1
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Zheng D, Nakabayashi M, Asano Y. Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex. J Biol Chem 2022; 298:101650. [PMID: 35101448 PMCID: PMC8892092 DOI: 10.1016/j.jbc.2022.101650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/02/2022] Open
Abstract
Hydroxynitrile lyase from Linum usitatissimum (LuHNL) is an enzyme involved in the catabolism of cyanogenic glycosides to release hydrogen cyanide upon tissue damage. This enzyme strictly conserves the substrate- and NAD(H)-binding domains of Zn2+-containing alcohol dehydrogenase (ADH); however, there is no evidence suggesting that LuHNL possesses ADH activity. Herein, we determined the ligand-free 3D structure of LuHNL and its complex with acetone cyanohydrin and (R)-2-butanone cyanohydrin using X-ray crystallography. These structures reveal that an A-form NAD+ is tightly but not covalently bound to each subunit of LuHNL. The restricted movement of the NAD+ molecule is due to the “sandwich structure” on the adenine moiety of NAD+. Moreover, the structures and mutagenesis analysis reveal a novel reaction mechanism for cyanohydrin decomposition involving the cyano-zinc complex and hydrogen-bonded interaction of the hydroxyl group of cyanohydrin with Glu323/Thr65 and H2O/Lys162 of LuHNL. The deprotonated Lys162 and protonated Glu323 residues are presumably stabilized by a partially desolvated microenvironment. In summary, the substrate binding geometry of LuHNL provides insights into the differences in activities of LuHNL and ADH, and identifying this novel reaction mechanism is an important contribution to the study of hydroxynitrile lyases.
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Affiliation(s)
- Daijun Zheng
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Makoto Nakabayashi
- Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Osaka, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan.
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2
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Chatterjee A, Rao DHS, Kumar Padhi S. One‐Pot Enzyme Cascade Catalyzed Asymmetrization of Primary Alcohols: Synthesis of Enantiocomplementary Chiral β‐Nitroalcohols. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ayon Chatterjee
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life Sciences University of Hyderabad 500 046 Hyderabad India
| | - D. H. Sreenivasa Rao
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life Sciences University of Hyderabad 500 046 Hyderabad India
| | - Santosh Kumar Padhi
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life Sciences University of Hyderabad 500 046 Hyderabad India
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3
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Pei X, Wang J, Zheng H, Xiao Q, Wang A, Su W. Catalytically active inclusion bodies (CatIBs) induced by terminally attached self-assembling coiled-coil domains: To enhance the stability of (R)-hydroxynitrile lyase. Enzyme Microb Technol 2021; 153:109915. [PMID: 34670185 DOI: 10.1016/j.enzmictec.2021.109915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 11/18/2022]
Abstract
The catalytically-active inclusion bodies (CatIBs) represent a promising strategy for immobilizing enzyme without additional carriers and chemicals, which has aroused great attention in academic and industrial communities. In this work, we discovered two natural parallel right-handed coiled-coil tetramer peptides from PDB database by a structural mining strategy. The two self-assembling peptides, NSPdoT from rotavirus and HVdoT from human Vasodilator-stimulated phosphoprotein, efficiently induced the CatIBs formation of a (R)-Hydroxynitrile lyase from Arabidopsis thaliana (AtHNL) in Escherichia coli cells. This is convenient to simultaneously purify and immobilize the target proteins as biocatalysts. As expected, HVdoT-AtHNL and NSPdoT-AtHNL possessed drastically increased tolerance toward lower pH values, which will be very critical to synthesize cyanohydrins under acidic condition for suppressing the non-enzymatic side reaction. In addition. AtHNL-CatIBs are produced at high yield in host cells as bioactive microparticles, which exhibited high thermal and pH stabilities. Therefore, the CatIBs method represent a promising application for the immobilization of enzymes in the biocatalysis field.
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Affiliation(s)
- Xiaolin Pei
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China; College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China.
| | - Jiapao Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Haoteng Zheng
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Qinjie Xiao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, China
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China.
