1
|
Milčić N, Švaco P, Sudar M, Tang L, Findrik Blažević Z, Majerić Elenkov M. Impact of organic solvents on the catalytic performance of halohydrin dehalogenase. Appl Microbiol Biotechnol 2023; 107:2351-2361. [PMID: 36881116 DOI: 10.1007/s00253-023-12450-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/08/2023]
Abstract
Biocatalytic transformations in organic synthesis often require the use of organic solvents to improve substrate solubility and promote the product formation. Halohydrin dehalogenases (HHDHs) are enzymes that catalyze the formation and conversion of epoxides, important synthetic class of compounds that are often sparingly soluble in water and prone to hydrolysis. In this study, the activity, stability, and enantioselectivity of HHDH from Agrobacterium radiobacter AD1 (HheC) in form of cell-free extract were evaluated in various aqueous-organic media. A correlation was discovered between the enzyme activity in the ring-closure reaction and logP of the solvent. Knowledge of such a relationship makes biocatalysis with organic solvents more predictable, which may reduce the need to experiment with a variety of solvents in the future. The results revealed a high enzyme compatibility with hydrophobic solvents (e.g., n-heptane) in terms of activity and stability. Regarding the HHDH applicability in an organic medium, inhibitions by a number of solvents (e.g., THF, toluene, chloroform) proved to be a more challenging problem than the protein stability, especially in the ring-opening reaction, thus suggesting which solvents should be avoided. In addition, solvent tolerance of the thermostable variant ISM-4 was also evaluated, revealing increased stability and to a lesser extent enantioselectivity compared to the wild-type. This is the first time such a systematic analysis has been reported, giving insight into the behavior of HHDHs in nonconventional media and opening new opportunities for the future biocatalytic applications. KEY POINTS: • HheC performs better in the presence of hydrophobic than hydrophilic solvents. • Enzyme activity in the PNSHH ring-closure reaction is a function of the logP. • Thermostability of ISM-4 variant is accompanied by superior solvent tolerance.
Collapse
Affiliation(s)
- Nevena Milčić
- Faculty of Chemical Engineering and Technology, University of Zagreb, Savska c, 16, Zagreb, Croatia
| | - Petra Švaco
- Ruđer Bošković Institute, Bijenička c, 54, Zagreb, Croatia
| | - Martina Sudar
- Faculty of Chemical Engineering and Technology, University of Zagreb, Savska c, 16, Zagreb, Croatia
| | - Lixia Tang
- University of Electronic Science and Technology, No. 4, Section 2, North Jianshe Road, Chengdu, China
| | | | | |
Collapse
|
2
|
Milčić N, Stepanić V, Crnolatac I, Findrik Blažević Z, Brkljača Z, Majerić Elenkov M. Inhibitory Effect of DMSO on Halohydrin Dehalogenase: Experimental and Computational Insights into the Influence of an Organic Co‐solvent on the Structural and Catalytic Properties of a Biocatalyst. Chemistry 2022; 28:e202201923. [DOI: 10.1002/chem.202201923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Nevena Milčić
- Faculty of Chemical Engineering and Technology University of Zagreb Savska c. 16 10000 Zagreb Croatia
| | - Višnja Stepanić
- Laboratory for Machine Learning and Knowledge Representation Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | | | - Zlatko Brkljača
- Division of Organic Chemistry and Biochemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Maja Majerić Elenkov
- Division of Organic Chemistry and Biochemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| |
Collapse
|
3
|
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
| | | |
Collapse
|
4
|
Gul I, Wang Q, Jiang Q, Fang R, Tang L. Enzyme immobilization on glass fiber membrane for detection of halogenated compounds. Anal Biochem 2020; 609:113971. [PMID: 32979368 DOI: 10.1016/j.ab.2020.113971] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023]
Abstract
Enzyme immobilization using inorganic membranes has enticed increased attention as they not only improve enzyme stability, but also furnish user-friendly biodevices that can be tailored to different applications. Herein, we explored the suitability of the glass fiber membrane for enzyme immobilization and its application for halocarbon detection. For this, halohydrin dehalogenase (HheC) and bovine serum albumin were crosslinked and immobilized on a glass fiber membrane without membrane functionalization. Immobilized HheC exhibited higher storage stability than its free counterpart over 60 days at 4 °C (67% immobilized vs. 8.1% free) and 30 °C (77% immobilized vs. 57% free). Similarly, the thermal endurance of the immobilized HheC was significantly improved. The practical utility of the membrane-immobilized enzyme was demonstrated by colorimetric detection of 1,3-dichloro-2-propanol (1,3-DCP) and 2,3-dibromo-1-propanol (2,3-DBP) as model analytes. Under optimized conditions, the detection limits of 0.06 mM and 0.09 mM were achieved for 1,3-DCP and 2,3-DBP, respectively. The satisfactory recoveries were observed with spiked river and lake water samples, which demonstrate the application potential of immobilized HheC for screening contaminants in water samples. Our results revealed that the proposed frugal and facile approach could be useful for enzyme stabilization, and mitigation of halocarbon pollution.
