1
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Adak S, Ye N, Calderone LA, Duan M, Lubeck W, Schäfer RJB, Lukowski AL, Houk KN, Pandelia ME, Drennan CL, Moore BS. A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile. Nat Chem 2024:10.1038/s41557-024-01603-z. [PMID: 39285206 DOI: 10.1038/s41557-024-01603-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 07/12/2024] [Indexed: 09/25/2024]
Abstract
Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes.
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Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Naike Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Meng Duan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Wilson Lubeck
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Rebecca J B Schäfer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - April L Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | | | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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2
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Pei X, Xiao Q, Feng Y, Chen L, Yang F, Wang Q, Li N, Wang A. Enzymatic properties of a non-classical aldoxime dehydratase capable of producing alkyl and arylalkyl nitriles. Appl Microbiol Biotechnol 2023; 107:7089-7104. [PMID: 37733049 DOI: 10.1007/s00253-023-12767-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/22/2023]
Abstract
Nitriles are of significant interest in the flavor and fragrance industries with potential application in cosmetics due to their higher stability than analogous aldehydes. However, the traditional methods to prepare nitriles need toxic reagents and hash conditions. This work aimed to develop a chemoenzymatic strategy to synthesize nitriles from natural aldehydes with aldoxime as the intermediate. A non-classical aldoxime dehydratase (Oxd) was discovered from the fungus Aspergillus ibericus (OxdAsp) to catalyze the dehydration of aldoximes to corresponding nitriles under mild conditions. The amino acid sequence of OxdAsp exhibits an approximately 20% identity with bacterial Oxds. OxdAsp contains a heme prosthetic group bound with the axial H287 in the catalytic pocket. The structure models of OxdAsp with substrates suggest that its catalytic triad is Y138-R141-E192, which is different from the classically bacterial Oxds of His-Arg-Ser/Thr. The catalytic mechanism of OxdAsp was proposed based on the mutagenesis of key residues. The hydroxyl group of the substrate is fixed by E192 to increase its basicity. Y138 acts as a general acid-based catalyst, and its phenolic proton is polarized by the adjacent R141. The protonated Y138 would donate a proton to the hydroxyl group of the substrate and eliminate a water molecule from aldoxime to produce nitrile. The recombinant OxdAsp can efficiently dehydrate citronellal oxime and cinnamaldoxime to citronellyl nitrile and cinnamonitrile in aqueous media, which are applied as fragrance ingredients in the food and cosmetic fields. KEY POINTS: • A novel aldoxime dehydratase from the Aspergillus genus was first characterized as a heme-binding protein. • The catalytic mechanism was predicted based on the molecular interactions of the catalytic pocket with the substrate. • A chemoenzymatic strategy was developed to synthesize nitriles from natural aldehydes with aldoxime as the intermediate.
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Affiliation(s)
- Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Qinjie Xiao
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yumin Feng
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China
| | - Li Chen
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China
| | - Fengling Yang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qiuyan Wang
- School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Nanxing Li
- Zhejiang Medicine Co. Ltd, Xinchang, 312500, China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, 311121, China.
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3
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Adak S, Ye N, Calderone LA, Schäfer RJB, Lukowski AL, Pandelia ME, Drennan CL, Moore BS. Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551874. [PMID: 37577561 PMCID: PMC10418191 DOI: 10.1101/2023.08.03.551874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Nitriles are uncommon in nature and are typically constructed from oximes via the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third strategy of nitrile biosynthesis featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the 'eagle-killing' neurotoxin, aetokthonotoxin, AetD converts the alanyl side chain of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical, and biophysical techniques, we characterized AetD as a non-heme diiron enzyme that belongs to the emerging Heme Oxygenase-like Diiron Oxidase and Oxygenase (HDO) superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation that we propose proceeds via an aziridine intermediate. Our work presents a new paradigm for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other HDO enzymes.
