1
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Liu H, Gao Q, Zhang K, Xu M, Wang H, Wei D. Combining binding pocket mutagenesis and substrate tunnel engineering to improve an (R)-selective transaminase for the efficient synthesis of (R)-3-aminobutanol. Biochem Biophys Res Commun 2024; 731:150383. [PMID: 39024977 DOI: 10.1016/j.bbrc.2024.150383] [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: 03/27/2024] [Revised: 06/28/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
(R)-selective transaminases have the potential to act as efficient biocatalysts for the synthesis of important pharmaceutical intermediates. However, their low catalytic efficiency and unfavorable equilibrium limit their industrial application. Seven (R)-selective transaminases were identified using homologous sequence mining. Beginning with the optimal candidate from Mycolicibacterium hippocampi, virtual mutagenesis and substrate tunnel engineering were performed to improve catalytic efficiency. The obtained variant, T282S/Q137E, exhibited 3.68-fold greater catalytic efficiency (kcat/Km) than the wild-type enzyme. Using substrate fed-batch and air sweeping processes, effective conversion of 100 mM 4-hydroxy-2-butanone was achieved with a conversion rate of 93 % and an ee value > 99.9 %. This study provides a basis for mutation of (R)-selective transaminases and offers an efficient biocatalytic process for the asymmetric synthesis of (R)-3-aminobutanol.
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Affiliation(s)
- He Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Qian Gao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Kaiyue Zhang
- Ludong University Laishan Experimental Middle School, 264000, China
| | - Meng Xu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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2
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Zhou SP, Xue YP, Zheng YG. Maximizing the potential of nitrilase: Unveiling their diversity, catalytic proficiency, and versatile applications. Biotechnol Adv 2024; 72:108352. [PMID: 38574900 DOI: 10.1016/j.biotechadv.2024.108352] [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: 11/21/2023] [Revised: 03/10/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
Nitrilases represent a distinct class of enzymes that play a pivotal role in catalyzing the hydrolysis of nitrile compounds, leading to the formation of corresponding carboxylic acids. These enzymatic entities have garnered significant attention across a spectrum of industries, encompassing pharmaceuticals, agrochemicals, and fine chemicals. Moreover, their significance has been accentuated by mounting environmental pressures, propelling them into the forefront of biodegradation and bioremediation endeavors. Nevertheless, the natural nitrilases exhibit intrinsic limitations such as low thermal stability, narrow substrate selectivity, and inadaptability to varying environmental conditions. In the past decade, substantial efforts have been made in elucidating the structural underpinnings and catalytic mechanisms of nitrilase, providing basis for engineering of nitrilases. Significant breakthroughs have been made in the regulation of nitrilases with ideal catalytic properties and application of the enzymes for industrial productions. This review endeavors to provide a comprehensive discourse and summary of recent research advancements related to nitrilases, with a particular emphasis on the elucidation of the structural attributes, catalytic mechanisms, catalytic characteristics, and strategies for improving catalytic performance of nitrilases. Moreover, the exploration extends to the domain of process engineering and the multifarious applications of nitrilases. Furthermore, the future development trend of nitrilases is prospected, providing important guidance for research and application in the related fields.
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Affiliation(s)
- Shi-Peng Zhou
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ya-Ping Xue
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yu-Guo Zheng
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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3
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Shilova SA, Matyuta IO, Khrenova MG, Nikolaeva AY, Klyachko NL, Minyaev ME, Khomutov AR, Boyko KM, Popov VO, Bezsudnova EY. In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity. Biochem J 2023; 480:1267-1284. [PMID: 37548495 DOI: 10.1042/bcj20230233] [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: 06/09/2023] [Revised: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 08/08/2023]
Abstract
The development of biocatalysts requires reorganization of the enzyme's active site to facilitate the productive binding of the target substrate and improve turnover number at desired conditions. Pyridoxal-5'-phosphate (PLP) - dependent transaminases are highly efficient biocatalysts for asymmetric amination of ketones and keto acids. However, transaminases, being stereoselective enzymes, have a narrow substrate specificity due to the ordered structure of the active site and work only in neutral-alkaline media. Here, we investigated the d-amino acid transaminase from Aminobacterium colombiense, with the active site organized differently from that of the canonical d-amino acid transaminase from Bacillus sp. YM-1. Using a combination of site-directed mutagenesis, kinetic analysis, molecular modeling, and structural analysis we determined the active site residues responsible for substrate binding, substrate differentiation, thermostability of a functional dimer, and affecting the pH optimum. We demonstrated that the high specificity toward d-glutamate/α-ketoglutarate is due to the interactions of a γ-carboxylate group with K237 residue, while binding of other substrates stems from the effectiveness of their accommodation in the active site optimized for d-glutamate/α-ketoglutarate binding. Furthermore, we showed that the K237A substitution shifts the catalytic activity optimum to acidic pH. Our findings are useful for achieving target substrate specificity and demonstrate the potential for developing and optimizing transaminases for various applications.
