1
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Wang QQ, Song J, Wei D. Origin of Chemoselectivity of Halohydrin Dehalogenase-Catalyzed Epoxide Ring-Opening Reactions. J Chem Inf Model 2024. [PMID: 38808649 DOI: 10.1021/acs.jcim.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
By performing molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and QM cluster calculations, the origin of chemoselectivity of halohydrin dehalogenase (HHDH)-catalyzed ring-opening reactions of epoxide with the nucleophilic reagent NO2- has been explored. Four possible chemoselective pathways were considered, and the computed results indicate that the pathway associated with the nucleophilic attack on the Cα position of epoxide by NO2- is most energetically favorable and has an energy barrier of 12.9 kcal/mol, which is close to 14.1 kcal/mol derived from experimental kinetic data. A hydrogen bonding network formed by residues Ser140, Tyr153, and Arg157 can strengthen the electrophilicity of the active site of the epoxide substrate to affect chemoselectivity. To predict the energy barrier trends of the chemoselective transition states, multiple analyses including distortion analysis and electrophilic Parr function (Pk+) analysis were carried out with or without an enzyme environment. The obtained insights should be valuable for the rational design of enzyme-catalyzed and biomimetic organocatalytic epoxide ring-opening reactions with special chemoselectivity.
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Affiliation(s)
- Qian-Qian Wang
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Jinshuai Song
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Donghui Wei
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
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2
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Ma R, Hua X, He CL, Wang HH, Wang ZX, Cui BD, Han WY, Chen YZ, Wan NW. Biocatalytic Thionation of Epoxides for Enantioselective Synthesis of Thiiranes. Angew Chem Int Ed Engl 2022; 61:e202212589. [PMID: 36328962 DOI: 10.1002/anie.202212589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Indexed: 11/06/2022]
Abstract
Expanding the enzymatic toolbox for the green synthesis of valuable molecules is still of high interest in synthetic chemistry and the pharmaceutical industry. Chiral thiiranes are valuable sulfur-containing heterocyclic compounds, but relevant methods for their enantioselective synthesis are limited. Herein, we report a biocatalytic thionation strategy for the enantioselective synthesis of thiiranes, which was developed based on the halohydrin dehalogenase (HHDH)-catalyzed enantioselective ring-opening reaction of epoxides with thiocyanate and a subsequent nonenzymatic rearrangement process. A novel HHDH was identified and engineered for enantioselective biocatalytic thionation of various aryl- and alkyl-substituted epoxides on a preparative scale, affording the corresponding thiiranes in up to 43 % isolated yield and 98 % ee. Large-scale synthesis and useful transformations of chiral thiiranes were also performed to demonstrate the utility and scalability of the biocatalytic thionation strategy.
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Affiliation(s)
- Ran Ma
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Xia Hua
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Cheng-Li He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Hui-Hui Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Zhu-Xiang Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Bao-Dong Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Wen-Yong Han
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Yong-Zheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Nan-Wei Wan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
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3
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Dokli I, Brkljača Z, Švaco P, Tang L, Stepanić V, Majerić Elenkov M. Biocatalytic approach to chiral fluoroaromatic scaffolds. Org Biomol Chem 2022; 20:9734-9741. [PMID: 36440739 DOI: 10.1039/d2ob01955h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ten different fluorinated aromatic epoxides have been tested as potential substrates for halohydrin dehalogenase (HHDH) HheC. The majority of investigated epoxides are useful building blocks in synthetic chemistry applications, with a number of them being polysubstituted. Moderate to high enantioselectivities (ER = 15 → 200) were observed in azidolysis, allowing the synthesis of enantioenriched (R)-azido alcohols containing fluorine in the molecule. In the case where a reaction runs over 50% conversion, enantiopure (S)-epoxides are also available. While o-F-styrene oxide was easily converted into a product, a sterically challenging o-CF3-derivative was not accepted by HheC. In silico probing of the binding site indicates that, in order to accommodate an o-CF3-derivative in the HheC active site, it is necessary to eliminate steric hindrance. Hence, we extended our research by probing several available HheC variants containing relevant modifications in the active site. The active mutant P84V/F86P/T134A/N176A (named HheC-M4) was identified, showing not only high activity towards o-CF3-styrene oxide, but also inverted enantioselectivity (ES = 27). Since (S)-enantioselective HHDHs are rare and therefore valuable for their synthetic application, this enzyme was screened on the initial panel of substrates. The observed (S)-enantioselectivity (ES = 1-111) is ascribed to the formation of the additional space by introduced mutations in HheC-M4, which is also confirmed by classical MD simulations. Successive molecular docking demonstrated that this newly formed tunnel located close to the protein surface is a critical feature of HheC-M4, representing a novel binding site.
