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Zheng D, Asano Y. A Cyanide‐free Biocatalytic Process for Synthesis of Complementary Enantiomers of 4‐Chloro‐3‐hydroxybutanenitrile From Allyl Chloride. ChemCatChem 2021. [DOI: 10.1002/cctc.202100835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Daijun Zheng
- 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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2
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Betke T, Higuchi J, Rommelmann P, Oike K, Nomura T, Kato Y, Asano Y, Gröger H. Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases. Chembiochem 2018; 19:768-779. [PMID: 29333684 DOI: 10.1002/cbic.201700571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Indexed: 11/05/2022]
Abstract
Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high-volume, low-price sectors, such as polymers, to low-volume, high-price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas-phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a "synthetic platform technology". Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2-arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.
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Affiliation(s)
- Tobias Betke
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.,Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Jun Higuchi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Philipp Rommelmann
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Keiko Oike
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Taiji Nomura
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
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3
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Nitrile Metabolizing Enzymes in Biocatalysis and Biotransformation. Appl Biochem Biotechnol 2018; 185:925-946. [DOI: 10.1007/s12010-018-2705-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/19/2018] [Indexed: 11/26/2022]
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4
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Sørensen M, Neilson EHJ, Møller BL. Oximes: Unrecognized Chameleons in General and Specialized Plant Metabolism. MOLECULAR PLANT 2018; 11:95-117. [PMID: 29275165 DOI: 10.1016/j.molp.2017.12.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 05/19/2023]
Abstract
Oximes (R1R2C=NOH) are nitrogen-containing chemical constituents that are formed in species representing all kingdoms of life. In plants, oximes are positioned at important metabolic bifurcation points between general and specialized metabolism. The majority of plant oximes are amino acid-derived metabolites formed by the action of a cytochrome P450 from the CYP79 family. Auxin, cyanogenic glucosides, glucosinolates, and a number of other bioactive specialized metabolites including volatiles are produced from oximes. Oximes with the E configuration have high biological activity compared with Z-oximes. Oximes or their derivatives have been demonstrated or proposed to play roles in growth regulation, plant defense, pollinator attraction, and plant communication with the surrounding environment. In addition, oxime-derived products may serve as quenchers of reactive oxygen species and storage compounds for reduced nitrogen that may be released on demand by the activation of endogenous turnover pathways. As highly bioactive molecules, chemically synthesized oximes have found versatile uses in many sectors of society, especially in the agro- and medical sectors. This review provides an update on the structural diversity, occurrence, and biosynthesis of oximes in plants and discusses their role as key players in plant general and specialized metabolism.
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Affiliation(s)
- Mette Sørensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Elizabeth H J Neilson
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark.
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5
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Yamada M, Hashimoto Y, Kumano T, Tsujimura S, Kobayashi M. New function of aldoxime dehydratase: Redox catalysis and the formation of an unexpected product. PLoS One 2017; 12:e0175846. [PMID: 28410434 PMCID: PMC5391958 DOI: 10.1371/journal.pone.0175846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/31/2017] [Indexed: 11/21/2022] Open
Abstract
In general, hemoproteins are capable of catalyzing redox reactions. Aldoxime dehydratase (OxdA), which is a unique heme-containing enzyme, catalyzes the dehydration of aldoximes to the corresponding nitriles. Its reaction is a rare example of heme directly activating an organic substrate, unlike the utilization of H2O2 or O2 as a mediator of catalysis by other heme-containing enzymes. While it is unknown whether OxdA catalyzes redox reactions or not, we here for the first time detected catalase activity (which is one of the redox activities) of wild-type OxdA, OxdA(WT). Furthermore, we constructed a His320 → Asp mutant of OxdA [OxdA(H320D)], and found it exhibits catalase activity. Determination of the kinetic parameters of OxdA(WT) and OxdA(H320D) revealed that their Km values for H2O2 were similar to each other, but the kcat value of OxdA(H320D) was 30 times higher than that of OxdA(WT). Next, we examined another redox activity and found it was the peroxidase activity of OxdAs. While both OxdA(WT) and OxdA(H320D) showed the activity, the activity of OxdA(H320D) was dozens of times higher than that of OxdA(WT). These findings demonstrated that the H320D mutation enhances the peroxidase activity of OxdA. OxdAs (WT and H320D) were found to catalyze another redox reaction, a peroxygenase reaction. During this reaction of OxdA(H320D) with 1-methoxynaphthalene as a substrate, surprisingly, the reaction mixture changed to a color different from that with OxdA(WT), which was due to the known product, Russig’s blue. We purified and identified the new product as 1-methoxy-2-naphthalenol, which has never been reported as a product of the peroxygenase reaction, to the best of our knowledge. These findings indicated that the H320D mutation not only enhanced redox activities, but also significantly altered the hydroxylation site of the substrate.
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Affiliation(s)
- Masatoshi Yamada
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiteru Hashimoto
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takuto Kumano
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Seiya Tsujimura
- Division of Materials Science, Faculty of Pure and Applied Sciences, The University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail:
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6
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Miao Y, Metzner R, Asano Y. Kemp Elimination Catalyzed by Naturally Occurring Aldoxime Dehydratases. Chembiochem 2017; 18:451-454. [PMID: 28120515 DOI: 10.1002/cbic.201600596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 11/10/2022]
Abstract
Recently, the Kemp elimination reaction has been extensively studied in computational enzyme design of new catalysts, as no natural enzyme has evolved to catalyze this reaction. In contrast to in silico enzyme design, we were interested in searching for Kemp eliminase activity in natural enzymes with catalytic promiscuity. Based on similarities of substrate structures and reaction mechanisms, we assumed that the active sites of naturally abundant aldoxime dehydratases have the potential to catalyze the non-natural Kemp elimination reaction. We found several aldoxime dehydratases that are efficient catalysts of this reaction. Although a few natural enzymes have been identified with promiscuous Kemp eliminase activity, to the best of our knowledge, this is a rare example of Kemp elimination catalyzed by naturally occurring enzymes with high catalytic efficiency.