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Affiliation(s)
- Sofia A Shilova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya O Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maria G Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alena Y Nikolaeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Natalia L Klyachko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail E Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alex R Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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4
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Shilova SA, Khrenova MG, Matyuta IO, Nikolaeva AY, Rakitina TV, Klyachko NL, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY. To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense. Molecules 2023; 28:molecules28052109. [PMID: 36903355 PMCID: PMC10003956 DOI: 10.3390/molecules28052109] [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: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Pyridoxal-5'-phosphate (PLP)-dependent transaminases are highly efficient biocatalysts for stereoselective amination. D-amino acid transaminases can catalyze stereoselective transamination producing optically pure D-amino acids. The knowledge of substrate binding mode and substrate differentiation mechanism in D-amino acid transaminases comes down to the analysis of the transaminase from Bacillus subtilis. However, at least two groups of D-amino acid transaminases differing in the active site organization are known today. Here, we present a detailed study of D-amino acid transaminase from the gram-negative bacterium Aminobacterium colombiense with a substrate binding mode different from that for the transaminase from B. subtilis. We study the enzyme using kinetic analysis, molecular modeling, and structural analysis of holoenzyme and its complex with D-glutamate. We compare the multipoint binding of D-glutamate with the binding of other substrates, D-aspartate and D-ornithine. QM/MM MD simulation reveals that the substrate can act as a base and its proton can be transferred from the amino group to the α-carboxylate group. This process occurs simultaneously with the nucleophilic attack of the PLP carbon atom by the nitrogen atom of the substrate forming gem-diamine at the transimination step. This explains the absence of the catalytic activity toward (R)-amines that lack an α-carboxylate group. The obtained results clarify another substrate binding mode in D-amino acid transaminases and underpinned the substrate activation mechanism.
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Affiliation(s)
- Sofia A. Shilova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya O. Matyuta
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alena Y. Nikolaeva
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Tatiana V. Rakitina
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Natalia L. Klyachko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mikhail E. Minyaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina Yu. Bezsudnova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence:
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5
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Wegner U, Matthes F, von Wirén N, Hajirezaei MR, Bode R, Kunze G, Rauter M. A transaminase with β-activity from Variovorax boronicumulans for the production of enantiopure β-amino acids. Heliyon 2022; 9:e12729. [PMID: 36685366 PMCID: PMC9850050 DOI: 10.1016/j.heliyon.2022.e12729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/11/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023] Open
Abstract
Enantioselective transamination of amino acids is a great challenge in biotechnology as suitable enzymes with wide substrate spectrum are rare. Here, we present a new transaminase from Variovorax boronicumulans (VboTA, Variovorax boronicumulansω-transaminase) which is specific for β-amino acids. The amino acid sequence of VboTA is similar to an ω-transaminase from Variovorax paradoxus, for which a crystal-structure is available. This similarity is allowing us to classify VboTA as a fold type 1 ω-transaminase (ω-TA). Although both enzymes have a high sequence similarity (86% identities, 92% positives), there are differences in the active center, which allow VboTA to accept a broader substrate spectrum. Both enzymes have also a different temperature stability and temperature optimum. VboTA deaminates the D-form of aromatic β-amino acids, such as β-homophenylalanine and β-phenylalanine as well as aliphatic β-amino acids, such as β-homoalanine and β-leucine. The optimal reaction conditions turned out to be 32 °C and pH 9. Kinetic resolution lead to high enantiomeric excess of 86.6% to >99.9%, depending on the amino donor/acceptor pair. In contrast to many other ω-TAs, VboTA has a broad substrate spectrum and uses both aromatic or aliphatic amino acids. With γ-amino acids as substrates, VboTA showed no activity at all.