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Affiliation(s)
- Irena Dokli
- Ruđer Bošković Institute, Bijenička c. 54, Zagreb 10000, Croatia.
| | - Zlatko Brkljača
- Selvita Ltd, Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Petra Švaco
- Ruđer Bošković Institute, Bijenička c. 54, Zagreb 10000, Croatia.
| | - Lixia Tang
- University of Electronic Science and Technology, No. 4, Section 2, North Jianshe Road, Chengdu, China
| | - Višnja Stepanić
- Ruđer Bošković Institute, Bijenička c. 54, Zagreb 10000, Croatia.
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4
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Nastke A, Gröger H. Biocatalytic Synthesis of Heterocycles. HETEROCYCLES 2022. [DOI: 10.1002/9783527832002.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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5
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Xu Q, Huang KS, Wang YF, Wang HH, Cui BD, Han WY, Chen YZ, Wan NW. Stereodivergent Synthesis of Epoxides and Oxazolidinones via the Halohydrin Dehalogenase-Catalyzed Desymmetrization Strategy. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qin Xu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Kai-Shun Huang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Yuan-Fei Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Hui-Hui Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Bao-Dong Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Wen-Yong Han
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Yong-Zheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Nan-Wei Wan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
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6
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Wessel J, Petrillo G, Estevez-Gay M, Bosch S, Seeger M, Dijkman WP, Iglesias-Fernández J, Hidalgo A, Uson I, Osuna S, Schallmey A. Insights into the molecular determinants of thermal stability in halohydrin dehalogenase HheD2. FEBS J 2021; 288:4683-4701. [PMID: 33605544 DOI: 10.1111/febs.15777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/07/2021] [Accepted: 02/15/2021] [Indexed: 11/30/2022]
Abstract
Halohydrin dehalogenases (HHDHs) are promising enzymes for application in biocatalysis due to their promiscuous epoxide ring-opening activity with various anionic nucleophiles. So far, seven different HHDH subtypes A to G have been reported with subtype D containing the by far largest number of enzymes. Moreover, several characterized members of subtype D have been reported to display outstanding characteristics such as high catalytic activity, broad substrate spectra or remarkable thermal stability. Yet, no structure of a D-type HHDH has been reported to date that could be used to investigate and understand those features on a molecular level. We therefore solved the crystal structure of HheD2 from gamma proteobacterium HTCC2207 at 1.6 Å resolution and used it as a starting point for targeted mutagenesis in combination with molecular dynamics (MD) simulation, in order to study the low thermal stability of HheD2 in comparison with other members of subtype D. This revealed a hydrogen bond between conserved residues Q160 and D198 to be connected with a high catalytic activity of this enzyme. Moreover, a flexible surface region containing two α-helices was identified to impact thermal stability of HheD2. Exchange of this surface region by residues of HheD3 yielded a variant with 10 °C higher melting temperature and reaction temperature optimum. Overall, our results provide important insights into the structure-function relationship of HheD2 and presumably for other D-type HHDHs. DATABASES: Structural data are available in PDB database under the accession number 7B73.
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Affiliation(s)
- Julia Wessel
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
| | - Giovanna Petrillo
- Molecular Biology Institute of Barcelona, IBMB-CSIC, Barcelona, Spain
| | - Miquel Estevez-Gay
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Spain
| | - Sandra Bosch
- Centro de Biología Molecular 'Severo Ochoa', UAM-CSIC, Madrid, Spain
| | - Margarita Seeger
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
| | - Willem P Dijkman
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
| | - Javier Iglesias-Fernández
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Spain
| | - Aurelio Hidalgo
- Centro de Biología Molecular 'Severo Ochoa', UAM-CSIC, Madrid, Spain
| | - Isabel Uson
- Molecular Biology Institute of Barcelona, IBMB-CSIC, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Spain.,ICREA, Barcelona, Spain
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
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7
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Conformational Landscapes of Halohydrin Dehalogenases and Their Accessible Active Site Tunnels. Catalysts 2020. [DOI: 10.3390/catal10121403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Halohydrin dehalogenases (HHDH) are industrially relevant biocatalysts exhibiting a promiscuous epoxide-ring opening reactivity in the presence of small nucleophiles, thus giving access to novel carbon–carbon, carbon–oxygen, carbon–nitrogen, and carbon–sulfur bonds. Recently, the repertoire of HHDH has been expanded, providing access to some novel HHDH subclasses exhibiting a broader epoxide substrate scope. In this work, we develop a computational approach based on the application of linear and non-linear dimensionality reduction techniques to long time-scale Molecular Dynamics (MD) simulations to study the HHDH conformational landscapes. We couple the analysis of the conformational landscapes to CAVER calculations to assess their impact on the active site tunnels and potential ability towards bulky epoxide ring opening reaction. Our study indicates that the analyzed HHDHs subclasses share a common breathing motion of the halide binding pocket, but present large deviations in the loops adjacent to the active site pocket and N-terminal regions. Such conformational differences affect the available tunnels for epoxide binding to the active site. The superior activity of the HHDH G subclass towards bulkier substrates is explained by the additional structural elements delimiting the active site region, its rich conformational heterogeneity, and the substantially wider and frequently observed active site tunnels. This study therefore provides key information for HHDH promiscuity and engineering.