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Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Naike Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Logan A. Calderone
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Rebecca J. B. Schäfer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - April L. Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
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4
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Engineered aldoxime dehydratase to enable the chemoenzymatic conversion of benzyl amines to aromatic nitriles. Bioorg Chem 2023; 134:106468. [PMID: 36933338 DOI: 10.1016/j.bioorg.2023.106468] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
A chemoenzymatic strategy has been implemented to synthesize nitriles from benzyl amines under mild conditions. Aldoxime dehydratase (Oxd) plays a decisive role to convert aldoximes into corresponding nitriles. However, natural Oxds commonly exhibit extremely low catalytic capacity toward benzaldehyde oximes. Here, we engineered the OxdF1 from Pseudomonas putida F1 to enhance its catalytic efficiency toward benzaldehyde oximes by a semi-rational design strategy. The protein structure-based CAVER analysis indicates that M29, A147, F306, and L318 are located adjacent to the substrate tunnel entrance of OxdF1, which were responsible for the transportation of substrate into the active site. After two rounds of mutagenesis, the maximum activities of the mutants L318F and L318F/F306Y were 2.6 and 2.8 U/mg respectively, which were significantly higher than the wild OxdF1 of 0.7 U/mg. Meanwhile, the lipase type B from Candida antarctica was functionally expressed in Escherichia coli cells to selectively oxidize benzyl amines to aldoximes using urea-hydrogen peroxide adduct (UHP) as an oxidant in ethyl acetate. To merge the oxidation and dehydration reactions, a reductive extraction solution was added to remove the residue UHP, which is critical to eliminate its inhibition on the Oxd activity. Consequently, nine benzyl amines were efficiently converted into corresponding nitriles by the chemoenzymatic sequence.
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5
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Gao H, Chen JY, Peng Z, Feng L, Tung CH, Wang W. Bioinspired Iron-Catalyzed Dehydration of Aldoximes to Nitriles: A General N-O Redox-Cleavage Method. J Org Chem 2022; 87:10848-10857. [PMID: 35914249 DOI: 10.1021/acs.joc.2c01122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inspired by OxdA that operates biocatalytic aldoxime dehydration, we have developed an efficient iron catalyst, Cp*Fe(1,2-Cy2PC6H4O) (1), which rapidly converts various aliphatic and aromatic aldoximes to nitriles with release of H2O at room temperature. The catalysis involves redox activation of the N-O bond by a 1e- transfer from the iron catalyst to the oxime. Such redox-mediated N-O cleavage was demonstrated by the isolation of a ferrous iminato intermediate from the reaction of the ketoxime substrate. This iron-catalyzed acceptorless dehydration approach represents a general method for the preparation of nitriles, and it also delivers salicylonitriles by catalyzing the Kemp elimination reaction.
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Affiliation(s)
- Hongjie Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jia-Yi Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhiqiang Peng
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lei Feng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Wenguang Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.,College of Chemistry, Beijing Normal University, Beijing 100875, China
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6
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Zheng H, Xiao Q, Mao F, Wang A, Li M, Wang Q, Zhang P, Pei X. Programing a cyanide-free transformation of aldehydes to nitriles and one-pot synthesis of amides through tandem chemo-enzymatic cascades. RSC Adv 2022; 12:17873-17881. [PMID: 35765330 PMCID: PMC9201870 DOI: 10.1039/d2ra03256b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