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Affiliation(s)
- Uwe Wegner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Falko Matthes
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Mohammad-Reza Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Rüdiger Bode
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany,Corresponding author.
| | - Marion Rauter
- Orgentis Chemicals GmbH, Bahnhofstr. 3-5, OT Gatersleben, D-06466 Seeland, Germany
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6
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Wang Y, Subrizi F, Carter EM, Sheppard TD, Ward JM, Hailes HC. Enzymatic synthesis of benzylisoquinoline alkaloids using a parallel cascade strategy and tyrosinase variants. Nat Commun 2022; 13:5436. [PMID: 36114194 PMCID: PMC9481557 DOI: 10.1038/s41467-022-33122-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Benzylisoquinoline alkaloid derived pharmaceuticals are widely applied in modern medicines. Recent studies on the microbial production of benzylisoquinolines have highlighted key biological syntheses towards these natural products. Routes to non-natural benzylisoquinolines have been less explored, particularly halogenated compounds which are more challenging. Here, we show the use of a tyrosinase, tyrosine decarboxylase, transaminase, and norcoclaurine synthase which are combined in a parallel cascade design, in order to generate halogenated benzylisoquinoline alkaloids in high enantiomeric excess. Notably, mutagenesis studies are applied to generate tyrosinase mutants, which enhance the acceptance of halogenated tyrosines for use in the biocatalytic cascades developed.
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Affiliation(s)
- Yu Wang
- Department of Chemistry, Christopher Ingold Building, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Fabiana Subrizi
- Department of Chemistry, Christopher Ingold Building, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Eve M Carter
- Department of Chemistry, Christopher Ingold Building, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Tom D Sheppard
- Department of Chemistry, Christopher Ingold Building, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - John M Ward
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, WC1E 6BT, UK
| | - Helen C Hailes
- Department of Chemistry, Christopher Ingold Building, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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7
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Yeom SJ, Kwon KK, An JU, Park SH, Lee JY, Rha E, Lee H, Kim H, Lee DH, Lee SG. Single-Cell-Based Screening and Engineering of d-Amino Acid Amidohydrolases Using Artificial Amidophenol Substrates and Microbial Biosensors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1203-1211. [PMID: 34994555 DOI: 10.1021/acs.jafc.1c05834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enantiomerically pure d-amino acids are important intermediates as chiral building blocks for peptidomimetics and semisynthetic antibiotics. Here, a transcriptional factor-based screening strategy was used for the rapid screening of d-stereospecific amino acid amidase via an enzyme-specific amidophenol substrate. We used a d-threonine amidophenyl derivative to produce 2-aminophenol that serves as a putative enzyme indicator in the presence of d-threonine amidases. Comparative analyses of known bacterial species indicated that several Bacillus strains produce amidase and form putative indicators in culture media. The estimated amidase was cloned and subjected to rapid directed evolution through biosensor cells. Consequently, we characterized the F119A mutation that significantly improved the catalytic activity toward d-alanine, d-threonine, and d-glutamate. Its beneficial effects were confirmed by higher conversions and recurrent applications of the mutant enzyme, compared to the wild-type. This study showed that rapid directed evolution with biosensors coupled to designed substrates is useful to develop biocatalytic processes.
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Affiliation(s)
- Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- School of Biological Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jung-Ung An
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sung Hyun Park
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Jin-Young Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eugene Rha
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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8
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Computer Modeling Explains the Structural Reasons for the Difference in Reactivity of Amine Transaminases Regarding Prochiral Methylketones. Int J Mol Sci 2022; 23:ijms23020777. [PMID: 35054965 PMCID: PMC8776209 DOI: 10.3390/ijms23020777] [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: 12/07/2021] [Revised: 12/30/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Amine transaminases (ATAs) are pyridoxal-5′-phosphate (PLP)-dependent enzymes that catalyze the transfer of an amino group from an amino donor to an aldehyde and/or ketone. In the past decade, the enzymatic reductive amination of prochiral ketones catalyzed by ATAs has attracted the attention of researchers, and more traditional chemical routes were replaced by enzymatic ones in industrial manufacturing. In the present work, the influence of the presence of an α,β-unsaturated system in a methylketone model substrate was investigated, using a set of five wild-type ATAs, the (R)-selective from Aspergillus terreus (Atr-TA) and Mycobacterium vanbaalenii (Mva-TA), the (S)-selective from Chromobacterium violaceum (Cvi-TA), Ruegeria pomeroyi (Rpo-TA), V. fluvialis (Vfl-TA) and an engineered variant of V. fluvialis (ATA-256 from Codexis). The high conversion rate (80 to 99%) and optical purity (78 to 99% ee) of both (R)- and (S)-ATAs for the substrate 1-phenyl-3-butanone, using isopropylamine (IPA) as an amino donor, were observed. However, the double bond in the α,β-position of 4-phenylbut-3-en-2-one dramatically reduced wild-type ATA reactivity, leading to conversions of <10% (without affecting the enantioselectivity). In contrast, the commercially engineered V. fluvialis variant, ATA-256, still enabled an 87% conversion, yielding a corresponding amine with >99% ee. Computational docking simulations showed the differences in orientation and intermolecular interactions in the active sites, providing insights to rationalize the observed experimental results.
