2CP) in the active site. The ideal position of DehE residues that allowed a direct attack mechanism was then assessed via molecular dynamics (MD) simulation. It was revealed that the essential catalytic water was hydrogen bonded to the 'water-bearer', Asn114, at a relatively constant distance of ∼2.0 Å after 50 ns. The same water molecule was also closely sited to the catalytic Asp189 at an average distance of ∼2.0 Å, signifying the imperative role of the latter to initiate proton abstraction for water activation. This reaction was crucial to promote a direct attack on the α-carbon of 2CP to eject the halide ion. The water molecule was oriented favourably towards the α-carbon of 2CP at an angle of ∼75°, mirrored by the formation of stable enzyme-substrate orientations throughout the simulation. The data therefore substantiated that the degradation of a haloacid by DehE followed a 'direct attack mechanism'. Hence, this study offers valuable information into future advancements in the engineering of haloacid dehalogenases with improved activity and selectivity, as well as functionality in solvents other than water.
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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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10
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Kondo H, Fujimoto KJ, Tanaka S, Deki H, Nakamura T. Theoretical prediction and experimental verification on enantioselectivity of haloacid dehalogenase l-DEX YL with chloropropionate. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.01.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Affiliation(s)
- Fahrul Huyop
- Universiti Teknologi Malaysia, Faculty of Biosciences and Bioengineering, Johor, Malaysia
| | - Ismaila Yada Sudi
- Universiti Teknologi Malaysia, Faculty of Biosciences and Bioengineering, Johor, Malaysia
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Siwek A, Omi R, Hirotsu K, Jitsumori K, Esaki N, Kurihara T, Paneth P. Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies. Arch Biochem Biophys 2013; 540:26-32. [DOI: 10.1016/j.abb.2013.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 09/14/2013] [Accepted: 09/17/2013] [Indexed: 11/30/2022]
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13
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Hamid AAA, Tengku Abdul Hamid TH, Wahab RA, Huyop F. Identification of functional residues essential for dehalogenation by the non-stereospecific α-haloalkanoic acid dehalogenase fromRhizobiumsp. RC1. J Basic Microbiol 2013; 55:324-30. [DOI: 10.1002/jobm.201300526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Azzmer Azzar Abdul Hamid
- Department of Biotechnology; Kulliyyah of Science, IIUM, Bandar Indera Mahkota; Kuantan Pahang Malaysia
| | | | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science; Universiti Teknologi Malaysia (UTM); Johor Bahru Johor Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering; Universiti Teknologi Malaysia (UTM); Johor Bahru Johor Malaysia
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Schober M, Faber K. Inverting hydrolases and their use in enantioconvergent biotransformations. Trends Biotechnol 2013; 31:468-78. [PMID: 23809848 PMCID: PMC3725421 DOI: 10.1016/j.tibtech.2013.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/14/2013] [Accepted: 05/14/2013] [Indexed: 01/23/2023]
Abstract
Enantioconvergent processes overcome the 50%-yield limits of kinetic resolution. Inverting enzymes are key catalysts for enantioconvergent processes. Enzyme engineering provided improved variants of inverting enzymes.
Owing to the more abundant occurrence of racemic compounds compared to prochiral or meso forms, most enantiomerically pure products are obtained via racemate resolution. This review summarizes (chemo)enzymatic enantioconvergent processes based on the use of hydrolytic enzymes, which are able to invert a stereocenter during catalysis that can overcome the 50%-yield limitation of kinetic resolution. Recent developments are presented in the fields of inverting or retaining sulfatases, epoxide hydrolases and dehalogenases, which allow the production of secondary alcohols or vicinal diols at a 100% theoretical yield from a racemate via enantioconvergent processes.
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Affiliation(s)
- Markus Schober
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Bagherbaigi S, Gicana RG, Lamis RJ, Nemati M, Huyop F. Characterisation of Arthrobacter sp. S1 that can degrade α and β-haloalkanoic acids isolated from contaminated soil. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0595-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Nakayama T, Kamachi T, Jitsumori K, Omi R, Hirotsu K, Esaki N, Kurihara T, Yoshizawa K. Substrate specificity of fluoroacetate dehalogenase: an insight from crystallographic analysis, fluorescence spectroscopy, and theoretical computations. Chemistry 2012; 18:8392-402. [PMID: 22674735 DOI: 10.1002/chem.201103369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 04/19/2012] [Indexed: 11/11/2022]
Abstract
The high substrate specificity of fluoroacetate dehalogenase was explored by using crystallographic analysis, fluorescence spectroscopy, and theoretical computations. A crystal structure for the Asp104Ala mutant of the enzyme from Burkholderia sp. FA1 complexed with fluoroacetate was determined at 1.2 Å resolution. The orientation and conformation of bound fluoroacetate is different from those in the crystal structure of the corresponding Asp110Asn mutant of the enzyme from Rhodopseudomonas palustris CGA009 reported recently (J. Am. Chem. Soc. 2011, 133, 7461). The fluorescence of the tryptophan residues of the wild-type and Trp150Phe mutant enzymes from Burkholderia sp. FA1 incubated with fluoroacetate and chloroacetate was measured to gain information on the environment of the tryptophan residues. The environments of the tryptophan residues were found to be different between the fluoroacetate- and chloroacetate-bound enzymes; this would come from different binding modes of these two substrates in the active site. Docking simulations and QM/MM optimizations were performed to predict favorable conformations and orientations of the substrates. The F atom of the substrate is oriented toward Arg108 in the most stable enzyme-fluoroacetate complex. This is a stable but unreactive conformation, in which the small O-C-F angle is not suitable for the S(N)2 displacement of the F(-) ion. The cleavage of the C-F bond is initiated by the conformational change of the substrate to a near attack conformation (NAC) in the active site. The second lowest energy conformation is appropriate for NAC; the C-O distance and the O-C-F angle are reasonable for the S(N) 2 reaction. The activation energy is greatly reduced in this conformation because of three hydrogen bonds between the leaving F atom and surrounding amino acid residues. Chloroacetate cannot reach the reactive conformation, due to the longer C-Cl bond; this results in an increase of the activation energy despite the weaker C-Cl bond.
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Affiliation(s)
- Tomonori Nakayama
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
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Enhancement of haloacetate dehalogenase production by strain mutation and condition optimization. BIOTECHNOL BIOPROC E 2011. [DOI: 10.1007/s12257-011-0186-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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