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4
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Liu M, Wei D, Wen Z, Wang JB. Progress in Stereoselective Construction of C-C Bonds Enabled by Aldolases and Hydroxynitrile Lyases. Front Bioeng Biotechnol 2021; 9:653682. [PMID: 33968915 PMCID: PMC8097096 DOI: 10.3389/fbioe.2021.653682] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
The creation of C-C bonds is an effective strategy for constructing complex compounds from simple synthetic blocks. Although many methods have been developed for C-C bond construction, the stereoselective creation of new C-C bonds remains a challenge. The selectivities (enantioselectivity, regioselectivity, and chemoselectivity) of biocatalysts are higher than those of chemical catalysts, therefore biocatalysts are excellent candidates for use in stereoselective C-C bond formation. Here, we summarize progress made in the past 10 years in stereoselective C-C bond formation enabled by two classic types of enzyme, aldolases and hydroxynitrile lyases. The information in this review will enable the development of new routes to the stereoselective construction of C-C bonds.
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Affiliation(s)
- Mi Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Dan Wei
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Zexing Wen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
| | - Jian-Bo Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.,Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China
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5
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Jones BJ, Evans RL, Mylrea NJ, Chaudhury D, Luo C, Guan B, Pierce CT, Gordon WR, Wilmot CM, Kazlauskas RJ. Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity. PLoS One 2020; 15:e0235341. [PMID: 32603354 PMCID: PMC7326234 DOI: 10.1371/journal.pone.0235341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/14/2020] [Indexed: 12/02/2022] Open
Abstract
Hydroxynitrile lyases (HNL's) belonging to the α/β-hydrolase-fold superfamily evolved from esterases approximately 100 million years ago. Reconstruction of an ancestral hydroxynitrile lyase in the α/β-hydrolase fold superfamily yielded a catalytically active hydroxynitrile lyase, HNL1. Several properties of HNL1 differ from the modern HNL from rubber tree (HbHNL). HNL1 favors larger substrates as compared to HbHNL, is two-fold more catalytically promiscuous for ester hydrolysis (p-nitrophenyl acetate) as compared to mandelonitrile cleavage, and resists irreversible heat inactivation to 35 °C higher than for HbHNL. We hypothesized that the x-ray crystal structure of HNL1 may reveal the molecular basis for the differences in these properties. The x-ray crystal structure solved to 1.96-Å resolution shows the expected α/β-hydrolase fold, but a 60% larger active site as compared to HbHNL. This larger active site echoes its evolution from esterases since related esterase SABP2 from tobacco also has a 38% larger active site than HbHNL. The larger active site in HNL1 likely accounts for its ability to accept larger hydroxynitrile substrates. Site-directed mutagenesis of HbHNL to expand the active site increased its promiscuous esterase activity 50-fold, consistent with the larger active site in HNL1 being the primary cause of its promiscuous esterase activity. Urea-induced unfolding of HNL1 indicates that it unfolds less completely than HbHNL (m-value = 0.63 for HNL1 vs 0.93 kcal/mol·M for HbHNL), which may account for the ability of HNL1 to better resist irreversible inactivation upon heating. The structure of HNL1 shows changes in hydrogen bond networks that may stabilize regions of the folded structure.
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Affiliation(s)
- Bryan J. Jones
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Robert L. Evans
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Nathan J. Mylrea
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Debayan Chaudhury
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Christine Luo
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Bo Guan
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Colin T. Pierce
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Wendy R. Gordon
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
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6
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Jones BJ, Evans RL, Mylrea NJ, Chaudhury D, Luo C, Guan B, Pierce CT, Gordon WR, Wilmot CM, Kazlauskas RJ. Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity.. [DOI: 10.1101/2020.04.06.027797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
AbstractHydroxynitrile lyases (HNL’s) belonging to the α/β-hydrolase-fold superfamily evolved from esterases approximately 100 million years ago. Reconstruction of an ancestral hydroxynitrile lyase in the α/β-hydrolase fold superfamily yielded a catalytically active hydroxynitrile lyase, HNL1. Several properties of HNL1 differ from the modern HNL from rubber tree (HbHNL). HNL1 favors larger substrates as compared to HbHNL, is two-fold more catalytically promiscuous for ester hydrolysis (p-nitrophenyl acetate) as compared to mandelonitrile cleavage, and resists irreversible heat inactivation to 35 °C higher than for HbHNL. We hypothesized that the x-ray crystal structure of HNL1 may reveal the molecular basis for the differences in these properties. The x-ray crystal structure solved to 1.96-Å resolution shows the expected α/β-hydrolase fold, but a 60% larger active site as compared to HbHNL. This larger active site echoes its evolution from esterases since related esterase SABP2 from tobacco also has a 38% larger active site than HbHNL. The larger active site in HNL1 likely accounts for its ability to accept larger hydroxynitrile substrates. Site-directed mutagenesis of HbHNL to expand the active site increased its promiscuous esterase activity 50-fold, consistent with the larger active site in HNL1 being the primary cause of its promiscuous esterase activity. Urea-induced unfolding of HNL1 indicates that it unfolds less completely than HbHNL (m-value = 0.63 for HNL1 vs 0.93 kcal/ mol·M for HbHNL), which may account for the ability of HNL1 to better resist irreversible inactivation upon heating. The structure of HNL1 shows changes in hydrogen bond networks that may stabilize regions of the folded structure.