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9
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Adhikari A, Bhattarai BR, Aryal A, Thapa N, Kc P, Adhikari A, Maharjan S, Chanda PB, Regmi BP, Parajuli N. Reprogramming natural proteins using unnatural amino acids. RSC Adv 2021; 11:38126-38145. [PMID: 35498070 PMCID: PMC9044140 DOI: 10.1039/d1ra07028b] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Unnatural amino acids have gained significant attention in protein engineering and drug discovery as they allow the evolution of proteins with enhanced stability and activity. The incorporation of unnatural amino acids into proteins offers a rational approach to engineer enzymes for designing efficient biocatalysts that exhibit versatile physicochemical properties and biological functions. This review highlights the biological and synthetic routes of unnatural amino acids to yield a modified protein with altered functionality and their incorporation methods. Unnatural amino acids offer a wide array of applications such as antibody-drug conjugates, probes for change in protein conformation and structure-activity relationships, peptide-based imaging, antimicrobial activities, etc. Besides their emerging applications in fundamental and applied science, systemic research is necessary to explore unnatural amino acids with novel side chains that can address the limitations of natural amino acids.
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Affiliation(s)
- Anup Adhikari
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Bibek Raj Bhattarai
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Ashika Aryal
- Department of Chemistry, Birendra Multiple Campus, Tribhuvan University Bharatpur Chitwan Nepal
| | - Niru Thapa
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Puja Kc
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Ashma Adhikari
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Sushila Maharjan
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
| | - Prem B Chanda
- Department of Chemistry and Physics, Southeastern Louisiana University Hammond Louisiana 70402 USA
| | - Bishnu P Regmi
- Department of Chemistry, Florida Agricultural and Mechanical University Tallahassee Florida 32307 USA
| | - Niranjan Parajuli
- Biological Chemistry Lab, Central Department of Chemistry, Tribhuvan University Kritipur 44618 Kathmandu Nepal
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10
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Cárdenas-Fernández M, Sinclair O, Ward JM. Novel transaminases from thermophiles: from discovery to application. Microb Biotechnol 2021; 15:305-317. [PMID: 34713952 PMCID: PMC8719814 DOI: 10.1111/1751-7915.13940] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 01/26/2023] Open
Abstract
Transaminases (TAs) are promising biocatalysts for chiral amine synthesis; however, only few thermophilic TAs have been described to date. In this work, a genome mining approach was taken to seek novel TAs from nine thermophilic microorganisms. TA sequences were identified from their respective genome sequences and their Pfam were predicted confirming that TAs class I–II are the most abundant (50%), followed by class III (26%), V (16%), IV (8%) and VI (1%). The percentage of open reading frames (ORFs) that are TAs ranges from 0.689% in Thermococcus litoralis to 0.424% in Sulfolobus solfataricus. A total of 94 putative TAs were successfully cloned and expressed into E. coli, showing mostly good expression levels when using a chemical chaperone media containing d‐sorbitol. Kinetic and end‐point colorimetric assays with different amino donors–acceptors confirmed TAs activity allowing for initial exploration of the substrate scope. Stereoselective and non‐stereoselective serine‐TAs were selected for the synthesis of hydroxypyruvate (HPA). Low HPA reaction yields were observed with four non‐stereoselective serine‐TAs, whilst two stereoselective serine‐TAs showed significantly higher yields. Coupling serine‐TA reactions to a transketolase to yield l‐erythrulose (Ery) substantially increased serine conversion into HPA. Combining both stereoselective serine‐TAs and transketolase using the inexpensive racemic D/L‐serine led to high Ery yield (82%). Thermal characterization of stereoselective serine‐TAs confirmed they have excellent thermostability up to 60°C and high optimum temperatures.
