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Musa MA, Wahab RA, Huyop F. Homology modelling and in silico substrate-binding analysis of a Rhizobium sp. RC1 haloalkanoic acid permease. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1432417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Muhammed Adamu Musa
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences & Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences & Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
- Biology Department, Faculty of Mathematics and Sciences, Universitas Negeri Semarang, Indonesia
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2
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Bajaj A, Kumar A, Yadav S, Kaur G, Bala M, Singh NK, Mathan Kumar R, Manickam N, Mayilraj S. Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes. Int J Syst Evol Microbiol 2016; 66:5228-5235. [PMID: 27619232 DOI: 10.1099/ijsem.0.001500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a Gram-stain negative, non-violaceinpigmented bacterium isolated from an insecticide-contaminated site was characterized by a polyphasic approach. The bacterium was able to grow on three different halogenated compounds namely 1-hlorobutane, 1-hloropropane and 1,2-ichloroethane. As a critical step in the degradation of these haloalkanes, stoichiometric amounts of dechlorination were estimated. Based on selective enrichment method for three months, using a highly contaminated mixed chemical soil, a bacterium was obtained and designated as IITR-71T. Its versatility and novelty led us to further characterize it by polyphasic taxonomy. The 16S rRNA gene sequence (1446 bases) comparison showed highest similarity with those of members of the genus Chromobacterium with the most closely related species to strain IITR-71T being Chromobacterium aquaticum (99.3 %) followed by Chromobacterium haemolyticum (98.6 %) and Chromobacterium piscinae (97.1 %). The major ubiquinone was Q-8. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The DNA G+C content of IITR-71T was estimated to be 61.2 mol%. The genotypic and phenotypic distinctiveness of IITR-71T and its phylogenetic relationships indicate that IITR-71T represents a novel species, for which the name Chromobacterium alkanivorans sp. nov. is proposed. The type strain is IITR-71T (=MTCC 11059T=JCM 30068T=KCTC 52433T).
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Affiliation(s)
- Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Anand Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Shivani Yadav
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Gurwinder Kaur
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Monu Bala
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Nitin Kumar Singh
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Rajendran Mathan Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
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Recent advances on halohydrin dehalogenases-from enzyme identification to novel biocatalytic applications. Appl Microbiol Biotechnol 2016; 100:7827-39. [PMID: 27502414 PMCID: PMC4989007 DOI: 10.1007/s00253-016-7750-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/16/2016] [Accepted: 07/20/2016] [Indexed: 10/25/2022]
Abstract
Halohydrin dehalogenases are industrially relevant enzymes that catalyze the reversible dehalogenation of vicinal haloalcohols with formation of the corresponding epoxides. In the reverse reaction, also other negatively charged nucleophiles such as azide, cyanide, or nitrite are accepted besides halides to open the epoxide ring. Thus, novel C-N, C-C, or C-O bonds can be formed by halohydrin dehalogenases, which makes them attractive biocatalysts for the production of various β-substituted alcohols. Despite the fact that only five individual halohydrin dehalogenase enzyme sequences have been known until recently enabling their heterologous production, a large number of different biocatalytic applications have been reported using these enzymes. The recent characterization of specific sequence motifs has facilitated the identification of novel halohydrin dehalogenase sequences available in public databases and has largely increased the number of recombinantly available enzymes. These will help to extend the biocatalytic repertoire of this enzyme family and to foster novel biotechnological applications and developments in the future. This review gives a general overview on the halohydrin dehalogenase enzyme family and their biochemical properties and further focuses on recent developments in halohydrin dehalogenase biocatalysis and protein engineering.