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8
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Findrik Blažević Z, Milčić N, Sudar M, Majerić Elenkov M. Halohydrin Dehalogenases and Their Potential in Industrial Application – A Viewpoint of Enzyme Reaction Engineering. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000984] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zvjezdana Findrik Blažević
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia
| | - Nevena Milčić
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia
| | - Martina Sudar
- University of Zagreb Faculty of Chemical Engineering and Technology Savska c. 16 HR-10000 Zagreb Croatia
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9
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Tang XL, Ye GY, Wan XY, Li HW, Zheng RC, Zheng YG. Rational design of halohydrin dehalogenase for efficient chiral epichlorohydrin production with high activity and enantioselectivity in aqueous-organic two-phase system. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Solarczek J, Klünemann T, Brandt F, Schrepfer P, Wolter M, Jacob CR, Blankenfeldt W, Schallmey A. Position 123 of halohydrin dehalogenase HheG plays an important role in stability, activity, and enantioselectivity. Sci Rep 2019; 9:5106. [PMID: 30911023 PMCID: PMC6434027 DOI: 10.1038/s41598-019-41498-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/11/2019] [Indexed: 12/28/2022] Open
Abstract
HheG from Ilumatobacter coccineus is a halohydrin dehalogenase with synthetically useful activity in the ring opening of cyclic epoxides with various small anionic nucleophiles. This enzyme provides access to chiral β-substituted alcohols that serve as building blocks in the pharmaceutical industry. Wild-type HheG suffers from low thermostability, which poses a significant drawback for potential applications. In an attempt to thermostabilize HheG by protein engineering, several single mutants at position 123 were identified which displayed up to 14 °C increased apparent melting temperatures and up to three-fold higher activity. Aromatic amino acids at position 123 resulted even in a slightly higher enantioselectivity. Crystal structures of variants T123W and T123G revealed a flexible loop opposite to amino acid 123. In variant T123G, this loop adopted two different positions resulting in an open or partially closed active site. Classical molecular dynamics simulations confirmed a high mobility of this loop. Moreover, in variant T123G this loop adopted a position much closer to residue 123 resulting in denser packing and increased buried surface area. Our results indicate an important role for position 123 in HheG and give first structural and mechanistic insight into the thermostabilizing effect of mutations T123W and T123G.
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Affiliation(s)
- Jennifer Solarczek
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Thomas Klünemann
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106, Braunschweig, Germany
| | - Patrick Schrepfer
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106, Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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11
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Biocatalyzed Synthesis of Statins: A Sustainable Strategy for the Preparation of Valuable Drugs. Catalysts 2019. [DOI: 10.3390/catal9030260] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Statins, inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, are the largest selling class of drugs prescribed for the pharmacological treatment of hypercholesterolemia and dyslipidaemia. Statins also possess other therapeutic effects, called pleiotropic, because the blockade of the conversion of HMG-CoA to (R)-mevalonate produces a concomitant inhibition of the biosynthesis of numerous isoprenoid metabolites (e.g., geranylgeranyl pyrophosphate (GGPP) or farnesyl pyrophosphate (FPP)). Thus, the prenylation of several cell signalling proteins (small GTPase family members: Ras, Rac, and Rho) is hampered, so that these molecular switches, controlling multiple pathways and cell functions (maintenance of cell shape, motility, factor secretion, differentiation, and proliferation) are regulated, leading to beneficial effects in cardiovascular health, regulation of the immune system, anti-inflammatory and immunosuppressive properties, prevention and treatment of sepsis, treatment of autoimmune diseases, osteoporosis, kidney and neurological disorders, or even in cancer therapy. Thus, there is a growing interest in developing more sustainable protocols for preparation of statins, and the introduction of biocatalyzed steps into the synthetic pathways is highly advantageous—synthetic routes are conducted under mild reaction conditions, at ambient temperature, and can use water as a reaction medium in many cases. Furthermore, their high selectivity avoids the need for functional group activation and protection/deprotection steps usually required in traditional organic synthesis. Therefore, biocatalysis provides shorter processes, produces less waste, and reduces manufacturing costs and environmental impact. In this review, we will comment on the pleiotropic effects of statins and will illustrate some biotransformations nowadays implemented for statin synthesis.