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Affiliation(s)
- Max Cárdenas-Fernández
- Department of Biochemical Engineering, University College London, Gower St, WC1E 6BT, London, UK.,School of Biosciences, University of Kent, CT2 7NJ, Kent, UK
| | - Oliver Sinclair
- Department of Biochemical Engineering, University College London, Gower St, WC1E 6BT, London, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, Gower St, WC1E 6BT, London, UK
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11
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Khobragade TP, Sarak S, Pagar AD, Jeon H, Giri P, Yun H. Synthesis of Sitagliptin Intermediate by a Multi-Enzymatic Cascade System Using Lipase and Transaminase With Benzylamine as an Amino Donor. Front Bioeng Biotechnol 2021; 9:757062. [PMID: 34692666 PMCID: PMC8526967 DOI: 10.3389/fbioe.2021.757062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/21/2021] [Indexed: 01/30/2023] Open
Abstract
Herein, we report the development of a multi-enzyme cascade using transaminase (TA), esterase, aldehyde reductase (AHR), and formate dehydrogenase (FDH), using benzylamine as an amino donor to synthesize the industrially important compound sitagliptin intermediate. A panel of 16 TAs was screened using ethyl 3-oxo-4-(2,4,5-trifluorophenyl) butanoate as a substrate (1). Amongst these enzymes, TA from Roseomonas deserti (TARO) was found to be the most suitable, showing the highest activity towards benzylamine (∼70%). The inhibitory effect of benzaldehyde was resolved by using AHR from Synechocystis sp. and FDH from Pseudomonas sp., which catalyzed the conversion of benzaldehyde to benzyl alcohol at the expense of NAD(P)H. Reaction parameters, such as pH, buffer system, and concentration of amino donor, were optimized. A single whole-cell system was developed for co-expressing TARO and esterase, and the promoter engineering strategy was adopted to control the expression level of each biocatalyst. The whole-cell reactions were performed with varying substrate concentrations (10-100 mM), resulting in excellent conversions (ranging from 72 to 91%) into the desired product. Finally, the applicability of this cascade was highlighted on Gram scale, indicating production of 70% of the sitagliptin intermediate with 61% isolated yield. The protocol reported herein may be considered an alternative to existing methods with respect to the use of cheaper amine donors as well as improved synthesis of (R) and (S) enantiomers with the use of non-chiral amino donors.
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Affiliation(s)
| | | | | | | | | | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
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12
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Tauheed AM, Mamman M, Ahmed A, Sani NA, Suleiman MM, Sulaiman MH, Balogun EO. Acute, sub-acute, sub-chronic and chronic toxicity studies of four important Nigerian ethnomedicinal plants in rats. CLINICAL PHYTOSCIENCE 2021. [DOI: 10.1186/s40816-020-00244-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AbstractBackgroundAzadirachta indica,Khaya senegalensis,Anogeissus leiocarpusandTamarindus indicaare important ethnomedicinal plants used for health mitigation since the history of mankind. They are used discretionarily in folkloric medicine on the premise that they are natural products devoid of synthetic preservatives. However, nature endows plants with metabolites for warding off potential attacks from animals and the environment. Some of these metabolites are responsible for toxicity of some plants. Furthermore, drug-induced liver injuries and nephrotoxicity are the leading causes of pharmaceutical attrition of promising drug candidates in clinical trials. Thus, we aimed to evaluate the safety of four ethnomedicinal plants in short-, medium- and long-term usage.MethodsRats dosed once with 5000 mg/kg extracts of each of these plants served as acute study (AS) while rats dosed daily with 2000 mg/kg for 2, 12 and 14 weeks served as sub-acute (SAS), sub-chronic (SCS) and chronic (CS) studies, respectively. Rats administered distilled water served as the negative control (NC).ResultsA. leiocarpusandT. indicasignificantly reduced percentage weight gain in the SCS compared to the NC.A. leiocarpussignificantly (P< 0.05) increased transaminases and alkaline phosphatase in the AS only; and total protein (TP) in the AS, SAS, SCS and CS compared to the NC.K. senegalensissignificantly (P< 0.05) increased alanine aminotransferase but significantly (P< 0.05) decreased TP in the AS only compared to the NC. However,A. indica and T. indicasignificantly (P< 0.05) increased globulin and aspartate transaminase in the CS only. WhereasA. leiocarpusandK. senegalensissignificantly (P< 0.05) increased urea and creatinine in the AS than SAS, SCS and CS; Na+and K+were significantly higher in the SCS and CS studies compared to the NC. The histological lesions seen ranged from cellular degeneration, congestion, fibrosis to necrosis.ConclusionThus, nonlethal, reversible toxic insults occur in short-term usage (AS); while, insidious lethal toxic effects occur in medium-term (SAS) and long-term usage (SCS and CS). The ability of these plant to maintain adequate hematological parameters, bodyweight and absence of mortality may explain free usage of preparations made from these plants in folkloric medicine.