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7
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Nuylert A, Motojima F, Khanongnuch C, Hongpattarakere T, Asano Y. Stabilization of Hydroxynitrile Lyases from Two Variants of Passion Fruit, Passiflora edulis Sims and Passiflora edulis Forma flavicarpa, by C-Terminal Truncation. Chembiochem 2020; 21:181-189. [PMID: 31562666 DOI: 10.1002/cbic.201900468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Indexed: 11/07/2022]
Abstract
Because the synthesis of chiral compounds generally requires a broad range of substrate specificity and stable enzymes, screening for better enzymes and/or improvement of enzyme properties through molecular approaches is necessary for sustainable industrial development. Herein, the discovery of unique hydroxynitrile lyases (HNLs) from two species of passion fruits, Passiflora edulis forma flavicarpa (yellow passion fruit, PeHNL-Ny) and Passiflora edulis Sims (purple passion fruit, PeHNL-Np), isolated and purified from passion fruit leaves is reported. These are the smallest HNLs (comprising 121 amino acids). Amino acid sequences of both enzymes are 99 % identical; there is a difference of one amino acid in a consensus sequence. PeHNL-Np has an Ala residue at position 107 and is nonglycosylated at Asn105. Because it was confirmed that natural and glycosylated PeHNL-Ny showed superior thermostability, pH stability, and organic tolerance to that of PeHNL-Np, it has been speculated that protein engineering around the only glycosylation site, Asn105, located at the C-terminal region of PeHNL-Ny, might contribute to the stabilization of PeHNL. Therefore, the focus is on improved stability of the nonglycosylated PeHNL by truncating its C-terminal region. The C-terminal-truncated PeHNLΔ107 was obtained by truncating 15 amino acids from the C terminus followed by expression in Escherichia coli. PeHNLΔ107 expressed in E. coli was not glycosylated, and showed improved thermostability, solvent stability, and reusability similar to that of the wild-type glycosylated form of PeHNL expressed in Pichia pastoris. These data reveal that the lack of the high-flexibility region at the C terminus of PeHNL might be a possible reason for improving the stability of PeHNL.
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Affiliation(s)
- Aem Nuylert
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Fumihiro Motojima
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Chartchai Khanongnuch
- Division of Biotechnology, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Tipparat Hongpattarakere
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Yasuhisa Asano
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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8
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Jangir N, Preeti, Padhi SK. A study on increasing enzymatic stability and activity of Baliospermum montanum hydroxynitrile lyase in biocatalysis. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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9
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Jangir N, Padhi SK. Immobilized Baliospermum montanum hydroxynitrile lyase catalyzed synthesis of chiral cyanohydrins. Bioorg Chem 2018; 84:32-40. [PMID: 30481644 DOI: 10.1016/j.bioorg.2018.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
Abstract
Hydroxynitrile lyase (HNL) catalyzed enantioselective CC bond formation is an efficient approach to synthesize chiral cyanohydrins which are important building blocks in the synthesis of a number of fine chemicals, agrochemicals and pharmaceuticals. Immobilization of HNL is known to provide robustness, reusability and in some cases also enhances activity and selectivity. We optimized the preparation of immobilization of Baliospermium montanum HNL (BmHNL) by cross linking enzyme aggregate (CLEA) method and characterized it by SEM. Optimization of biocatalytic parameters was performed to obtain highest % conversion and ee of (S)-mandelonitrile from benzaldehyde using CLEA-BmHNL. The optimized reaction parameters were: 20 min of reaction time, 7 U of CLEA-BmHNL, 1.2 mM substrate, and 300 mM citrate buffer pH 4.2, that synthesized (S)-mandelonitrile in ∼99% ee and ∼60% conversion. Addition of organic solvent in CLEA-BmHNL biocatalysis did not improve in % ee or conversion of product unlike other CLEA-HNLs. CLEA-BmHNL could be successfully reused for eight consecutive cycles without loss of conversion or product formation and five cycles with a little loss in enantioselectivity. Eleven different chiral cyanohydrins were synthesized under optimal biocatalytic conditions in up to 99% ee and 59% conversion, however the % conversion and ee varied for different products. CLEA-BmHNL has improved the enantioselectivity of (S)-mandelonitrile synthesis compared to the use of purified BmHNL. Nine aldehydes not tested earlier with BmHNL were converted into their corresponding (S)-cyanohydrins for the first time using CLEA-BmHNL. Among the eleven (S)-cyanohydrins syntheses reported here, eight of them have not been synthesized by any CLEA-HNL. Overall, this study showed preparation, characterization of a stable, robust and recyclable biocatalyst i.e. CLEA-BmHNL and its biocatalytic application in the synthesis of different (S)-aromatic cyanohydrins.