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12
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Zhang XJ, Deng HZ, Liu N, Gong YC, Liu ZQ, Zheng YG. Molecular modification of a halohydrin dehalogenase for kinetic regulation to synthesize optically pure (S)-epichlorohydrin. BIORESOURCE TECHNOLOGY 2019; 276:154-160. [PMID: 30623870 DOI: 10.1016/j.biortech.2018.12.103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/24/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Asymmetric synthesis of chiral epichlorohydrin (ECH) from 1,3-dichloro-2-propanol (1,3-DCP) using halohydrin dehalogenases (HHDHs) is of great value due to the 100% theoretical yield and high enantioselectivity. The vital problem in the asymmetric synthesis is to prepare optically pure ECH. In this study, key amino acid residues located at halide ion channels of HheC (P175S/W249P) (HheCPS) were modified to regulate the kinetic parameters. HheCPS I81W, F86N and V94R were constructed with the corresponding halide ion channels destroyed. The catalytically efficiencies (kcat/Km) of the three mutants exhibited 0.38-, 0.23- and 0.23-fold decrease toward (S)-ECH and the reverse reaction was significantly inhibited. As the results, (S)-ECH was synthesized with >99% enantiomeric excess (e.e.) and 63.42%, 67.08% and 57.01% yields, respectively, under 20 mM 1,3-DCP as substrate. To our knowledge, this is the first investigation of the molecule kinetic modification of HHDHs and also the first report for the biosynthesis of optically pure (S)-ECH from 1,3-DCP using HHDHs.
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Affiliation(s)
- Xiao-Jian Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Han-Zhong Deng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Nan Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yi-Chuan Gong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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13
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Wan N, Tian J, Wang H, Tian M, He Q, Ma R, Cui B, Han W, Chen Y. Identification and characterization of a highly S-enantioselective halohydrin dehalogenase from Tsukamurella sp. 1534 for kinetic resolution of halohydrins. Bioorg Chem 2018; 81:529-535. [PMID: 30245234 DOI: 10.1016/j.bioorg.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 02/05/2023]
Abstract
Halohydrin dehalogenases are remarkable enzymes which possess promiscuous catalytic activity and serve as potential biocatalysts for the synthesis of chiral halohydrins, epoxides and β-substituted alcohols. The enzyme HheC exhibits a highly R enantioselectivity in the processes of dehalogenation of vicinal halohydrins and ring-opening of epoxides, which attracts more attentions in organic synthesis. Recently dozens of novel potential halohydrin dehalogenases have been identified by gene mining, however, most of the characterized enzymes showed low stereoselectivity. In this study, a novel halohydrin dehalogenase of HheA10 from Tsukamurella sp. 1534 has been heterologously expressed, purified and characterized. Substrate spectrum and kinetic resolution studies indicated the HheA10 was a highly S enantioselective enzyme toward several halohydrins, which produced the corresponding epoxides with the ee (enantiomeric excess) and E values up to >99% and >200 respectively. Our results revealed the HheA10 was a promising biocatalyst for the synthesis of enantiopure aromatic halohydrins and epoxides via enzymatic kinetic resolution of racemic halohydrins. What's more important, the HheA10 as the first individual halohydrin dehalogenase with the highly S enantioselectivity provides a complementary enantioselectivity to the HheC.
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Affiliation(s)
- Nanwei Wan
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China.
| | - Jiawei Tian
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Huihui Wang
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Meiting Tian
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Qing He
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Ran Ma
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Baodong Cui
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Wenyong Han
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Yongzheng Chen
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China.
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14
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Cross-linked enzyme aggregates (CLEAs) of halohydrin dehalogenase from Agrobacterium radiobacter AD1: Preparation, characterization and application as a biocatalyst. J Biotechnol 2018; 272-273:48-55. [DOI: 10.1016/j.jbiotec.2017.12.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 02/01/2023]
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15
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Dong JJ, Fernández-Fueyo E, Li J, Guo Z, Renirie R, Wever R, Hollmann F. Halofunctionalization of alkenes by vanadium chloroperoxidase from Curvularia inaequalis. Chem Commun (Camb) 2018; 53:6207-6210. [PMID: 28548142 DOI: 10.1039/c7cc03368k] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vanadium-dependent chloroperoxidase from Curvularia inaequalis is a stable and efficient biocatalyst for the hydroxyhalogenation of a broad range of alkenes into halohydrins. Up to 1 200 000 TON with 69 s-1 TOF were observed for the biocatalyst. A bienzymatic cascade to yield epoxides as reaction products is presented.