Nitriles are broadly applied to synthesize pharmaceuticals, agrochemicals, and materials because of their versatile transformation. Although various methods have been developed for introducing a nitrile group into organic molecules, most of them entail the use of highly toxic chemicals, transition metals, or harsh conditions. In this work, we reported a greener chemo-enzymatic cascade to synthesize alky and aryl nitriles from readily accessible aldehydes, that were further transformed into corresponding amides via an artificial enzyme cascade. A biphasic reaction system was designed to bridge chemical synthesis and enzymatic catalysis through simple phase separation. The biphasic system mainly perfectly avoided the inactivation of hydroxylamine on aldoxime dehydratase from Pseudomonas putida (OxdF1) and nitrile hydratase from Aurantimonas manganoxydans ATCC BAA-1229 (NHase1229). For the synthesis of various nitriles, moderate isolation yields of approximately 60% were obtained by the chemo-enzymatic cascade. Interestingly, two seemingly conflicting reactions of dehydration and hydration were sequentially proceeded to synthesize amides by the synergistic catalysis of OxdF1 and NHase1229 in E. coli cells. An isolation yield of approximately 62% was achieved for benzamide at the one-liter scale. In addition, the shuttle transport of substrates and products between two phases is convenient for the product separation and n-hexane recycling. Thus, the chemo-enzymatic cascade shows a potential application in the cyanide-free and large-scale synthesis of nitriles and amides. A chemo-enzymatic cascade was developed for the cyanide-free synthesis of nitriles from aldehydes and further one-pot transformation into amides.![]()
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Affiliation(s)
- Haoteng Zheng
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University Hangzhou 311121 PR China
| | - Qinjie Xiao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University Hangzhou 311121 PR China
| | - Feiying Mao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University Hangzhou 311121 PR China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University Hangzhou 311121 PR China
| | - Mu Li
- College of Food Science and Technology, Huazhong Agricultural University Wuhan 430070 PR China
| | - Qiuyan Wang
- School of Basic Medical Sciences, Hangzhou Normal University Hangzhou 311121 PR China
| | - Pengfei Zhang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University Hangzhou 311121 PR China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University Hangzhou 311121 PR China
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7
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Chen Z, Mao F, Zheng H, Xiao Q, Ding Z, Wang A, Pei X. Cyanide-free synthesis of aromatic nitriles from aldoximes: Discovery and application of a novel heme-containing aldoxime dehydratase. Enzyme Microb Technol 2021; 150:109883. [PMID: 34489036 DOI: 10.1016/j.enzmictec.2021.109883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/15/2021] [Accepted: 07/27/2021] [Indexed: 01/03/2023]
Abstract
Aromatic nitriles are important structural motifs that frequently existed in pharmaceutical drugs. Due to the convenient synthesis of aldoximes from aldehydes, the dehydration of aldoximes to corresponding nitriles by aldoxime dehydratases (Oxds) is considered as a safe and robust enzymatic production route. Although the Oxd genes are widely distributed in microbial kingdom, so far less than ten Oxds were expressed and further characterized. In this study, we found 26 predicted putative Oxd genes from the GenBank database using a genome mining strategy. The Oxd gene from Pseudomonas putida F1 was cloned and functionally expressed in Escherichia coli BL21 (DE3). The amino acid sequence of OxdF1 shows high identities of 33∼85 % to other characterized Oxds, and contained a ferrous heme as the catalytic site. The optimum reaction pH and temperature of recombinant OxdF1 were 7.0 and 35 °C, respectively. OxdF1 was stable in pH 7.0 potassium phosphate buffer at 30 °C, and its half-life was approximately 3.8 h. OxdF1 can efficiently dehydrate aromatic and heterocyclic aldoximes to nitriles, such as 2-bromobenzaldoxime, 2-chloro-6-fluorobenzaldoxime, thiophene-2-carboxaldoxime, and pyridine-3-aldoxime. Therefore, the recombinant OxdF1 shows a potential application in the cyanide-free synthesis of aromatic nitriles.
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Affiliation(s)
- Zhiji Chen
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Feiying Mao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Haoteng Zheng
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qinjie Xiao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhihao Ding
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 311121, China.