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Affiliation(s)
- Nisha Jangir
- Biocatalysis and Enzyme Engineering Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Santosh Kumar Padhi
- Biocatalysis and Enzyme Engineering Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
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10
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Isobe K, Kitagawa A, Kanamori K, Kashiwagi N, Matsui D, Yamaguchi T, Fuhshuku KI, Semba H, Asano Y. Characterization of a novel hydroxynitrile lyase from Nandina domestica Thunb. Biosci Biotechnol Biochem 2018; 82:1760-1769. [DOI: 10.1080/09168451.2018.1490171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
ABSTRACT
The leaves of Nandina domestica Thunb. exhibited high hydroxynitrile lyase (HNL) activity in (R)-mandelonitrile synthesis. The specific activity of young leaves was significantly higher than that of mature leaves. We isolated two HNLs with molecular mass of 24.9 kDa (NdHNL-S) and 28.0 kDa (NdHNL-L) from the young leaves. Both NdHNLs were composed of two identical subunits, without FAD and carbohydrates. We purified NdHNL-L and revealed its enzymatic properties. The whole deduced amino acid sequence of NdHNL-L was not homologous to any other HNLs, and the specific activity for mandelonitrile synthesis by NdHNL-L was higher than that by other plant HNLs. The enzyme catalyzed enantioselective synthesis of (R)-cyanohydrins, exhibited high activity at pH 4.0, and high stability in the pH range of 3.5–8.0 and below 55°C. Thus, NdHNL-L is a novel HNL with novel amino acid sequence and has a potential for the efficient production of (R)-cyanohydrins.
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Affiliation(s)
- Kimiyasu Isobe
- Biotechnology Research Center andDepartment of Biotechnology, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, Kurokawa, Imizu, Toyama, Japan
| | - Asuka Kitagawa
- Biotechnology Research Center andDepartment of Biotechnology, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
| | - Kazuma Kanamori
- Biotechnology Research Center andDepartment of Biotechnology, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
| | - Nozomi Kashiwagi
- Biotechnology Research Center andDepartment of Biotechnology, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
| | - Daisuke Matsui
- Biotechnology Research Center andDepartment of Biotechnology, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, Kurokawa, Imizu, Toyama, Japan
| | - Takuya Yamaguchi
- Asano Active Enzyme Molecule Project, ERATO, JST, Kurokawa, Imizu, Toyama, Japan
| | - Ken-ichi Fuhshuku
- Biotechnology Research Center andDepartment of Biotechnology, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
| | - Hisashi Semba
- Suita Research Laboratory, Nippon Shokubai Co. Ltd, Suita, Osaka, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center andDepartment of Biotechnology, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, Kurokawa, Imizu, Toyama, Japan
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11
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Jangir N, Sangoji D, Padhi SK. Baliospermum montanum hydroxynitrile lyase catalyzed synthesis of chiral cyanohydrins in a biphasic solvent. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Yao L, Li H, Yang J, Li C, Shen Y. Purification and characterization of a hydroxynitrile lyase from Amygdalus pedunculata Pall. Int J Biol Macromol 2018; 118:189-194. [DOI: 10.1016/j.ijbiomac.2018.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/03/2018] [Accepted: 06/07/2018] [Indexed: 10/28/2022]
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13
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Yildirim D, Toprak A, Alagöz D, Tukel SS. Protein-coated microcrystals of Prunus armeniaca hydroxynitrile lyase: an effective and recyclable biocatalyst for synthesis of (R)-mandelonitrile. CHEMICAL PAPERS 2018. [DOI: 10.1007/s11696-018-0577-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Bracco P, Busch H, von Langermann J, Hanefeld U. Enantioselective synthesis of cyanohydrins catalysed by hydroxynitrile lyases - a review. Org Biomol Chem 2018; 14:6375-89. [PMID: 27282284 DOI: 10.1039/c6ob00934d] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The first enantioselective synthesis was the selective addition of cyanide to benzaldehyde catalysed by a hydroxynitrile lyase (HNL). Since then these enzymes have been developed into a reliable tool in organic synthesis. HNLs to prepare either the (R)- or the (S)-enantiomer of the desired cyanohydrin are available and a wide variety of reaction conditions can be applied. As a result of this, numerous applications of these enzymes in organic synthesis have been described. Here the examples of the last decade are summarised, the enzyme catalysed step is discussed and the follow-up chemistry is shown. This proves HNLs to be part of main stream organic synthesis. Additionally the newest approaches via immobilisation and reaction engineering are introduced.