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Affiliation(s)
- Jia Jia Dong
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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16
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Arabnejad H, Dal Lago M, Jekel PA, Floor RJ, Thunnissen AMWH, Terwisscha van Scheltinga AC, Wijma HJ, Janssen DB. A robust cosolvent-compatible halohydrin dehalogenase by computational library design. Protein Eng Des Sel 2017; 30:173-187. [PMID: 27999093 DOI: 10.1093/protein/gzw068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/02/2016] [Indexed: 01/05/2023] Open
Abstract
To improve the applicability of halohydrin dehalogenase as a catalyst for reactions in the presence of organic cosolvents, we explored a computational library design strategy (Framework for Rapid Enzyme Stabilization by Computational libraries) that involves discovery and in silico evaluation of stabilizing mutations. Energy calculations, disulfide bond predictions and molecular dynamics simulations identified 218 point mutations and 35 disulfide bonds with predicted stabilizing effects. Experiments confirmed 29 stabilizing point mutations, most of which were located in two distinct regions, whereas introduction of disulfide bonds was not effective. Combining the best mutations resulted in a 12-fold mutant (HheC-H12) with a 28°C higher apparent melting temperature and a remarkable increase in resistance to cosolvents. This variant also showed a higher optimum temperature for catalysis while activity at low temperature was preserved. Mutant H12 was used as a template for the introduction of mutations that enhance enantioselectivity or activity. Crystal structures showed that the structural changes in the H12 mutant mostly agreed with the computational predictions and that the enhanced stability was mainly due to mutations that redistributed surface charges and improved interactions between subunits, the latter including better interactions of water molecules at the subunit interfaces.
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Affiliation(s)
- Hesam Arabnejad
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco Dal Lago
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Peter A Jekel
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robert J Floor
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anke C Terwisscha van Scheltinga
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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17
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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18
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Wu Z, Deng W, Tong Y, Liao Q, Xin D, Yu H, Feng J, Tang L. Exploring the thermostable properties of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by a combinatorial directed evolution strategy. Appl Microbiol Biotechnol 2017; 101:3201-3211. [PMID: 28074221 DOI: 10.1007/s00253-017-8090-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/19/2016] [Accepted: 12/23/2016] [Indexed: 01/26/2023]
Abstract
As a crucial factor for biocatalysts, protein thermostability often arises from a combination of factors that are often difficult to rationalize. In this work, the thermostable nature of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) was systematically explored using a combinatorial directed evolution approach. For this, a mutagenesis library of HheC mutants was first constructed using error-prone PCR with low mutagenesis frequency. After screening approximately 2000 colonies, six mutants with eight mutation sites were obtained. Those mutation sites were subsequently combined by adopting several rounds of iterative saturation mutagenesis (ISM) approach. After four rounds of saturation mutagenesis, one best mutant ISM-4 with a 3400-fold improvement in half-life (t 1/2) inactivation at 65 °C, 18 °C increase in apparent T m value, and 20 °C increase in optimum temperature was obtained, compared to wild-type HheC. To the best of our knowledge, the mutant represents the most thermostable HheC variant reported up to now. Moreover, the mutant was as active as wild-type enzyme for the substrate 1,3-dichloro-2-propanol, and they remained most enantioselectivity of wild-type enzyme in the kinetic resolution of rac-2-chloro-1-phenolethanol, exhibiting a great potential for industrial applications. Our structural investigation highlights that surface loop regions are hot spots for modulating the thermostability of HheC, the residues located at these regions contribute to the thermostability of HheC in a cooperative way, and protein rigidity and oligomeric interface connections contribute to the thermostability of HheC. All of these essential factors could be used for further design of an even more thermostable HheC, which, in turn, could greatly facilitate the application of the enzyme as a biocatalyst.
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Affiliation(s)
- Zhiyun Wu
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China
| | - Wenfeng Deng
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China
| | - Yapei Tong
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China
| | - Qian Liao
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China
| | - Dongmin Xin
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China
| | - Huashun Yu
- Research and Development Center, Angel Yeast Co., Ltd., Yichang, China
| | - Juan Feng
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, China. .,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
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19
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Ferrari AR, Rozeboom HJ, Dobruchowska JM, van Leeuwen SS, Vugts ASC, Koetsier MJ, Visser J, Fraaije MW. Discovery of a Xylooligosaccharide Oxidase from Myceliophthora thermophila C1. J Biol Chem 2016; 291:23709-23718. [PMID: 27629413 PMCID: PMC5095424 DOI: 10.1074/jbc.m116.741173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/12/2016] [Indexed: 11/06/2022] Open
Abstract
By inspection of the predicted proteome of the fungus Myceliophthora thermophila C1 for vanillyl-alcohol oxidase (VAO)-type flavoprotein oxidases, a putative oligosaccharide oxidase was identified. By homologous expression and subsequent purification, the respective protein could be obtained. The protein was found to contain a bicovalently bound FAD cofactor. By screening a large number of carbohydrates, several mono- and oligosaccharides could be identified as substrates. The enzyme exhibits a strong substrate preference toward xylooligosaccharides; hence it is named xylooligosaccharide oxidase (XylO). Chemical analyses of the product formed upon oxidation of xylobiose revealed that the oxidation occurs at C1, yielding xylobionate as product. By elucidation of several XylO crystal structures (in complex with a substrate mimic, xylose, and xylobiose), the residues that tune the unique substrate specificity and regioselectivity could be identified. The discovery of this novel oligosaccharide oxidase reveals that the VAO-type flavoprotein family harbors oxidases tuned for specific oligosaccharides. The unique substrate profile of XylO hints at a role in the degradation of xylan-derived oligosaccharides by the fungus M. thermophila C1.