Collapse
Affiliation(s)
- Ijaz Gul
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qian Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qifa Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Ruiqin Fang
- School of Life Science and Technology, University of Electronic Science and Technology of China, 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, Chengdu, 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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]
|
7
|
One-Pot Combination of Metal- and Bio-Catalysis in Water for the Synthesis of Chiral Molecules. Catalysts 2018. [DOI: 10.3390/catal8020075] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
During the last decade, the combination of different metal- and bio-catalyzed organic reactions in aqueous media has permitted the flourishing of a variety of one-pot asymmetric multi-catalytic reactions devoted to the construction of enantiopure and high added-value chemicals under mild reaction conditions (usually room temperature) and in the presence of air. Herein, a comprehensive account of the state-of-the-art in the development of catalytic networks by combining metallic and biological catalysts in aqueous media (the natural environment of enzymes) is presented. Among others, the combination of metal-catalyzed isomerizations, cycloadditions, hydrations, olefin metathesis, oxidations, C-C cross-coupling and hydrogenation reactions, with several biocatalyzed transformations of organic groups (enzymatic reduction, epoxidation, halogenation or ester hydrolysis), are discussed.
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Luo Y, Chen Y, Ma H, Tian Z, Zhang Y, Zhang J. Enhancing the biocatalytic manufacture of the key intermediate of atorvastatin by focused directed evolution of halohydrin dehalogenase. Sci Rep 2017; 7:42064. [PMID: 28165015 PMCID: PMC5292711 DOI: 10.1038/srep42064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/05/2017] [Indexed: 11/09/2022] Open
Abstract
Halohydrin dehalogenases (HHDHs) are biocatalytically interesting enzymes due to their ability to form C-C, C-N, C-O, and C-S bonds. One of most important application of HHDH was the protein engineering of HheC (halohydrin dehalogenase from Agrobacterium radiobacter AD1) for the industrial manufacturing of ethyl (R)-4-cyano-3-hydroxybutanoate (HN), a key chiral synthon of a cholesterol-lowering drug of atorvastatin. During our development of an alternative, more efficient and economic route for chemo-enzymatic preparation of the intermediate of atorvastatin, we found that the HheC2360 previously reported for HN manufacture, had insufficient activity for the cyanolysis production of tert-butyl (3 R,5 S)-6-cyano-3,5-dihydroxyhexanoate (A7). Herein, we present the focused directed evolution of HheC2360 with higher activity and enhanced biocatalytic performance using active site mutagenesis. Through docking of the product, A7, into the crystal structure of HheC2360, 6 residues was selected for combined active sites testing (CASTing). After library screening, the variant V84G/W86F was identified to have a 15- fold increase in activity. Time course analysis of the cyanolysis reaction catalyzed by this variant, showed 2- fold increase in space time productivity compared with HheC2360. These results demonstrate the applicability of the variant V84G/W86F as a biocatalyst for the efficient and practical production of atorvastatin intermediate.
Collapse
Affiliation(s)
- Yu Luo
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Abiochem Co. LTD, Shanghai, China
| | - Yangzi Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Hongmin Ma
- Key Laboratory of Combinational Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | | | - Yeqi Zhang
- Key Laboratory of Combinational Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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]
|
12
|
Wang X, Han S, Yang Z, Tang L. Improvement of the thermostability and activity of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by engineering C-terminal amino acids. J Biotechnol 2015; 212:92-8. [DOI: 10.1016/j.jbiotec.2015.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/14/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
|
13
|
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]
|
14
|
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]
|
15
|
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.