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Affiliation(s)
- Yufeng Miao
- 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
| | - Richard Metzner
- 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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7
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Clausen M, Kannangara RM, Olsen CE, Blomstedt CK, Gleadow RM, Jørgensen K, Bak S, Motawie MS, Møller BL. The bifurcation of the cyanogenic glucoside and glucosinolate biosynthetic pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:558-73. [PMID: 26361733 DOI: 10.1111/tpj.13023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 08/18/2015] [Accepted: 09/02/2015] [Indexed: 05/08/2023]
Abstract
The biosynthetic pathway for the cyanogenic glucoside dhurrin in sorghum has previously been shown to involve the sequential production of (E)- and (Z)-p-hydroxyphenylacetaldoxime. In this study we used microsomes prepared from wild-type and mutant sorghum or transiently transformed Nicotiana benthamiana to demonstrate that CYP79A1 catalyzes conversion of tyrosine to (E)-p-hydroxyphenylacetaldoxime whereas CYP71E1 catalyzes conversion of (E)-p-hydroxyphenylacetaldoxime into the corresponding geometrical Z-isomer as required for its dehydration into a nitrile, the next intermediate in cyanogenic glucoside synthesis. Glucosinolate biosynthesis is also initiated by the action of a CYP79 family enzyme, but the next enzyme involved belongs to the CYP83 family. We demonstrate that CYP83B1 from Arabidopsis thaliana cannot convert the (E)-p-hydroxyphenylacetaldoxime to the (Z)-isomer, which blocks the route towards cyanogenic glucoside synthesis. Instead CYP83B1 catalyzes the conversion of the (E)-p-hydroxyphenylacetaldoxime into an S-alkyl-thiohydroximate with retention of the configuration of the E-oxime intermediate in the final glucosinolate core structure. Numerous microbial plant pathogens are able to detoxify Z-oximes but not E-oximes. The CYP79-derived E-oximes may play an important role in plant defense.
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Affiliation(s)
- Mette Clausen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Rubini M Kannangara
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Carl E Olsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | | | - Roslyn M Gleadow
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Kirsten Jørgensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Søren Bak
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Mohammed S Motawie
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- VILLUM Research Center for 'Plant Plasticity', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Center for Synthetic Biology 'bioSYNergy', Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
- Carlsberg Laboratory, 10 Gamle Carlsberg Vej, DK-1799, Copenhagen V, Denmark
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8
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Celis AI, DuBois JL. Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme. Arch Biochem Biophys 2015; 574:3-17. [PMID: 25778630 PMCID: PMC4414885 DOI: 10.1016/j.abb.2015.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 12/21/2022]
Abstract
PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most important small molecules.
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Affiliation(s)
- Arianna I Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States.
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9
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Pavlou A, Martínková M, Shimizu T, Kitanishi K, Stranava M, Loullis A, Pinakoulaki E. Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy. Phys Chem Chem Phys 2015; 17:17007-15. [DOI: 10.1039/c5cp01708d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present time-resolved step-scan FTIR evidence for the role of the distal Y43 and L65 residues in controlling the ligand dynamics in the signal transducer protein YddV.
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Affiliation(s)
- Andrea Pavlou
- Department of Chemistry
- University of Cyprus
- 1678 Nicosia
- Cyprus
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Kenichi Kitanishi
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Martin Stranava
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Andreas Loullis
- Department of Chemistry
- University of Cyprus
- 1678 Nicosia
- Cyprus
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10
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Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis. Proc Natl Acad Sci U S A 2013; 110:2810-5. [PMID: 23382199 DOI: 10.1073/pnas.1200338110] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aldoxime dehydratase (OxdA), which is a unique heme protein, catalyzes the dehydration of an aldoxime to a nitrile even in the presence of water in the reaction mixture. Unlike the utilization of H(2)O(2) or O(2) as a mediator of catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron. Here, we determined the crystal structure of OxdA. We then constructed OxdA mutants in which each of the polar amino acids lying within ∼6 Å of the iron atom of the heme was converted to alanine. Among the purified mutant OxdAs, S219A had completely lost and R178A exhibited a reduction in the activity. Together with this finding, the crystal structural analysis of OxdA and spectroscopic and electrostatic potential analyses of the wild-type and mutant OxdAs suggest that S219 plays a key role in the catalysis, forming a hydrogen bond with the substrate. Based on the spatial arrangement of the OxdA active site and the results of a series of mutagenesis experiments, we propose the detailed catalytic mechanism of general aldoxime dehydratases: (i) S219 stabilizes the hydroxy group of the substrate to increase its basicity; (ii) H320 acts as an acid-base catalyst; and (iii) R178 stabilizes the heme, and would donate a proton to and accept one from H320.
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11
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Liao RZ, Thiel W. Why Is the Oxidation State of Iron Crucial for the Activity of Heme-Dependent Aldoxime Dehydratase? A QM/MM Study. J Phys Chem B 2012; 116:9396-408. [DOI: 10.1021/jp305510c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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