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Affiliation(s)
| | | | - Justyna M Dobruchowska
- Microbial Physiology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen
| | - Sander S van Leeuwen
- Microbial Physiology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen
| | | | | | - Jaap Visser
- the Fungal Genetics and Technology Consultancy, 6700 AJ Wageningen, The Netherlands
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20
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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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21
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Koopmeiners J, Halmschlag B, Schallmey M, Schallmey A. Biochemical and biocatalytic characterization of 17 novel halohydrin dehalogenases. Appl Microbiol Biotechnol 2016; 100:7517-27. [DOI: 10.1007/s00253-016-7493-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/19/2016] [Accepted: 03/22/2016] [Indexed: 01/30/2023]
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22
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Efficient synthesis of (S)-epichlorohydrin in high yield by cascade biocatalysis with halohydrin dehalogenase and epoxide hydrolase mutants. CATAL COMMUN 2015. [DOI: 10.1016/j.catcom.2015.09.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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23
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Hu D, Ye HH, Wu MC, Feng F, Zhu LJ, Yin X, Li JF. Chemoenzymatic preparation of (S)-p-nitrostyrene oxide from p-nitrophenacyl bromide by recombinant Escherichia coli cells expressing a novel halohydrin dehalogenase. CATAL COMMUN 2015. [DOI: 10.1016/j.catcom.2015.05.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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24
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Biocatalysts for the formation of three- to six-membered carbo- and heterocycles. Biotechnol Adv 2015; 33:457-80. [DOI: 10.1016/j.biotechadv.2015.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022]
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25
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Tang L, Liu Y, Jiang R, Zheng Y, Zheng K, Zheng H. A high-throughput adrenaline test for the exploration of the catalytic potential of halohydrin dehalogenases in epoxide ring-opening reactions. Biotechnol Appl Biochem 2015; 62:451-7. [PMID: 25099782 DOI: 10.1002/bab.1278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 08/02/2014] [Indexed: 11/06/2022]
Abstract
The principle of the adrenaline test for enzymes is based on the quantification of periodate-sensitive reaction products with adrenaline to produce a chromogenic compound adrenochrome that can be easily detected. Here, a rapid whole-cell -based adrenaline assay for the activity measurement of halohydrin dehalogenases (HHDHs) in nucleophile-mediated epoxide ring-opening reactions is presented. The assay was validated using two types of model reactions (glycidol with nucleophiles and nitrite with epoxides). Moreover, the reliability of the assay was confirmed by gas chromatography analysis. Our results demonstrated that the developed assay is efficient in both library screening and the evaluation of catalytic diversity and specificity of HHDHs. Thus, the assay represents a valuable tool in the evolution of HHDHs for its industrial applications. Moreover, the adrenaline test exhibits a great potential for enzyme assay and could be easily adopted for other suitable enzymes.