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Konti A, Mamma D, Hatzinikolaou DG, Kekos D. 3-Chloro-1,2-propanediol biodegradation by Ca-alginate immobilized Pseudomonas putida DSM 437 cells applying different processes: mass transfer effects. Bioprocess Biosyst Eng 2016; 39:1597-609. [PMID: 27262716 DOI: 10.1007/s00449-016-1635-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/30/2016] [Indexed: 10/21/2022]
Abstract
3-Chloro-1,2-propanediol (3-CPD) biodegradation by Ca-alginate immobilized Pseudomonas putida cells was performed in batch system, continuous stirred tank reactor (CSTR), and packed-bed reactor (PBR). Batch system exhibited higher biodegradation rates and 3-CPD uptakes compared to CSTR and PBR. The two continuous systems (CSTR and PBR) when compared at 200 mg/L 3-CPD in the inlet exhibited the same removal of 3-CPD at steady state. External mass-transfer limitations are found negligible at all systems examined, since the observable modulus for external mass transfer Ω ≪ 1 and the Biot number Bi > 1. Intra-particle diffusion resistance had a significant effect on 3-CPD biodegradation in all systems studied, but to a different extent. Thiele modulus was in the range of 2.5 in batch system, but it was increased at 11 when increasing cell loading in the beads, thus lowering significantly the respective effectiveness factor. Comparing the systems at the same cell loading in the beads PBR was less affected by internal diffusional limitations compared to CSTR and batch system, and, as a result, exhibited the highest overall effectiveness factor.
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Affiliation(s)
- Aikaterini Konti
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 157 80, Zografou, Greece
| | - Diomi Mamma
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 157 80, Zografou, Greece
| | - Dimitios G Hatzinikolaou
- Microbial Biotechnology Unit, Sector of Botany, Department of Biology, National and Kapodistrian University of Athens, Athens, Zografou, Greece
| | - Dimitris Kekos
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 157 80, Zografou, Greece.
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Li J, Yi Y, Cheng X, Zhang D, Irfan M. Study on the effect of magnetic field treatment of newly isolated Paenibacillus sp. BOTANICAL STUDIES 2015; 56:2. [PMID: 28510811 PMCID: PMC5430345 DOI: 10.1186/s40529-015-0083-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 01/13/2015] [Indexed: 06/07/2023]
Abstract
BACKGROUND Symbiotic nitrogen fixation in plants occurs in roots with the help of some bacteria which help in soil nitrogen fertility management. Isolation of significant environment friendly bacteria for nitrogen fixation is very important to enhance yield in plants. RESULTS In this study effect of different magnetic field intensity and treatment time was studied on the morphology, physiology and nitrogen fixing capacity of newly isolated Paenibaccilus sp. from brown soil. The bacterium was identified by 16S rDNA sequence having highest similarity (99%) with Paenibacillus sp as revealed by BLAST. Different magnetic intensities such as 100mT, 300mT and 500mT were applied with processing time of 0, 5, 10, 20 and 30 minutes. Of all these treatment 300mT with processing time of 10 minutes was found to be most suitable treatment. Results revealed that magnetic treatment improve the growth rate with shorter generation time leading to increased enzyme activities (catalase, peroxidase and superoxide dismutase) and nitrogen fixing efficiencies. High magnetic field intensity (500mT) caused ruptured cell morphology and decreased enzyme activities which lead to less nitrogen fixation. CONCLUSION It is concluded that appropriate magnetic field intensity and treatment time play a vital role in the growth of soil bacteria which increases the nitrogen fixing ability which affects the yield of plant. These results were very helpful in future breading programs to enhance the yield of soybean.
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Affiliation(s)
- Jie Li
- Key Laboratory of Preservation of Northeast Cultivated Land, Ministry of Agriculture, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer, College of Land and Enviroment, Shenyang Agricultural University, 120 dongling road, Shenyang, 110866 Liaoning China
| | - Yanli Yi
- Key Laboratory of Preservation of Northeast Cultivated Land, Ministry of Agriculture, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer, College of Land and Enviroment, Shenyang Agricultural University, 120 dongling road, Shenyang, 110866 Liaoning China
| | - Xilei Cheng
- Liaoning Academy of Environmental Sciences, Shenyang, China
| | - Dageng Zhang
- Key Laboratory of Preservation of Northeast Cultivated Land, Ministry of Agriculture, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer, College of Land and Enviroment, Shenyang Agricultural University, 120 dongling road, Shenyang, 110866 Liaoning China
| | - Muhammad Irfan
- Bioscience and Biotechnology College, Shenyang Agricultural University, 120 dongling road, Shenyang, 110866 China
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Abstract
Enantiomerically pure epichlorohydrin is a key chiral synthon in the preparation of 4-chloro-3-hydroxybutyrate, pheromones,l-carnitine, and β-adrenergic blockers.