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8
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Hashimoto Y, Ube Y, Doi S, Kumano T, Kobayashi M. Metal chaperone, NhpC, involved in the metallocenter biosynthesis of nitrile hydratase. J GEN APPL MICROBIOL 2021; 67:24-32. [DOI: 10.2323/jgam.2020.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yoshiteru Hashimoto
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
| | - Yuko Ube
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
| | - Shiori Doi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
| | - Takuto Kumano
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
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9
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Betke T, Maier M, Gruber-Wölfler H, Gröger H. Biocatalytic production of adiponitrile and related aliphatic linear α,ω-dinitriles. Nat Commun 2018; 9:5112. [PMID: 30504854 PMCID: PMC6269433 DOI: 10.1038/s41467-018-07434-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022] Open
Abstract
Linear α,ω-dinitriles are important precursors for the polymer industry. Most prominently, adiponitrile is produced on an annual scale of ca. 1 million tons. However, a drawback of today’s dominating process is the need for large amounts of highly toxic hydrogen cyanide. In this contribution, an alternative approach towards such linear dinitriles is presented based on dehydration of readily available α,ω-dialdoximes at ambient conditions by means of aldoxime dehydratases. In contrast to existing production routes this biocatalytic route enables a highly regio- and chemoselective approach towards dinitriles without the use of hydrogen cyanide or harsh reaction conditions. In addition, a selective synthesis of adiponitrile with substrate loadings of up to 100 g/L and high yields of up to 80% was achieved. Furthermore, a lab scale process on liter scale leading to > 99% conversion at 50 g/L underlines the potential and robustness of this method for technical applicability. Typically, preparation of the polymer precursors α,ω-dinitriles requires hydrogen cyanide. Here, the authors use aldoxime hydratase to produce adiponitrile and related aliphatic linear dinitriles under ambient conditions starting from readily available substrates without needing hydrogen cyanide.
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Affiliation(s)
- Tobias Betke
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Manuel Maier
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13/III, 8010, Graz, Austria
| | - Heidrun Gruber-Wölfler
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13/III, 8010, Graz, Austria
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.
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10
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Overproduction and characterization of the first enzyme of a new aldoxime dehydratase family in Bradyrhizobium sp. Int J Biol Macromol 2018; 115:746-753. [PMID: 29698761 DOI: 10.1016/j.ijbiomac.2018.04.103] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/23/2022]
Abstract
Almost 100 genes within the genus Bradyrhizobium are known to potentially encode aldoxime dehydratases (Oxds), but none of the corresponding proteins have been characterized yet. Aldoximes are natural substances involved in plant defense and auxin synthesis, and Oxds are components of enzymatic cascades enabling bacteria to transform, utilize and detoxify them. The aim of this work was to characterize a representative of the highly conserved Oxds in Bradyrhizobium spp. which include both plant symbionts and members of the soil communities. The selected oxd gene from Bradyrhizobium sp. LTSPM299 was expressed in Escherichia coli, and the corresponding gene product (OxdBr1; GenBank: WP_044589203) was obtained as an N-His6-tagged protein (monomer, 40.7 kDa) with 30-47% identity to Oxds characterized previously. OxdBr1 was most stable at pH ca. 7.0-8.0 and at up to 30 °C. As substrates, the enzyme acted on (aryl)aliphatic aldoximes such as E/Z-phenylacetaldoxime, E/Z-2-phenylpropionaldoxime, E/Z-3-phenylpropionaldoxime, E/Z-indole-3-acetaldoxime, E/Z-propionaldoxime, E/Z-butyraldoxime, E/Z-valeraldoxime and E/Z-isovaleraldoxime. Some of the reaction products of OxdBr1 are substrates of nitrilases occurring in the same genus. Regions upstream of the oxd gene contained genes encoding a putative aliphatic nitrilase and its transcriptional activator, indicating the participation of OxdBr1 in the metabolic route from aldoximes to carboxylic acids.