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Affiliation(s)
- Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Yu Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Rongxiang Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Yu Zheng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Kai Zheng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Huayu Zheng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
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26
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Wan NW, Liu ZQ, Xue F, Shen ZY, Zheng YG. A One-Step Biocatalytic Process for (S)-4-Chloro-3-hydroxybutyronitrile using Halohydrin Dehalogenase: A Chiral Building Block for Atorvastatin. ChemCatChem 2015. [DOI: 10.1002/cctc.201500453] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Ricklefs E, Girhard M, Koschorreck K, Smit MS, Urlacher VB. Two-Step One-Pot Synthesis of Pinoresinol from Eugenol in an Enzymatic Cascade. ChemCatChem 2015. [DOI: 10.1002/cctc.201500182] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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28
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Xue F, Liu ZQ, Wang YJ, Wan NW, Zheng YG. Biochemical characterization and biosynthetic application of a halohydrin dehalogenase from Tistrella mobilis ZJB1405. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Wang X, Lin H, Zheng Y, Feng J, Yang Z, Tang L. MDC-Analyzer-facilitated combinatorial strategy for improving the activity and stability of halohydrin dehalogenase from Agrobacterium radiobacter AD1. J Biotechnol 2015; 206:1-7. [PMID: 25896949 DOI: 10.1016/j.jbiotec.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 01/05/2023]
Abstract
Halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) displays a broad substrate range with high regio- and enantioselectivity of both ring-closure and ring-opening reactions, making the enzyme a useful catalyst for the production of optically pure epoxides and β-substituted alcohols. In this study, we report a novel method using an MDC-Analyzer-facilitated combinatorial strategy to improve the activity and stability of HheC by simultaneously randomizing multiple contiguous residues. Six contiguous active-site residues, which are the hotspots for improving the activity of HheC, were simultaneously selected and randomized using the MDC-Analyzer-facilitated combinatorial strategy, resulting in a high-quality mutagenesis library. After screening a total of 1152 clones, three positive mutants were obtained, which exhibited approximately 3.5-5.9-fold higher kcat values than the wild-type HheC toward 1,3-dichloro-2-propanol (1,3-DCP). However, the inactivation half-life of the best mutant (DG9) at 55 °C decreased 9-fold compared with that of the wild-type HheC. To improve the stability of mutant DG9, seven contiguous potential surface amino acids were revealed by using the B-FITTER tool. Two charged amino acids, Glu and Lys, which are more abundant in thermophilic proteins than in their mesophilic counterparts, were selected to substitute those seven amino acids and were combined together via an MDC-Analyzer-facilitated combinatorial strategy. Two mutants displaying 1.6- and 2.3-fold higher half-life τ1/2 (55 °C) values than their DG9 template were obtained after screening only 384 clones. The results indicated that an MDC-Analyzer-facilitated combinatorial strategy represents an efficient tool for the directed evolution of functional enzymes with multiple contiguous targeting sites.
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Affiliation(s)
- Xiong Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Yu Zheng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Juan Feng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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30
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An efficient high-throughput screening assay for rapid directed evolution of halohydrin dehalogenase for preparation of β-substituted alcohols. Appl Microbiol Biotechnol 2015; 99:4019-29. [DOI: 10.1007/s00253-015-6527-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/04/2015] [Accepted: 03/07/2015] [Indexed: 10/23/2022]
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31
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Floor RJ, Wijma HJ, Jekel PA, Terwisscha van Scheltinga AC, Dijkstra BW, Janssen DB. X-ray crystallographic validation of structure predictions used in computational design for protein stabilization. Proteins 2015; 83:940-51. [PMID: 25739581 DOI: 10.1002/prot.24791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/11/2015] [Accepted: 02/14/2015] [Indexed: 11/10/2022]
Abstract
Protein engineering aimed at enhancing enzyme stability is increasingly supported by computational methods for calculation of mutant folding energies and for the design of disulfide bonds. To examine the accuracy of mutant structure predictions underlying these computational methods, crystal structures of thermostable limonene epoxide hydrolase variants obtained by computational library design were determined. Four different predicted effects indeed contributed to the obtained stabilization: (i) enhanced interactions between a flexible loop close to the N-terminus and the rest of the protein; (ii) improved interactions at the dimer interface; (iii) removal of unsatisfied hydrogen bonding groups; and (iv) introduction of additional positively charged groups at the surface. The structures of an eightfold and an elevenfold mutant showed that most mutations introduced the intended stabilizing interactions, and side-chain conformations were correctly predicted for 72-88% of the point mutations. However, mutations that introduced a disulfide bond in a flexible region had a larger influence on the backbone conformation than predicted. The enzyme active sites were unaltered, in agreement with the observed preservation of catalytic activities. The structures also revealed how a c-Myc tag, which was introduced for facile detection and purification, can reduce access to the active site and thereby lower the catalytic activity. Finally, sequence analysis showed that comprehensive mutant energy calculations discovered stabilizing mutations that are not proposed by the consensus or B-FIT methods.