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Affiliation(s)
- Huo-Xi Jin
- School of Food Science and Pharmaceutics
- Zhejiang Ocean University
- Zhoushan 316022
- P. R. China
| | - Xiao-Kun OuYang
- School of Food Science and Pharmaceutics
- Zhejiang Ocean University
- Zhoushan 316022
- P. R. China
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Xue F, Liu ZQ, Wan NW, Zheng YG. Purification, gene cloning, and characterization of a novel halohydrin dehalogenase from Agromyces mediolanus ZJB120203. Appl Biochem Biotechnol 2014; 174:352-64. [PMID: 25069405 DOI: 10.1007/s12010-014-1111-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/22/2014] [Indexed: 11/29/2022]
Abstract
A novel halohydrin dehalogenase (HHDH), catalyzing the transformation of 1,3-dichloro-2-propanol (1,3-DCP) to epichlorohydrin (ECH), was purified from Agromyces mediolanus ZJB120203. The molecular mass of the enzyme was estimated to be 28 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A 735-bp nucleotide fragment was obtained based on the N-terminal and internal amino acid sequences of the purified HHDH. The gene codes a protein sequence with 244 amino acid residues, and the protein sequence shows high similarity to Hhe AAD2 (HHDH from Arthrobacter sp. AD2), defined as Hhe AAm, which is the seventh reported HHDH. Expression of Hhe AAm was carried out in Escherichia coli and purification was performed by nickel-affinity chromatography. The recombinant HheAAm possessed an optimal pH of 8.5 and an optimal temperature of 50 °C and manifested a K m of 4.58 mM and a V max of 3.84 μmol/min(/)mg. The activity of Hhe AAm was not significantly affected by metal ions such as Zn(2+), Ca(2+), Cu(2+), and EDTA, but was strongly inhibited by Hg(2+) and Ag(+). In particular, the Hhe AAm exhibits an enantioselectivity for the conversion of prochiral 1,3-DCP to (S)-ECH. The applications of the Hhe AAm as a catalyst for asymmetric synthesis are promising.
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Affiliation(s)
- Feng Xue
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Huyop F, Cooper R. Degradation of Millimolar Concentration of the Herbicide Dalapon (2,2-Dichloropropionic Acid) byRhizobiumSp. Isolated from Soil. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Carro A, González P, Lorenzo R. Simultaneous derivatization and ultrasound-assisted dispersive liquid–liquid microextraction of chloropropanols in soy milk and other aqueous matrices combined with gas-chromatography–mass spectrometry. J Chromatogr A 2013; 1319:35-45. [DOI: 10.1016/j.chroma.2013.10.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 12/31/2022]
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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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Arif MI, Samin G, van Leeuwen JGE, Oppentocht J, Janssen DB. Novel dehalogenase mechanism for 2,3-dichloro-1-propanol utilization in Pseudomonas putida strain MC4. Appl Environ Microbiol 2012; 78:6128-36. [PMID: 22752160 PMCID: PMC3416625 DOI: 10.1128/aem.00760-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 06/14/2012] [Indexed: 11/20/2022] Open
Abstract
A Pseudomonas putida strain (MC4) that can utilize 2,3-dichloro-1-propanol (DCP) and several aliphatic haloacids and haloalcohols as sole carbon and energy source for growth was isolated from contaminated soil. Degradation of DCP was found to start with oxidation and concomitant dehalogenation catalyzed by a 72-kDa monomeric protein (DppA) that was isolated from cell lysate. The dppA gene was cloned from a cosmid library and appeared to encode a protein equipped with a signal peptide and that possessed high similarity to quinohemoprotein alcohol dehydrogenases (ADHs), particularly ADH IIB and ADH IIG from Pseudomonas putida HK. This novel dehalogenating dehydrogenase has a broad substrate range, encompassing a number of nonhalogenated alcohols and haloalcohols. With DCP, DppA exhibited a k(cat) of 17 s(-1). (1)H nuclear magnetic resonance experiments indicated that DCP oxidation by DppA in the presence of 2,6-dichlorophenolindophenol (DCPIP) and potassium ferricyanide [K(3)Fe(CN)(6)] yielded 2-chloroacrolein, which was oxidized to 2-chloroacrylic acid.