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11
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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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12
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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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13
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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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14
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Kumano T, Takizawa Y, Shimizu S, Kobayashi M. Nitrile-synthesizing enzyme: Gene cloning, overexpression and application for the production of useful compounds. J GEN APPL MICROBIOL 2016; 62:174-80. [DOI: 10.2323/jgam.2016.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Takuto Kumano
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Yuko Takizawa
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Sakayu Shimizu
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
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15
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Kumano T, Suzuki T, Shimizu S, Kobayashi M. Nitrile-synthesizing enzyme: Screening, purification and characterization. J GEN APPL MICROBIOL 2016; 62:167-73. [DOI: 10.2323/jgam.2016.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Takuto Kumano
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Takahisa Suzuki
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Sakayu Shimizu
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
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16
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Rapeyko A, Climent MJ, Corma A, Concepción P, Iborra S. Postsynthesis-Treated Iron-Based Metal-Organic Frameworks as Selective Catalysts for the Sustainable Synthesis of Nitriles. CHEMSUSCHEM 2015; 8:3270-3282. [PMID: 26333197 DOI: 10.1002/cssc.201500695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Indexed: 06/05/2023]
Abstract
The dehydration of aldoximes to the corresponding nitriles can be performed with excellent activity and selectivity by using iron trimesate as a homogeneous catalyst. Iron trimesate has been heterogenized by synthesizing metal-organic frameworks (MOFs) from iron trimesate, that is, Fe(BTC), and MIL-100 (Fe). These materials were active and selective aldoxime dehydration catalysts, and postsynthesis-treated MIL-100 (Fe) produced the desired nitriles with 100 % conversion and selectivities >90 % under mild reaction conditions and in short reaction times. X-ray photoelectron spectroscopy showed the presence of different Fe species in the catalyst, and in situ IR spectroscopy combined with catalytic results indicates that the catalytic activity is associated with Fe framework species. The postsynthesis-treated MIL-100 (Fe)-NH4 F can be recycled several times and has an excellent reaction scope, which gives better catalytic results than other solid acid or base catalysts.
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Affiliation(s)
- Anastasia Rapeyko
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain
| | - Maria J Climent
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain
| | - Avelino Corma
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain.
- King Fahd University of Petroleum and Minerals, P.O. Box 989, Dhahran, 31261, Saudi Arabia.
| | - Patricia Concepción
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain
| | - Sara Iborra
- Instituto de Tecnología Química (UPV-CSIC), Universitat Politécnica de València, Avda dels Tarongers s/n, 46022, Valencia, Spain.
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A new synthetic route to N-benzyl carboxamides through the reverse reaction of N-substituted formamide deformylase. Appl Environ Microbiol 2013; 80:61-9. [PMID: 24123742 DOI: 10.1128/aem.02429-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we isolated a new enzyme, N-substituted formamide deformylase, that catalyzes the hydrolysis of N-substituted formamide to the corresponding amine and formate (H. Fukatsu, Y. Hashimoto, M. Goda, H. Higashibata, and M. Kobayashi, Proc. Natl. Acad. Sci. U. S. A. 101:13726-13731, 2004, doi:10.1073/pnas.0405082101). Here, we discovered that this enzyme catalyzed the reverse reaction, synthesizing N-benzylformamide (NBFA) from benzylamine and formate. The reverse reaction proceeded only in the presence of high substrate concentrations. The effects of pH and inhibitors on the reverse reaction were almost the same as those on the forward reaction, suggesting that the forward and reverse reactions are both catalyzed at the same catalytic site. Bisubstrate kinetic analysis using formate and benzylamine and dead-end inhibition studies using a benzylamine analogue, aniline, revealed that the reverse reaction of this enzyme proceeds via an ordered two-substrate, two-product (bi-bi) mechanism in which formate binds first to the enzyme active site, followed by benzylamine binding and the subsequent release of NBFA. To our knowledge, this is the first report of the reverse reaction of an amine-forming deformylase. Surprisingly, analysis of the substrate specificity for acids demonstrated that not only formate, but also acetate and propionate (namely, acids with numbers of carbon atoms ranging from C1 to C3), were active as acid substrates for the reverse reaction. Through this reaction, N-substituted carboxamides, such as NBFA, N-benzylacetamide, and N-benzylpropionamide, were synthesized from benzylamine and the corresponding acid substrates.