Collapse
|
16
|
Dvorak P, Bidmanova S, Damborsky J, Prokop Z. Immobilized synthetic pathway for biodegradation of toxic recalcitrant pollutant 1,2,3-trichloropropane. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6859-6866. [PMID: 24787668 DOI: 10.1021/es500396r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The anthropogenic compound 1,2,3-trichloropropane (TCP) has recently drawn attention as an emerging groundwater contaminant. No living organism, natural or engineered, is capable of the efficient aerobic utilization of this toxic industrial waste product. We describe a novel biotechnology for transforming TCP based on an immobilized synthetic pathway. The pathway is composed of three enzymes from two different microorganisms: engineered haloalkane dehalogenase from Rhodococcus rhodochrous NCIMB 13064, and haloalcohol dehalogenase and epoxide hydrolase from Agrobacterium radiobacter AD1. Together, they catalyze consecutive reactions converting toxic TCP to harmless glycerol. The pathway was immobilized in the form of purified enzymes or cell-free extracts, and its performance was tested in batch and continuous systems. Using a packed bed reactor filled with the immobilized biocatalysts, 52.6 mmol of TCP was continuously converted into glycerol within 2.5 months of operation. The efficiency of the TCP conversion to the intermediates was 97%, and the efficiency of conversion to the final product glycerol was 78% during the operational period. Immobilized biocatalysts are suitable for removing TCP from contaminated water up to a 10 mM solubility limit, which is an order of magnitude higher than the concentration tolerated by living microorganisms.
Collapse
Affiliation(s)
- Pavel Dvorak
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic
| | | | | | | |
Collapse
|
17
|
Expression, characterization, and improvement of a newly cloned halohydrin dehalogenase from Agrobacterium tumefaciens and its application in production of epichlorohydrin. J Ind Microbiol Biotechnol 2014; 41:1145-58. [PMID: 24777710 DOI: 10.1007/s10295-014-1443-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Abstract
A gene encoding halohydrin dehalogenase (HHDH) from Agrobacterium tumefaciens CCTCC M 87071 was cloned and expressed in Escherichia coli. To increase activity and stability of HHDH, 14 amino acid residues around the active site and substrate-binding pocket based on the structural analysis and molecular docking were selected as targets for site-directed mutagenesis. The studies showed that the mutant HHDH (Mut-HHDH) enzyme had a more accessible substrate-binding pocket than the wild-type HHDH (Wt-HHDH). Molecular docking revealed that the distance between the substrate and active site was closer in mutant which improved the catalytic activity. The expressed Wt-HHDH and Mut-HHDH were purified and characterized using 1,3-dichloro-2-propanol (1,3-DCP) as substrates. The specific activity of the mutant was enhanced 26-fold and the value of k cat was 18.4-fold as compared to the Wt-HHDH, respectively. The Mut-HHDH showed threefold extension of half-life at 45 °C than that of Wt-HHDH. Therefore it is possible to add 1,3-DCP concentration up to 100 mM and epichlorohydrin (ECH) was produced at a relatively high conversion and yield (59.6 %) using Mut-HHDH as catalyst. This Mut-HHDH could be a potential candidate for the upscale production of ECH.
Collapse
|
18
|
Chen SY, He XJ, Wu JP, Xu G, Yang LR. Identification of halohydrin dehalogenase mutants that resist COBE inhibition. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0457-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
19
|
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]
|
20
|
Schallmey M, Floor RJ, Hauer B, Breuer M, Jekel PA, Wijma HJ, Dijkstra BW, Janssen DB. Biocatalytic and structural properties of a highly engineered halohydrin dehalogenase. Chembiochem 2013; 14:870-81. [PMID: 23585096 DOI: 10.1002/cbic.201300005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Indexed: 01/30/2023]
Abstract
Two highly engineered halohydrin dehalogenase variants were characterized in terms of their performance in dehalogenation and epoxide cyanolysis reactions. Both enzyme variants outperformed the wild-type enzyme in the cyanolysis of ethyl (S)-3,4-epoxybutyrate, a conversion yielding ethyl (R)-4-cyano-3-hydroxybutyrate, an important chiral building block for statin synthesis. One of the enzyme variants, HheC2360, displayed catalytic rates for this cyanolysis reaction enhanced up to tenfold. Furthermore, the enantioselectivity of this variant was the opposite of that of the wild-type enzyme, both for dehalogenation and for cyanolysis reactions. The 37-fold mutant HheC2360 showed an increase in thermal stability of 8 °C relative to the wild-type enzyme. Crystal structures of this enzyme were elucidated with chloride and ethyl (S)-3,4-epoxybutyrate or with ethyl (R)-4-cyano-3-hydroxybutyrate bound in the active site. The observed increase in temperature stability was explained in terms of a substantial increase in buried surface area relative to the wild-type HheC, together with enhanced interfacial interactions between the subunits that form the tetramer. The structures also revealed that the substrate binding pocket was modified both by substitutions and by backbone movements in loops surrounding the active site. The observed changes in the mutant structures are partly governed by coupled mutations, some of which are necessary to remove steric clashes or to allow backbone movements to occur. The importance of interactions between substitutions suggests that efficient directed evolution strategies should allow for compensating and synergistic mutations during library design.