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Affiliation(s)
- Muhammad Irfan Arif
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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12
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Samin G, Janssen DB. Transformation and biodegradation of 1,2,3-trichloropropane (TCP). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2012; 19:3067-78. [PMID: 22875418 PMCID: PMC3414701 DOI: 10.1007/s11356-012-0859-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/09/2012] [Indexed: 05/04/2023]
Abstract
PURPOSE 1,2,3-Trichloropropane (TCP) is a persistent groundwater pollutant and a suspected human carcinogen. It is also is an industrial chemical waste that has been formed in large amounts during epichlorohydrin manufacture. In view of the spread of TCP via groundwater and its toxicity, there is a need for cheap and efficient technologies for the cleanup of TCP-contaminated sites. In situ or on-site bioremediation of TCP is an option if biodegradation can be achieved and stimulated. This paper presents an overview of methods for the remediation of TCP-contaminated water with an emphasis on the possibilities of biodegradation. CONCLUSIONS Although TCP is a xenobiotic chlorinated compound of high chemical stability, a number of abiotic and biotic conversions have been demonstrated, including abiotic oxidative conversion in the presence of a strong oxidant and reductive conversion by zero-valent zinc. Biotransformations that have been observed include reductive dechlorination, monooxygenase-mediated cometabolism, and enzymatic hydrolysis. No natural organisms are known that can use TCP as a carbon source for growth under aerobic conditions, but anaerobically TCP may serve as electron acceptor. The application of biodegradation is hindered by low degradation rates and incomplete mineralization. Protein engineering and genetic modification can be used to obtain microorganisms with enhanced TCP degradation potential.
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Affiliation(s)
- Ghufrana Samin
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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Jin HX, Hu ZC, Liu ZQ, Zheng YG. Nitrite-mediated synthesis of chiral epichlorohydrin using halohydrin dehalogenase from Agrobacterium radiobacter AD1. Biotechnol Appl Biochem 2012; 59:170-7. [DOI: 10.1002/bab.1004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/18/2012] [Indexed: 11/07/2022]
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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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González P, Racamonde I, Carro AM, Lorenzo RA. Combined solid-phase extraction and gas chromatography-mass spectrometry used for determination of chloropropanols in water. J Sep Sci 2011; 34:2697-704. [DOI: 10.1002/jssc.201100312] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 06/16/2011] [Accepted: 06/22/2011] [Indexed: 11/08/2022]
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Badawi HM, Ali SA. A study of the conformational stability and the vibrational spectra of 2,3-dichloro-1-propanol. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:734-738. [PMID: 20022293 DOI: 10.1016/j.saa.2009.11.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Revised: 11/16/2009] [Accepted: 11/18/2009] [Indexed: 05/28/2023]
Abstract
The conformational stability and the three rotor internal rotations in 2,3-dichloro-1-propanol were investigated at DFT-B3LYP/6-311+G**, MP2/6-311+G** and MP4(SDQ) levels of theory. From the calculated potential energy surface, ten distinct minima were located all of which were predicted to have real frequencies at the B3LYP level of theory. The calculated lowest energy minima in the potential curves of the molecule were predicted to correspond to the Ggg and Gtg1 structures. The observed broad and very intense infrared band centered at about 3370 cm(-1) supports the existence of the strong intermolecular H-bonding in 2,3-dichloro-1-propanol. The equilibrium constants for the conformational interconversion in the molecule were estimated from the calculated Gibb's energies at the B3LYP/6-311+G** level of calculation and found to correspond to an equilibrium mixture of about 49% Ggg, 27% Gtg1, 5% Ggt and 5% Tgg conformations at 298.15K.
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Affiliation(s)
- Hassan M Badawi
- Department of Chemistry, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia.