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18
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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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19
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Structures and mechanisms of the dehydration of benzaldoxime over Fe-ZSM-5 zeolites: a DFT study. Struct Chem 2012. [DOI: 10.1007/s11224-012-0161-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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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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21
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Pan XL, Cui FC, Liu W, Liu JY. QM/MM Study on the Catalytic Mechanism of Heme-Containing Aliphatic Aldoxime Dehydratase. J Phys Chem B 2012; 116:5689-93. [DOI: 10.1021/jp302114d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao-Liang Pan
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Feng-Chao Cui
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Wei Liu
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Jing-Yao Liu
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
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22
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Pinakoulaki E, Koutsoupakis C, Sawai H, Pavlou A, Kato Y, Asano Y, Aono S. Aldoxime Dehydratase: Probing the Heme Environment Involved in the Synthesis of the Carbon–Nitrogen Triple Bond. J Phys Chem B 2011; 115:13012-8. [DOI: 10.1021/jp205944e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | - Hitomi Sawai
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Andrea Pavlou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shigetoshi Aono
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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23
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Exploiting the interactions of PNA-DNA films with Ni2+ ions: detection of nucleobase mismatches and electrochemical genotyping of the single-nucleotide mismatch in apoE 4 related to Alzheimer's disease. Biosens Bioelectron 2011; 27:187-91. [PMID: 21752624 DOI: 10.1016/j.bios.2011.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/20/2011] [Accepted: 06/10/2011] [Indexed: 11/23/2022]
Abstract
The presence of Ni(2+) enables us to distinguish the presence of single-nucleotide mismatches in PNA (peptide nucleic acids)-DNA films on gold electrodes by electrochemical impedance spectroscopy (EIS). With the help of a modified Randles' equivalent circuit, differences in the charge transfer resistance (ΔR(CT)) before and after the addition of Ni(2+) are a diagnostic measure for the presence of single-nucleotide mismatch. The approach works under real-life conditions with concentrations of the DNA target strand down to 10 fM, and a PNA capture probe is used to genotype the single-nucleotide mismatch in apoE 4 related to Alzheimer's disease (AD).
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24
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Sato H, Hashimoto Y, Fukatsu H, Kobayashi M. Novel isonitrile hydratase involved in isonitrile metabolism. J Biol Chem 2010; 285:34793-802. [PMID: 20826798 DOI: 10.1074/jbc.m110.150227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously discovered N-substituted formamide deformylase (NfdA) in Arthrobacter pascens F164, which degrades N-substituted formamide (Fukatsu, H., Hashimoto, Y., Goda, M., Higashibata, H., and Kobayashi, M. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 13726-13731). In this study, we found an enzyme involved in the first step of isonitrile metabolism, isonitrile hydratase, that hydrates isonitrile to the corresponding N-substituted formamide. First, we investigated the optimum culture conditions for the production of isonitrile hydratase. The highest enzyme activity was obtained when A. pascens F164 was cultured in a nutrient medium containing N-benzylformamide. This Arthrobacter isonitrile hydratase was purified, characterized, and compared with Pseudomonas putida N19-2 isonitrile hydratase (InhA), which is the sole one reported at present. Arthrobacter isonitrile hydratase was found to have a molecular mass of about 530 kDa and to consist of 12 identical subunits. The apparent K(m) value for cyclohexyl isocyanide was 0.95 ± 0.05 mm. A. pascens F164 grew and exhibited the isonitrile hydratase and N-substituted formamide deformylase activities when cultured in a medium containing an isonitrile as the sole carbon and nitrogen sources. However, both enzyme activities were not observed on culture in a medium containing glycerol and (NH(4))(2)SO(4) as the sole carbon and nitrogen sources, respectively. These findings suggested that the Arthrobacter enzyme is an inducible enzyme, possibly involved in assimilation and/or detoxification of isonitrile. Moreover, gene cloning of the Arthrobacter enzyme revealed no sequence similarity between this enzyme and InhA. Comparison of their properties and features demonstrated that the two enzymes are biochemically, immunologically, and structurally different from each other. Thus, we discovered a new isonitrile hydratase named InhB.