Collapse
Affiliation(s)
- Marcus Schallmey
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
21
|
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]
|
22
|
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]
|
23
|
Behrens GA, Hummel A, Padhi SK, Schätzle S, Bornscheuer UT. Discovery and Protein Engineering of Biocatalysts for Organic Synthesis. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100446] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
24
|
Campbell-Verduyn LS, Szymański W, Postema CP, Dierckx RA, Elsinga PH, Janssen DB, Feringa BL. One pot 'click' reactions: tandem enantioselective biocatalytic epoxide ring opening and [3+2] azide alkyne cycloaddition. Chem Commun (Camb) 2010; 46:898-900. [PMID: 20107643 DOI: 10.1039/b919434g] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Halohydrin dehalogenase (HheC) can perform enantioselective azidolysis of aromatic epoxides to 1,2-azido alcohols which are subsequently ligated to alkynes producing chiral hydroxy triazoles in a one-pot procedure with excellent enantiomeric excess.
Collapse
|
25
|
Haak RM, Berthiol F, Jerphagnon T, Gayet AJA, Tarabiono C, Postema CP, Ritleng V, Pfeffer M, Janssen DB, Minnaard AJ, Feringa BL, de Vries JG. Dynamic kinetic resolution of racemic beta-haloalcohols: direct access to enantioenriched epoxides. J Am Chem Soc 2008; 130:13508-9. [PMID: 18800793 DOI: 10.1021/ja805128x] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The direct chemo-enzymatic DKR of racemic beta-haloalcohols is reported, yielding the corresponding optically active epoxides in a single step. The mutant haloalcohol dehalogenase HheC Cys153Ser Trp249Phe is used for the asymmetric ring closure, whereas racemization of the remaining enantiomer of the haloalcohol is achieved using the new iridacycle 3, one of the most effective racemization catalysts to date for beta-haloalcohols.
Collapse
Affiliation(s)
- Robert M Haak
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
|
27
|
Affiliation(s)
- Dick B Janssen
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
28
|
Haak RM, Tarabiono C, Janssen DB, Minnaard AJ, de Vries JG, Feringa BL. Synthesis of enantiopure chloroalcohols by enzymatic kinetic resolution. Org Biomol Chem 2006; 5:318-23. [PMID: 17205176 DOI: 10.1039/b613937j] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3-Alkenyl and heteroaryl chloroalcohols have been obtained in excellent enantiomeric excess (>99%) by enzymatic kinetic resolution using the haloalcohol dehalogenase HheC. Yields were close to the theoretical maximum for all substrates employed. Furthermore, the applicability of this methodology on multigram scale has been established.
Collapse
Affiliation(s)
- Robert M Haak
- Department of Organic and Molecular Inorganic Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
29
|
Enantioselective formation and ring-opening of epoxides catalysed by halohydrin dehalogenases. Biochem Soc Trans 2006. [DOI: 10.1042/bst0340291] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Halohydrin dehalogenases catalyse the conversion of vicinal halohydrins into their corresponding epoxides, while releasing halide ions. They can be found in several bacteria that use halogenated alcohols or compounds that are degraded via halohydrins as a carbon source for growth. Biochemical and structural studies have shown that halohydrin dehalogenases are evolutionarily and mechanistically related to enzymes of the SDR (short-chain dehydrogenase/reductase) superfamily. In the reverse reaction, which is epoxide-ring opening, different nucleophiles can be accepted, including azide, nitrite and cyanide. This remarkable catalytic promiscuity allows the enzymatic production of a broad range of β-substituted alcohols from epoxides. In these oxirane-ring-opening reactions, the halohydrin dehalogenase from Agrobacterium radiobacter displays high enantioselectivity, making it possible to use the enzyme for the preparation of enantiopure building blocks for fine chemicals.