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Affiliation(s)
- Paula Bracco
- Gebouw voor Scheikunde, Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628BL Delft, The Netherlands.
| | - Hanna Busch
- Gebouw voor Scheikunde, Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628BL Delft, The Netherlands.
| | - Jan von Langermann
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany
| | - Ulf Hanefeld
- Gebouw voor Scheikunde, Biokatalyse, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628BL Delft, The Netherlands.
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15
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Jones BJ, Bata Z, Kazlauskas RJ. Identical active sites in hydroxynitrile lyases show opposite enantioselectivity and reveal possible ancestral mechanism. ACS Catal 2017; 7:4221-4229. [PMID: 28798888 DOI: 10.1021/acscatal.7b01108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Evolutionarily related hydroxynitrile lyases from rubber tree (HbHNL) and from Arabidopsis thaliana (AtHNL) follow different catalytic mechanisms with opposite enantioselectivity toward mandelonitrile. We hypothesized that the HbHNL-like mechanism evolved from an enzyme with an AtHNL-like mechanism. We created ancestor-like composite active-sites in each scaffold to elucidate how this transition may have occurred. Surprisingly, a composite active site in HbHNL maintained (S)-selectivity, while the identical set of active site residues in AtHNL maintained (R)-selectivity. Composite active-site mutants that are (S)-selective without the Lys236 and Thr11 that are required for the classical (S)-HNL mechanism suggests a new mechanism. Modeling suggested a possibility for this new mechanism that does not exist in modern enzymes. Thus, the last common ancestor of HbHNL and AtHNL may have used an extinct mechanism, not the AtHNL-like mechanism. Multiple mechanisms are possible with the same catalytic residues and residues outside the active site strongly influence mechanism and enantioselectivity.
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Affiliation(s)
- Bryan J. Jones
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Zsófia Bata
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Department
of Organic Chemistry and Technology, Budapest University of Technology and Economics, 3 Műegyetem rkp, H-1111 Budapest, Hungary
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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16
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Zheng YC, Xu JH, Wang H, Lin GQ, Hong R, Yu HL. Hydroxynitrile Lyase Isozymes fromPrunus communis: Identification, Characterization and Synthetic Applications. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601332] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
| | - Hui Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
| | - Guo-Qiang Lin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; Shanghai 200032 People's Republic of China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; Shanghai 200032 People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing; East China University of Science and Technology; Shanghai 200237 People's Republic of China
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17
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Padhi SK. Modern Approaches to Discovering New Hydroxynitrile Lyases for Biocatalysis. Chembiochem 2016; 18:152-160. [DOI: 10.1002/cbic.201600495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Santosh Kumar Padhi
- Biocatalysis and Enzyme Engineering Laboratory; Department of Biochemistry; School of Life Sciences; University of Hyderabad; Hyderabad 500 046 India
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18
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Asano Y, Kawahara N. A New S-Hydroxynitrile Lyase from Baliospermum montanum—Its Structure, Molecular Dynamics Simulation, and Improvement by Protein Engineering. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1089/ind.2015.0029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
- Japan Science and Technology Agency, Exploratory Research for Advanced Technology, Asano Active Enzyme Molecule Project, Toyama, Japan
| | - Nobuhiro Kawahara
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
- Japan Science and Technology Agency, Exploratory Research for Advanced Technology, Asano Active Enzyme Molecule Project, Toyama, Japan
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19