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Badawi HM, Förner W. Analysis of vibrational spectra of 3-halo-1-propanols CH(2)XCH(2)CH(2)OH (X is Cl and Br). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 71:1095-1101. [PMID: 18417416 DOI: 10.1016/j.saa.2008.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 03/03/2008] [Indexed: 05/26/2023]
Abstract
The conformational stability and the three rotor internal rotations in 3-chloro- and 3-bromo-1-propanols were investigated by DFT-B3LYP/6-311+G and ab initio MP2/6-311+G, MP3/6-311+G and MP4(SDTQ)//MP3/6-311+G levels of theory. On the calculated potential energy surface twelve distinct minima were located all of which were not predicted to have imaginary frequencies at the B3LYP level of theory. The calculated lowest energy minimum in the potential curves of both molecules was predicted to correspond to the Gauche-gauche-trans (Ggt) conformer in excellent agreement with earlier microwave and electron diffraction results. The equilibrium constants for the conformational interconversion of the two 3-halo-1-propanols were calculated at the B3LYP/6-311+G level of calculation and found to correspond to an equilibrium mixture of about 32% Ggt, 18% Ggg1, 13% Tgt, 8% Tgg and 8% Gtt conformations for 3-chloro-1-propanol and 34% Ggt, 15% Tgt, 13% Ggg1, 9% Tgg and 7% Gtt conformations for 3-bromo-1-propanol at 298.15K. The nature of the high energy conformations was verified by carrying out solvent experiments using formamide ( epsilon=109.5) and MP3 and MP4//MP3 calculations. The vibrational frequencies of each molecule in its three most stable forms were computed at the B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecules.
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Affiliation(s)
- Hassan M Badawi
- Department of Chemistry, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
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Badawi HM, Förner W. Solvent dependence of conformational stability and analysis of vibrational spectra of 2,2,3,3,3-pentafluoro-1-propanol. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 71:388-397. [PMID: 18280783 DOI: 10.1016/j.saa.2007.12.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Revised: 12/26/2007] [Accepted: 12/27/2007] [Indexed: 05/25/2023]
Abstract
The conformational stability of 2,2,3,3,3-pentafluoro-1-propanol was investigated by the DFT-B3LYP/6-311+G** and the ab initio MP2/6-311+G** calculations. The calculated potential energy curves of 2,2,3,3,3-pentafluoro-1-propanol at both levels of theory were consistent with three distinct minima that correspond to Trans-gauche-gauche (Tgg), trans-trans-gauche (Ttg) and trans-gauche-gauche(-) (Tgg1) conformers in the order of decreasing relative stability. The equilibrium constants for the conformational interconversion of 2,2,3,3,3-pentafluoro-1-propanol were calculated and found to correspond to an equilibrium mixture of about 46% Tgg, 43% Ttg and 11% Tgg1 conformations at 298.15K. The calculated (%Ttg/%Tgg) ratio of 0.93 is consistent with the 0.85 ratio of the observed intensities of the 772 and 794 cm(-1) lines in the Raman spectrum of the liquid. The nature of the high energy Ttg conformation was verified by solvent experiments using formamide (epsilon = 109.5) and acetonitrile (epsilon = 37). The vibrational frequencies of the molecule in its stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.
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Affiliation(s)
- Hassan M Badawi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia.
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Holtze MS, Sørensen SR, Sørensen J, Aamand J. Microbial degradation of the benzonitrile herbicides dichlobenil, bromoxynil and ioxynil in soil and subsurface environments--insights into degradation pathways, persistent metabolites and involved degrader organisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2008; 154:155-168. [PMID: 17988770 DOI: 10.1016/j.envpol.2007.09.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 09/05/2007] [Accepted: 09/20/2007] [Indexed: 05/25/2023]
Abstract
The benzonitriles dichlobenil, bromoxynil and ioxynil are important broad-spectrum or selective herbicides used in agriculture, orchards and public areas worldwide. The dichlobenil metabolite 2,6-dichlorobenzamide is the most frequently encountered groundwater contaminant in Denmark, which suggests that the environmental fate of these three structurally related benzonitrile herbicides should be addressed in detail. This review summarises the current knowledge on microbial degradation of dichlobenil, bromoxynil and ioxynil with particular focus on common features of degradation rates and pathways, accumulation of persistent metabolites and diversity of the involved degrader organisms.