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Affiliation(s)
- Hiroyoshi Sato
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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25
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Sawai H, Sugimoto H, Kato Y, Asano Y, Shiro Y, Aono S. X-ray crystal structure of michaelis complex of aldoxime dehydratase. J Biol Chem 2009; 284:32089-96. [PMID: 19740758 DOI: 10.1074/jbc.m109.018762] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aldoxime dehydratase (Oxd) catalyzes the dehydration of aldoximes (R-CH=N-OH) to their corresponding nitrile (R-C triple bond N). Oxd is a heme-containing enzyme that catalyzes the dehydration reaction as its physiological function. We have determined the first two structures of Oxd: the substrate-free OxdRE at 1.8 A resolution and the n-butyraldoxime- and propionaldoxime-bound OxdREs at 1.8 and 1.6 A resolutions, respectively. Unlike other heme enzymes, the organic substrate is directly bound to the heme iron in OxdRE. We determined the structure of the Michaelis complex of OxdRE by using the unique substrate binding and activity regulation properties of Oxd. The Michaelis complex was prepared by x-ray cryoradiolytic reduction of the ferric dead-end complex in which Oxd contains a Fe(3+) heme form. The crystal structures reveal the mechanism of substrate recognition and the catalysis of OxdRE.
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Affiliation(s)
- Hitomi Sawai
- From the Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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26
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Bjarnholt N, Møller BL. Hydroxynitrile glucosides. PHYTOCHEMISTRY 2008; 69:1947-61. [PMID: 18539303 DOI: 10.1016/j.phytochem.2008.04.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 04/16/2008] [Indexed: 05/08/2023]
Abstract
beta- and gamma-Hydroxynitrile glucosides are structurally related to cyanogenic glucosides (alpha-hydroxynitrile glucosides) but do not give rise to hydrogen cyanide release upon hydrolysis. Structural similarities and frequent co-occurrence suggest that the biosynthetic pathways for these compounds share common features. Based on available literature data we propose that oximes produced by CYP79 orthologs are common intermediates and that their conversion into beta- and gamma-hydroxynitrile glucosides is mediated by evolutionary diversified multifunctional orthologs to CYP71E1. We designate these as CYP71(betagamma) and CYP71(alphabetagamma); in combination with the classical CYP71(alpha) (CYP71E1 and orthologs) these are able to hydroxylate any of the carbon atoms present in the amino acid and oxime derived nitriles. Subsequent dehydration reactions and hydroxylations and a final glycosylation step afford the unsaturated beta- and gamma-hydroxynitrile glucosides. This scheme would explain the distribution patterns of alpha-, beta- and gamma-hydroxynitrile glucosides found in plants. The possible biological functions of these hydroxynitriles are discussed.
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Affiliation(s)
- Nanna Bjarnholt
- Plant Biochemistry Laboratory and The VKR Research Centre Pro-Active Plants, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg C, Copenhagen, Denmark
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27
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Abe T, Hashimoto Y, Hosaka H, Tomita-Yokotani K, Kobayashi M. Discovery of amide (peptide) bond synthetic activity in Acyl-CoA synthetase. J Biol Chem 2008; 283:11312-21. [PMID: 18305111 DOI: 10.1074/jbc.m709654200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acyl-CoA synthetase, which is one of the acid-thiol ligases (EC 6.2.1), plays key roles in metabolic and regulatory processes. This enzyme forms a carbon-sulfur bond in the presence of ATP and Mg(2+), yielding acyl-CoA thioesters from the corresponding free acids and CoA. This enzyme belongs to the superfamily of adenylate-forming enzymes, whose three-dimensional structures are analogous to one another. We here discovered a new reaction while studying the short-chain acyl-CoA synthetase that we recently reported (Hashimoto, Y., Hosaka, H., Oinuma, K., Goda, M., Higashibata, H., and Kobayashi, M. (2005) J. Biol. Chem. 280, 8660-8667). When l-cysteine was used as a substrate instead of CoA, N-acyl-l-cysteine was surprisingly detected as a reaction product. This finding demonstrated that the enzyme formed a carbon-nitrogen bond (EC 6.3.1 acid-ammonia (or amide) ligase (amide synthase); EC 6.3.2 acid-amino acid ligase (peptide synthase)) comprising the amino group of the cysteine and the carboxyl group of the acid. N-Acyl-d-cysteine, N-acyl-dl-homocysteine, and N-acyl-l-cysteine methyl ester were also synthesized from the corresponding cysteine analog substrates by the enzyme. Furthermore, this unexpected enzyme activity was also observed for acetyl-CoA synthetase and firefly luciferase, indicating the generality of the new reaction in the superfamily of adenylate-forming enzymes.