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Devamani T, Rauwerdink AM, Lun-zer M, Jones BJ, Mooney JL, Tan MAO, Zhang ZJ, Xu JH, Dean AM, Kazlauskas RJ. Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases. J Am Chem Soc 2016; 138:1046-56. [PMID: 26736133 PMCID: PMC5466365 DOI: 10.1021/jacs.5b12209] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Catalytic promiscuity is a useful, but accidental, enzyme property, so finding catalytically promiscuous enzymes in nature is inefficient. Some ancestral enzymes were branch points in the evolution of new enzymes and are hypothesized to have been promiscuous. To test the hypothesis that ancestral enzymes were more promiscuous than their modern descendants, we reconstructed ancestral enzymes at four branch points in the divergence hydroxynitrile lyases (HNL's) from esterases ∼ 100 million years ago. Both enzyme types are α/β-hydrolase-fold enzymes and have the same catalytic triad, but differ in reaction type and mechanism. Esterases catalyze hydrolysis via an acyl enzyme intermediate, while lyases catalyze an elimination without an intermediate. Screening ancestral enzymes and their modern descendants with six esterase substrates and six lyase substrates found higher catalytic promiscuity among the ancestral enzymes (P < 0.01). Ancestral esterases were more likely to catalyze a lyase reaction than modern esterases, and the ancestral HNL was more likely to catalyze ester hydrolysis than modern HNL's. One ancestral enzyme (HNL1) along the path from esterase to hydroxynitrile lyases was especially promiscuous and catalyzed both hydrolysis and lyase reactions with many substrates. A broader screen tested mechanistically related reactions that were not selected for by evolution: decarboxylation, Michael addition, γ-lactam hydrolysis and 1,5-diketone hydrolysis. The ancestral enzymes were more promiscuous than their modern descendants (P = 0.04). Thus, these reconstructed ancestral enzymes are catalytically promiscuous, but HNL1 is especially so.
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Affiliation(s)
- Titu Devamani
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Alissa M. Rauwerdink
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Mark Lun-zer
- University of Minnesota, Department of Ecology, Evolution & Behavior and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Bryan J. Jones
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Joanna L. Mooney
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | | | - Zhi-Jun Zhang
- East China University of Science and Technology, School of Biotechnology, Meilong Road 130, Shanghai 200237 P. R. China
| | - Jian-He Xu
- East China University of Science and Technology, School of Biotechnology, Meilong Road 130, Shanghai 200237 P. R. China
| | - Antony M. Dean
- University of Minnesota, Department of Ecology, Evolution & Behavior and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
- Sun Yat-sen University, Institute of Ecology and Evolution, No.135, Xinggang West Road, Guangzhou, 510275 P. R. China
| | - Romas J. Kazlauskas
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
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20
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Discovery and molecular and biocatalytic properties of hydroxynitrile lyase from an invasive millipede, Chamberlinius hualienensis. Proc Natl Acad Sci U S A 2015; 112:10605-10. [PMID: 26261304 DOI: 10.1073/pnas.1508311112] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydroxynitrile lyase (HNL) catalyzes the degradation of cyanohydrins and causes the release of hydrogen cyanide (cyanogenesis). HNL can enantioselectively produce cyanohydrins, which are valuable building blocks for the synthesis of fine chemicals and pharmaceuticals, and is used as an important biocatalyst in industrial biotechnology. Currently, HNLs are isolated from plants and bacteria. Because industrial biotechnology requires more efficient and stable enzymes for sustainable development, we must continuously explore other potential enzyme sources for the desired HNLs. Despite the abundance of cyanogenic millipedes in the world, there has been no precise study of the HNLs from these arthropods. Here we report the isolation of HNL from the cyanide-emitting invasive millipede Chamberlinius hualienensis, along with its molecular properties and application in biocatalysis. The purified enzyme displays a very high specific activity in the synthesis of mandelonitrile. It is a glycosylated homodimer protein and shows no apparent sequence identity or homology with proteins in the known databases. It shows biocatalytic activity for the condensation of various aromatic aldehydes with potassium cyanide to produce cyanohydrins and has high stability over a wide range of temperatures and pH values. It catalyzes the synthesis of (R)-mandelonitrile from benzaldehyde with a 99% enantiomeric excess, without using any organic solvents. Arthropod fauna comprise 80% of terrestrial animals. We propose that these animals can be valuable resources for exploring not only HNLs but also diverse, efficient, and stable biocatalysts in industrial biotechnology.