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Affiliation(s)
- Maria S Holtze
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, 1350 Copenhagen K, Denmark
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Badawi HM, Förner W, Ali SA. Three rotor potential energy scans, conformational equilibrium constants and vibrational analysis of 3-fluoro-1-propanol CH(2)FCH(2)CH(2)OH. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 69:263-71. [PMID: 17485239 DOI: 10.1016/j.saa.2007.03.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 03/19/2007] [Indexed: 05/15/2023]
Abstract
The conformational stability and the three rotor internal rotations in 3-fluoro-1-propanol were investigated by the DFT-B3LYP/6-311+G** and the ab initio MP2/6-311+G** levels of theory. The calculated potential energy curves of the molecule at both levels of theory were consistent with complex conformational equilibria of about 12 minima, all of which were predicted to have real frequencies at both the B3LYP and the MP2 levels. The lowest energy minimum in the potential curves of 3-fluoro-1-propanol was predicted to correspond to the Gauche-gauche-trans (Ggt) conformer in excellent agreement with microwave and electron diffraction results. The equilibrium constants for the conformational interconversion of the molecule were calculated and found to correspond to an equilibrium mixture of about 33% Ggt, 14% Ggg1 and 13% Gg1g and about 43% Ggt, 12% Ggg1 and 10% Gg1g distribution by the B3LYP/6-311+G** and the MP2/6-311+G** calculations, respectively, at 298.15K. The vibrational frequencies of each molecule in its three stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.
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Affiliation(s)
- Hassan M Badawi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia.
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21
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Badawi HM, Förner W. Conformational analysis and vibrational assignments of 2,2,3,3-tetrafluoro-1-propanol CHF2CF2CH2OH as three-rotors system. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2007; 66:1352-60. [PMID: 16920008 DOI: 10.1016/j.saa.2006.04.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 04/27/2006] [Indexed: 05/11/2023]
Abstract
The conformational stability of 2,2,3,3-tetrafluoro-1-propanol was investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. The calculated potential energy curves of the molecule at DFT-B3LYP level were consistent with five distinct minima that correspond to gauche(-)-gauche-gauche (G1gg), trans-trans-gauche (Ttg), trans-gauche-gauche (Tgg), trans-gauche-gauche(-) (Tgg1) and gauche(-)-gauche-trans (G1gt) conformers in the order of decreasing relative stability. The equilibrium constants for the conformational interconversion of 2,2,3,3-tetrafluoro-1-propanol were calculated and found to correspond to an equilibrium mixture of about 38% G1gg, 28% Ttg, 13% Tgg, 11% Tggt and 10% G1gt conformations at 298.15K. The vibrational frequencies of 2,2,3,3,-tetrafluoro-1-propanol in its five stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.
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Affiliation(s)
- Hassan M Badawi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia.
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22
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Mamma D, Papadopoulou E, Petroutsos D, Christakopoulos P, Kekos D. Removal of 1,3-dichloro2-propanol and 3-chloro1,2-propanediol by the whole cell system of pseudomonas putida DSM 437. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2006; 41:303-13. [PMID: 16484065 DOI: 10.1080/10934520500423154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The removal of 1,3-dichloro-2-propanol (1,3-DCP), 3-chloro-1,2-propanediol (3-CPD) and their mixtures at concentrations up to 1,000 mg . L(-1) by the whole cell system of Pseudomonas putida DSM 437 was investigated. The 1,3-DCP removal rates ranged from 2.36 to 10.55 mg . L(-1) . h(-1); 3-CPD exhibited approximately two times higher removal rates compared to 1,3-DCP for all concentrations tested. Removal of 1,3-DCP and 3-CPD followed first-order kinetics with rate constants of 0.0109 h(-1) and 0.0206 h(-1), respectively. When the whole cell system of P. putida DSM 437 was applied to mixtures of the two halohdrins, complete removal of 1,3-DCP was achieved at 144 h while removal of 3-CPD was completed at times ranging from 72 to 144 h. Time to achieve 50% removal of both halohydrins depends on the initial concentration of each in the mixture. For 1,3-DCP, it ranged from 40.55 h at 200 mg . L(-1) to 53.28 h at 500 mg . L(-1) while the respected values for 3-CPD were 33.39 and 68.91 h.