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Affiliation(s)
- Tomoko Abe
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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28
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Kato Y, Tsuda T, Asano Y. Purification and partial characterization of N-hydroxy-l-phenylalanine decarboxylase/oxidase from Bacillus sp. strain OxB-1, an enzyme involved in aldoxime biosynthesis in the “aldoxime–nitrile pathway”. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:856-65. [PMID: 17544345 DOI: 10.1016/j.bbapap.2007.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 03/27/2007] [Accepted: 04/25/2007] [Indexed: 11/22/2022]
Abstract
An enzyme that catalyzes the conversion of N-hydroxy-l-phenylalanine to phenylacetaldoxime was shown to be present in the Z-phenylacetaldoxime-degrading bacterium, Bacillus sp. strain OxB-1. The aldoxime-forming enzyme, which is induced by L-phenylalanine, was purified 8,050-fold to apparent homogeneity with a yield of 15.2%. The enzyme has a subunit M(r) of about 86,000. The enzyme converts N-hydroxy-L-phenylalanine (K(m) 0.99 mM) to only one geometrical isomer, namely Z-phenylacetaldoxime. Relatively large amounts of pyridoxal 5'-phosphate (PLP) are required to be present in the reaction mixture because PLP reacts non-enzymatically with the N-hydroxy amino acid substrate to form a nitrone. Several characteristics of the enzyme were compared with those of other PLP-dependent aromatic amino acid-converting enzymes described in the literature. The enzyme is tentatively named "N-hydroxy-L-phenylalanine decarboxylase/oxidase". Finally, the possible biosynthesis and metabolism of phenylacetaldoxime in Bacillus sp. strain OxB-1 is discussed.
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Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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Kobayashi K, Kubo M, Yoshioka S, Kitagawa T, Kato Y, Asano Y, Aono S. Systematic Regulation of the Enzymatic Activity of Phenylacetaldoxime Dehydratase by Exogenous Ligands. Chembiochem 2006; 7:2004-9. [PMID: 17009275 DOI: 10.1002/cbic.200600261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Phenylacetaldoxime dehydratase from Bacillus sp. OxB-1 (OxdB) contains a heme that acts as the active site for the dehydration reaction of aldoxime. Ferrous heme is the active form, in which the heme is five coordinate with His282 as a proximal ligand. In this work, we evaluated the functional role of the proximal ligand for the catalytic properties of the enzyme by "the cavity mutant technique". The H282G mutant of OxdB lost enzymatic activity, although the heme, which was five coordinate with a water molecule (or OH-) as an axial ligand, existed in the protein matrix. The enzymatic activity was rescued by imidazole or pyridine derivatives that acted as the exogenous proximal ligand. By changing the electron-donation ability of the exogenous ligand with different substituents, the enzymatic activity could be regulated systematically. The stronger the electron-donation ability of the exogenous ligand, the higher was the restored enzymatic activity. Interestingly, H282G OxdB with 2-methyl imidazole showed a higher activity than the wild-type enzyme. Kinetic analyses revealed that the proximal His regulated not only the affinity of substrate binding to the heme but also the elimination of the OH group from the substrate.
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Affiliation(s)
- Katsuaki Kobayashi
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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