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21
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Kawahara N, Asano Y. Mutagenesis of an Asn156 Residue in a Surface Region ofS-Selective Hydroxynitrile Lyase fromBaliospermum montanumEnhances Catalytic Efficiency and Enantioselectivity. Chembiochem 2015; 16:1891-1895. [DOI: 10.1002/cbic.201500225] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 11/11/2022]
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22
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Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software. Sci Rep 2015; 5:8193. [PMID: 25645341 PMCID: PMC4648443 DOI: 10.1038/srep08193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/12/2015] [Indexed: 01/05/2023] Open
Abstract
Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.
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23
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Nakano S, Dadashipour M, Asano Y. Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2059-67. [PMID: 25220808 DOI: 10.1016/j.bbapap.2014.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
Abstract
Hydroxynitrile lyases (HNLs) catalyze degradation of cyanohydrins to hydrogen cyanide and the corresponding ketone or aldehyde. HNLs can also catalyze the reverse reaction, i.e., synthesis of cyanohydrins. Although several crystal structures of S-selective hydroxynitrile lyases (S-HNLs) have been reported, it remains unknown whether and how dynamics at the active site of S-HNLs influence their broad substrate specificity and affinity. In this study, we analyzed the structure, dynamics and function of S-HNL from Baliospermum montanum (BmHNL), which has an α/β hydrolase fold. Two crystal structures of BmHNL, apo1 and apo2, were determined at 2.55 and 1.9Å, respectively. Structural comparison between BmHNL (apo2) and S-HNL from Hevea brasiliensis with (S)-mandelonitrile bound to the active site revealed that hydrophobic residues at the entrance region of BmHNL formed hydrophobic interactions with the benzene ring of the substrate. The flexible structures of these hydrophobic residues were confirmed by a 15ns molecular dynamics simulation. This flexibility regulated the size of the active site cavity, enabling binding of various substrates to BmHNL. The high affinity of BmHNL toward substrates containing a benzene ring was also confirmed by comparing the kinetics of BmHNL and S-HNL from Manihot esculenta. Taken together, the results indicated that the flexibility and placement of the residues are important for the broad substrate specificity of S-HNLs.
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Affiliation(s)
- Shogo Nakano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Mohammad Dadashipour
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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24
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von Langermann J, Nedrud DM, Kazlauskas RJ. Increasing the reaction rate of hydroxynitrile lyase from Hevea brasiliensis toward mandelonitrile by copying active site residues from an esterase that accepts aromatic esters. Chembiochem 2014; 15:1931-8. [PMID: 25044660 DOI: 10.1002/cbic.201402081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 11/11/2022]
Abstract
The natural substrate of hydroxynitrile lyase from rubber tree (HbHNL, Hevea brasiliensis) is acetone cyanohydrin, but synthetic applications usually involve aromatic cyanohydrins such as mandelonitrile. To increase the activity of HbHNL toward this unnatural substrate, we replaced active site residues in HbHNL with the corresponding ones from esterase SABP2 (salicylic acid binding protein 2). Although this enzyme catalyzes a different reaction (hydrolysis of esters), its natural substrate (methyl salicylate) contains an aromatic ring. Three of the eleven single-amino-acid-substitution variants of HbHNL reacted more rapidly with mandelonitrile. The best was HbHNL-L121Y, with a kcat 4.2 times higher and high enantioselectivity. Site-saturation mutagenesis at position 121 identified three other improved variants. We hypothesize that the smaller active site orients the aromatic substrate more productively.
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Affiliation(s)
- Jan von Langermann
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 (USA); Institute of Chemistry, University of Rostock, Albert-Einstein-Strasse 3A, 18059 Rostock (Germany)
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25
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Alagöz D, Tükel SS, Yildirim D. Purification, immobilization and characterization of (R)-hydroxynitrile lyase from Prunus amygdalus turcomanica seeds and their applicability for synthesis of enantiopure cyanohydrins. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.12.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Abstract
Hydroxynitrile lyases are a versatile group of enzymes that are applied both in the laboratory and on an industrial scale. What makes them particularly interesting is that to date five structurally unrelated categories of hydroxynitrile lyases have been discovered. Given their great importance they have often been immobilised utilising many different methodologies. Therefore the hydroxynitrile lyases are ideally suited to compare different immobilisation methods and their dependence on the structural features of the enzyme in question, since the activity is the same in all cases. This review examines all the different immobilisation methods applied to hydroxynitrile lyases and draws conclusions on the effect of the approach.