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Affiliation(s)
- Diomi Mamma
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 157 80, Zografou, Greece
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23
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Higgins TP, Hope SJ, Effendi AJ, Dawson S, Dancer BN. Biochemical and molecular characterisation of the 2,3-dichloro-1-propanol dehalogenase and stereospecific haloalkanoic dehalogenases from a versatile Agrobacterium sp. Biodegradation 2005; 16:485-92. [PMID: 15865161 DOI: 10.1007/s10532-004-5670-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We previously reported the presence of both haloalcohol and haloalkanoate dehalogenase activity in the Agrobacterium sp. strain NHG3. The versatile nature of the organism led us to further characterise the genetic basis of these dehalogenation activities. Cloning and sequencing of the haloalcohol dehalogenase and subsequent analysis suggested that it was part of a highly conserved catabolic gene cluster. Characterisation of the haloalkanoate dehalogenase enzyme revealed the presence of two stereospecific enzymes with a narrow substrate range which acted on D-2-chloropropionic and L-2-chloropropionoic acid, respectively. Cloning and sequencing indicated that the two genes were separated by 87 bp of non-coding DNA and were preceded by a putative transporter gene 66 bp upstream of the D-specific enzyme.
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Affiliation(s)
- Timothy P Higgins
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, UK.
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Bel-Rhlid R, Talmon JP, Fay LB, Juillerat MA. Biodegradation of 3-chloro-1,2-propanediol with Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2004; 52:6165-6169. [PMID: 15453682 DOI: 10.1021/jf048980k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A novel enzymatic dehalogenating activity of 3-chloro-1,2-propanediol (3-MCPD) with Saccharomyces cerevisiae (baker's yeast) is reported. All bioconversion assays were carried out under aerobic conditions, at 28 degrees C, and the kinetics were monitored. The biodegradation was performed at different pH values (6.2, 7.0, and 8.2), in the presence and absence of glucose, using racemic 3-MCPD at two different concentrations (7.3 micromol/L and 27 mmol/L). Optimal conversion (68%) of racemic (R,S)-3-MCPD at a concentration of 27 mmol/L was achieved after 48 h of reaction time, at pH 8.2, and in the presence of glucose. At a concentration of 7.3 micromol/L, 73% degradation was observed after 72 h, at pH 8.2 and in the absence of glucose. Under the same experimental conditions, the conversion of pure (S)-3-MCPD (85%) was higher than that of the (R)-enantiomer (60%).
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Affiliation(s)
- Rachid Bel-Rhlid
- Nestlé Research Center, Nestec Ltd., Vers-Chez-les-Blanc, P.O. Box 44, 1000 Lausanne 26, Switzerland
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Yonetani R, Ikatsu H, Miyake-Nakayama C, Fujiwara E, Maehara Y, Miyoshi SI, Matsuoka H, Shinoda S. Isolation and Characterization of a 1,3-Dichloro-2-Propanol-Degrading Bacterium. ACTA ACUST UNITED AC 2004. [DOI: 10.1248/jhs.50.605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Risa Yonetani
- Faculty of Pharmaceutical Sciences, Okayama University
| | - Hisayoshi Ikatsu
- Center for Environmental Science and Technology, Okayama University
| | | | | | - Yoko Maehara
- Faculty of Pharmaceutical Sciences, Okayama University
| | | | - Hideomi Matsuoka
- Seiko PMC Cooperation, Research and Development Division, Ichihara Laboratory
| | - Sumio Shinoda
- Faculty of Pharmaceutical Sciences, Okayama University
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Sawada H, Kuykendall LD, Young JM. Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J GEN APPL MICROBIOL 2003; 49:155-79. [PMID: 12949698 DOI: 10.2323/jgam.49.155] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
As of February 2003, bacteria that form nitrogen-fixing symbiotic associations with legumes have been confirmed in 44 species of 12 genera. Phylogenies of these taxa containing legume symbionts based on the comparative analysis of 16S rDNA sequences show that they are not clustered in one lineage but are distributed in the classes Alphaproteobacteria and Betaproteobacteria, and dispersed over the following nine monophyletic groups, being intermingled with other taxa that do not contain legume symbionts (shown in parentheses below): Group 1, which comprises Rhizobium and Allorhizobium species containing legume symbionts (intermingled with Agrobacterium and Blastobacter species, which are nonsymbionts); Group 2, Sinorhizobium and