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Affiliation(s)
- Robert J Floor
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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Yao P, Wang L, Yuan J, Cheng L, Jia R, Xie M, Feng J, Wang M, Wu Q, Zhu D. Efficient Biosynthesis of Ethyl (R)-3-Hydroxyglutarate through a One-Pot Bienzymatic Cascade of Halohydrin Dehalogenase and Nitrilase. ChemCatChem 2015. [DOI: 10.1002/cctc.201500061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Schallmey M, Jekel P, Tang L, Majerić Elenkov M, Höffken HW, Hauer B, Janssen DB. A single point mutation enhances hydroxynitrile synthesis by halohydrin dehalogenase. Enzyme Microb Technol 2015; 70:50-7. [DOI: 10.1016/j.enzmictec.2014.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/14/2014] [Accepted: 12/16/2014] [Indexed: 12/19/2022]
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Exploring the enantioselective mechanism of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by iterative saturation mutagenesis. Appl Environ Microbiol 2015; 81:2919-26. [PMID: 25681194 DOI: 10.1128/aem.04153-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) shows great potential in producing valuable chiral epoxides and β-substituted alcohols. The wild-type (WT) enzyme displays a high R-enantiopreference toward most aromatic substrates, whereas no S-selective HheC has been reported to date. To obtain more enantioselective enzymes, seven noncatalytic active-site residues were subjected to iterative saturation mutagenesis (ISM). After two rounds of screening aspects of both activity and enantioselectivity (E), three outstanding mutants (Thr134Val/Leu142Met, Leu142Phe/Asn176His, and Pro84Val/Phe86Pro/Thr134Ala/Asn176Ala mutants) with divergent enantioselectivity were obtained. The two double mutants displayed approximately 2-fold improvement in R-enantioselectivity toward 2-chloro-1-phenylethanol (2-CPE) without a significant loss of enzyme activity compared with the WT enzyme. Strikingly, the Pro84Val/Phe86Pro/Thr134Ala/Asn176Ala mutant showed an inverted enantioselectivity (from an ER of 65 [WT] to an ES of 101) and approximately 100-fold-enhanced catalytic efficiency toward (S)-2-CPE. Molecular dynamic simulation and docking analysis revealed that the phenyl side chain of (S)-2-CPE bound at a different location than that of its R-counterpart; those mutations generated extra connections for the binding of the favored enantiomer, while the eliminated connections reduced binding of the nonfavored enantiomer, all of which could contribute to the observed inverted enantiopreference.
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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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Romashov LV, Khemchyan LL, Gordeev EG, Koshevoy IO, Tunik SP, Ananikov VP. Design of a Bimetallic Au/Ag System for Dechlorination of Organochlorides: Experimental and Theoretical Evidence for the Role of the Cluster Effect. Organometallics 2014. [DOI: 10.1021/om500620u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Leonid V. Romashov
- Zelinsky
Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 47, Moscow 119991, Russia
| | - Levon L. Khemchyan
- Zelinsky
Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 47, Moscow 119991, Russia
| | - Evgeniy G. Gordeev
- Zelinsky
Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 47, Moscow 119991, Russia
| | - Igor O. Koshevoy
- Department
of Chemistry, Saint Petersburg State University, Stary Petergof 198504, Russia
- Department
of Chemistry, University of Eastern Finland, Joensuu 80101, Finland
| | - Sergey P. Tunik
- Department
of Chemistry, Saint Petersburg State University, Stary Petergof 198504, Russia
| | - Valentine P. Ananikov
- Zelinsky
Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp. 47, Moscow 119991, Russia
- Department
of Chemistry, Saint Petersburg State University, Stary Petergof 198504, Russia
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Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining. Appl Environ Microbiol 2014; 80:7303-15. [PMID: 25239895 DOI: 10.1128/aem.01985-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/13/2014] [Indexed: 01/22/2023] Open
Abstract
Halohydrin dehalogenases are very rare enzymes that are naturally involved in the mineralization of halogenated xenobiotics. Due to their catalytic potential and promiscuity, many biocatalytic reactions have been described that have led to several interesting and industrially important applications. Nevertheless, only a few of these enzymes have been made available through recombinant techniques; hence, it is of general interest to expand the repertoire of these enzymes so as to enable novel biocatalytic applications. After the identification of specific sequence motifs, 37 novel enzyme sequences were readily identified in public sequence databases. All enzymes that could be heterologously expressed also catalyzed typical halohydrin dehalogenase reactions. Phylogenetic inference for enzymes of the halohydrin dehalogenase enzyme family confirmed that all enzymes form a distinct monophyletic clade within the short-chain dehydrogenase/reductase superfamily. In addition, the majority of novel enzymes are substantially different from previously known phylogenetic subtypes. Consequently, four additional phylogenetic subtypes were defined, greatly expanding the halohydrin dehalogenase enzyme family. We show that the enormous wealth of environmental and genome sequences present in public databases can be tapped for in silico identification of very rare but biotechnologically important biocatalysts. Our findings help to readily identify halohydrin dehalogenases in ever-growing sequence databases and, as a consequence, make even more members of this interesting enzyme family available to the scientific and industrial community.
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You ZY, Liu ZQ, Zheng YG. Chemical and enzymatic approaches to the synthesis of optically pure ethyl (R)-4-cyano-3-hydroxybutanoate. Appl Microbiol Biotechnol 2013; 98:11-21. [DOI: 10.1007/s00253-013-5357-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 11/29/2022]
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