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Affiliation(s)
- Ulf Hanefeld
- Gebouw voor Scheikunde, Afdeling Biotechnologie, Technische Universiteit Delft, Julianalaan 136, 2628BL Delft, The Netherlands.
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27
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Kassim MA, Rumbold K. HCN production and hydroxynitrile lyase: a natural activity in plants and a renewed biotechnological interest. Biotechnol Lett 2013; 36:223-8. [DOI: 10.1007/s10529-013-1353-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/06/2013] [Indexed: 11/28/2022]
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28
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Andexer JN, Staunig N, Eggert T, Kratky C, Pohl M, Gruber K. Hydroxynitrile lyases with α/β-hydrolase fold: two enzymes with almost identical 3D structures but opposite enantioselectivities and different reaction mechanisms. Chembiochem 2012; 13:1932-9. [PMID: 22851196 PMCID: PMC3444685 DOI: 10.1002/cbic.201200239] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Indexed: 11/20/2022]
Abstract
Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R-selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 Å. The structure exhibits an α/β-hydrolase fold, very similar to the homologous, but S-selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser-His-Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)- and (S)-mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)-mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main-chain amide groups and an α-helix dipole very similar to α/β-hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies.
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Affiliation(s)
- Jennifer N Andexer
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University FreiburgAlbertstrasse 25, 79104 Freiburg (Germany)
| | - Nicole Staunig
- Institute of Molecular Biosciences, University of GrazHumboldtstrasse 50/3, 8010 Graz (Austria) E-mail:
| | | | - Christoph Kratky
- Institute of Molecular Biosciences, University of GrazHumboldtstrasse 50/3, 8010 Graz (Austria) E-mail:
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH52425 Jülich (Germany)
| | - Karl Gruber
- Institute of Molecular Biosciences, University of GrazHumboldtstrasse 50/3, 8010 Graz (Austria) E-mail:
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29
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Fuhshuku KI, Asano Y. Organic Synthesis Catalyzed by Plant Enzyme Hydroxynitrile Lyase. J SYN ORG CHEM JPN 2012. [DOI: 10.5059/yukigoseikyokaishi.70.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ken-ichi Fuhshuku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University
- JST, ERATO
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30
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Dadashipour M, Asano Y. Hydroxynitrile Lyases: Insights into Biochemistry, Discovery, and Engineering. ACS Catal 2011. [DOI: 10.1021/cs200325q] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mohammad Dadashipour
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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31
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Asano Y, Dadashipour M, Yamazaki M, Doi N, Komeda H. Functional expression of a plant hydroxynitrile lyase in Escherichia coli by directed evolution: creation and characterization of highly in vivo soluble mutants. Protein Eng Des Sel 2011; 24:607-16. [DOI: 10.1093/protein/gzr030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Fuhshuku KI, Asano Y. Synthesis of (R)-β-nitro alcohols catalyzed by R-selective hydroxynitrile lyase from Arabidopsis thaliana in the aqueous-organic biphasic system. J Biotechnol 2011; 153:153-9. [PMID: 21439333 DOI: 10.1016/j.jbiotec.2011.03.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 03/02/2011] [Accepted: 03/10/2011] [Indexed: 10/18/2022]
Abstract
Both enantiomers of β-nitro alcohols are versatile chiral building blocks. However, their synthesis using enzymes as catalysts has received little attention, with the exception of (S)-β-nitro alcohols produced in a reaction catalyzed by an S-selective hydroxynitrile lyase (HNL) from Hevea brasiliensis (HbHNL). An R-selective HNL containing an α/β-hydrolase fold from the noncyanogenic plant Arabidopsis thaliana (AtHNL) accepts nitromethane (MeNO₂) as a donor in a reaction with aromatic aldehydes to yield (R)-β-nitro alcohols (Henry reaction; nitro aldol reaction). This reaction proceeded in an aqueous-organic biphasic system. The organic solvent giving the highest enantioselectivity was n-butyl acetate (AcOBu) with an optimum aqueous phase content of 50% (v/v). This is the first example of the R-HNL-catalyzed synthesis of (R)-β-nitro alcohols.
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Affiliation(s)
- Ken-Ichi Fuhshuku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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