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Diomi Mamma
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 157 80, Zografou, Greece
| | | | | | | | | |
Collapse
|
31
|
Tang L, Torres Pazmiño DE, Fraaije MW, de Jong RM, Dijkstra BW, Janssen DB. Improved Catalytic Properties of Halohydrin Dehalogenase by Modification of the Halide-Binding Site. Biochemistry 2005; 44:6609-18. [PMID: 15850394 DOI: 10.1021/bi047613z] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halohydrin dehalogenase (HheC) from Agrobacterium radiobacter AD1 catalyzes the dehalogenation of vicinal haloalcohols by an intramolecular substitution reaction, resulting in the formation of the corresponding epoxide, a halide ion, and a proton. Halide release is rate-limiting during the catalytic cycle of the conversion of (R)-p-nitro-2-bromo-1-phenylethanol by the enzyme. The recent elucidation of the X-ray structure of HheC showed that hydrogen bonds between the OH group of Tyr187 and between the Odelta1 atom of Asn176 and Nepsilon1 atom of Trp249 could play a role in stabilizing the conformation of the halide-binding site. The possibility that these hydrogen bonds are important for halide binding and release was studied using site-directed mutagenesis. Steady-state kinetic studies revealed that mutant Y187F, which has lost both hydrogen bonds, has a higher catalytic activity (k(cat)) with two of the three tested substrates compared to the wild-type enzyme. Mutant W249F also shows an enhanced k(cat) value with these two substrates, as well as a remarkable increase in enantiopreference for (R)-p-nitro-2-bromo-1-phenylethanol. In case of a mutation at position 176 (N176A and N176D), a 1000-fold lower catalytic efficiency (k(cat)/K(m)) was obtained, which is mainly due to an increase of the K(m) value of the enzyme. Pre-steady-state kinetic studies showed that a burst of product formation precedes the steady state, indicating that halide release is still rate-limiting for mutants Y187F and W249F. Stopped-flow fluorescence experiments revealed that the rate of halide release is 5.6-fold higher for the Y187F mutant than for the wild-type enzyme and even higher for the W249F enzyme. Taken together, these results show that the disruption of two hydrogen bonds around the halide-binding site increases the rate of halide release and can enhance the overall catalytic activity of HheC.
Collapse
Affiliation(s)
- Lixia Tang
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
32
|
Tang L, van Merode AEJ, Lutje Spelberg JH, Fraaije MW, Janssen DB. Steady-State Kinetics and Tryptophan Fluorescence Properties of Halohydrin Dehalogenase from Agrobacterium radiobacter. Roles of W139 and W249 in the Active Site and Halide-Induced Conformational Change. Biochemistry 2003; 42:14057-65. [PMID: 14636074 DOI: 10.1021/bi034941a] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halohydrin dehalogenase (HheC) from Agrobacterium radiobacter AD1 is a homotetrameric protein containing four tryptophan residues per subunit. The fluorescence properties of the enzyme are strongly influenced by halide binding. To examine the role of the tryptophans (W139, W192, W238, and W249) in halide binding and catalysis, they were individually mutated to a phenylalanine. All mutations, except for W238F, influenced the enzymatic properties. Mutating W192 to phenylalanine inactivated the enzyme and led to dissociation into dimers and monomers. In the structure of HheC, residue W139 and residue W249 from the opposite subunit are close to the active site of the enzyme. Substitution of W139 mainly affected K(m) values with all tested substrates and reduced the enantiopreference for p-nitro-2-bromo-1-phenylethanol. Replacing W249 increased both k(cat) and K(m) values with all tested substrates except for the (S)-enantiomer of p-nitro-2-bromo-1-phenylethanol, for which k(cat) was 3-fold decreased, resulting in a 6-fold increase of the enantioselectivity. Fluorescence measurements revealed that in the ligand-free state the intrinsic protein fluorescence of mutant W139F is higher than that of the wild-type enzyme, while the fluorescence intensity of mutants W238F and W249F was lower. The fluorescence intensities of the W238F and W249F enzymes were increased when they were unfolded or when bromide was added, whereas the fluorescence of mutant W139F was not increased by unfolding or addition of bromide. These results demonstrate that the fluorescence of residues W238 and W249 is partially quenched in the folded ligand-free state, and that W139 is completely quenched and acts as an energy acceptor for the other tryptophan residues as well. Changes of the maximum fluorescence emission wavelength of the HheC variants and the results of acrylamide quenching experiments confirmed that bromide binding induces a local conformational change around the active site, resulting in residue W139 and the quencher group being separated.
Collapse
Affiliation(s)
- Lixia Tang
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | | | | | | |
Collapse
|