Ensifer species (with unclassified nonsymbionts); Group 3, Mesorhizobium species (with nonsymbiotic Aminobacter and Pseudaminobacter species); Group 4, Bradyrhizobium species and Blastobacter denitrificans (with nonsymbiotic Agromonas, Nitrobacter, Afipia, and Rhodopseudomonas species); Group 5, 'Methylobacterium nodulans" (with nonsymbiotic Methylobacterium species); Group 6, Azorhizobium species (with nonsymbiotic Xanthobacter and Aquabacter species); Group 7, 'Devosia neptuniae" (with nonsymbiotic Devosia species and unclassified nonsymbionts); Group 8, symbiotic Burkholderia strains (with nonsymbiotic Burkholderia species); and Group 9, Ralstonia taiwanensis (with nonsymbiotic Ralstonia species). For Groups 5, 8, and 9, the present classification, in which 'each monophyletic group comprises one genus wherein legume symbionts and nonsymbionts are intermingled with each other, " is considered to be retained as is because they are clearly separated from other genera at high bootstrap values and have already been sufficiently characterized based on polyphasic taxonomy. As for the remaining six monophyletic groups, on the other hand, there are currently three options for emending their current classification (definitions and circumscriptions) at the generic level: A) the current classification shall be retained as is; B) all the genera within each monophyletic group shall be amalgamated into one single genus in conformity with the results of phylogenetic analysis; or C) each subordinate lineage in each monophyletic group shall be proposed as a genus. It is considered that research and discussions will be continuously conducted for emending the classification of these monophyletic groups based chiefly on Options B and C as preferable candidates.
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Affiliation(s)
- Hiroyucki Sawada
- National Institute for Agro-Environmental Sciences, Tsukuba 305-8604, Japan.
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Tang L, van Hylckama Vlieg JE, Lutje Spelberg JH, Fraaije MW, Janssen DB. Improved stability of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by replacement of cysteine residues. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(01)00488-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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van Hylckama Vlieg JE, Tang L, Lutje Spelberg JH, Smilda T, Poelarends GJ, Bosma T, van Merode AE, Fraaije MW, Janssen DB. Halohydrin dehalogenases are structurally and mechanistically related to short-chain dehydrogenases/reductases. J Bacteriol 2001; 183:5058-66. [PMID: 11489858 PMCID: PMC95381 DOI: 10.1128/jb.183.17.5058-5066.2001] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halohydrin dehalogenases, also known as haloalcohol dehalogenases or halohydrin hydrogen-halide lyases, catalyze the nucleophilic displacement of a halogen by a vicinal hydroxyl function in halohydrins to yield epoxides. Three novel bacterial genes encoding halohydrin dehalogenases were cloned and expressed in Escherichia coli, and the enzymes were shown to display remarkable differences in substrate specificity. The halohydrin dehalogenase of Agrobacterium radiobacter strain AD1, designated HheC, was purified to homogeneity. The k(cat) and K(m) values of this 28-kDa protein with 1,3-dichloro-2-propanol were 37 s(-1) and 0.010 mM, respectively. A sequence homology search as well as secondary and tertiary structure predictions indicated that the halohydrin dehalogenases are structurally similar to proteins belonging to the family of short-chain dehydrogenases/reductases (SDRs). Moreover, catalytically important serine and tyrosine residues that are highly conserved in the SDR family are also present in HheC and other halohydrin dehalogenases. The third essential catalytic residue in the SDR family, a lysine, is replaced by an arginine in halohydrin dehalogenases. A site-directed mutagenesis study, with HheC as a model enzyme, supports a mechanism for halohydrin dehalogenases in which the conserved Tyr145 acts as a catalytic base and Ser132 is involved in substrate binding. The primary role of Arg149 may be lowering of the pK(a) of Tyr145, which abstracts a proton from the substrate hydroxyl group to increase its nucleophilicity for displacement of the neighboring halide. The proposed mechanism is fundamentally different from that of the well-studied hydrolytic dehalogenases, since it does not involve a covalent enzyme-substrate intermediate.
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Affiliation(s)
- J E van Hylckama Vlieg
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NL-9747 AG Groningen, The Netherlands
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