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13
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Martínez-Rodríguez S, Torres JM, Sánchez P, Ortega E. Overview on Multienzymatic Cascades for the Production of Non-canonical α-Amino Acids. Front Bioeng Biotechnol 2020; 8:887. [PMID: 32850740 PMCID: PMC7431475 DOI: 10.3389/fbioe.2020.00887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The 22 genetically encoded amino acids (AAs) present in proteins (the 20 standard AAs together with selenocysteine and pyrrolysine), are commonly referred as proteinogenic AAs in the literature due to their appearance in ribosome-synthetized polypeptides. Beyond the borders of this key set of compounds, the rest of AAs are generally named imprecisely as non-proteinogenic AAs, even when they can also appear in polypeptide chains as a result of post-transductional machinery. Besides their importance as metabolites in life, many of D-α- and L-α-"non-canonical" amino acids (NcAAs) are of interest in the biotechnological and biomedical fields. They have found numerous applications in the discovery of new medicines and antibiotics, drug synthesis, cosmetic, and nutritional compounds, or in the improvement of protein and peptide pharmaceuticals. In addition to the numerous studies dealing with the asymmetric synthesis of NcAAs, many different enzymatic pathways have been reported in the literature allowing for the biosynthesis of NcAAs. Due to the huge heterogeneity of this group of molecules, this review is devoted to provide an overview on different established multienzymatic cascades for the production of non-canonical D-α- and L-α-AAs, supplying neophyte and experienced professionals in this field with different illustrative examples in the literature. Whereas the discovery of new or newly designed enzymes is of great interest, dusting off previous enzymatic methodologies by a "back and to the future" strategy might accelerate the implementation of new or improved multienzymatic cascades.
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14
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Valdez-Camacho JR, Pérez-Salgado Y, Espinoza-Guillén A, Gómez-Vidales V, Alberto Tavira-Montalvan C, Meneses-Acosta A, Leyva MA, Vázquez-Ríos MG, Juaristi E, Höpfl H, Ruiz-Azuara L, Escalante J. Synthesis, structural characterization and antiproliferative activity on MCF-7 and A549 tumor cell lines of [Cu(N-N)(β3-aminoacidate)]NO3 complexes (Casiopeínas®). Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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15
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Feng X, Guo J, Zhang R, Liu W, Cao Y, Xian M, Liu H. An Aminotransferase from Enhydrobacter aerosaccus to Obtain Optically Pure β-Phenylalanine. ACS OMEGA 2020; 5:7745-7750. [PMID: 32309682 PMCID: PMC7160847 DOI: 10.1021/acsomega.9b03416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/12/2020] [Indexed: 05/14/2023]
Abstract
An aminotransferase ω-TAEn was identified from Enhydrobacter aerosaccus. The ω-TAEn was successfully expressed in Escherichia coli and the obtained enzyme showed activity toward β-phenylalanine (β-phe) at optimal conditions. For optically pure (R)-β-phe, 50% yield was observed by kinetic resolution of racemic amino with pyruvate as the amino acceptor. To obtain (S)-β-phe, the lipase/ω-TAEn catalytic system was adopted. The ω-TAEn showed strict stereoselectivity to the amino donor. The formation of (S)-β-phe was observed using 3-aminobutyric acid as the amino donor, and (S)-β-phe was obtained by asymmetric synthesis with a yield of 82%.
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Affiliation(s)
- Xinming Feng
- CAS
Key Laboratory of Biobased Materials, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Guo
- CAS
Key Laboratory of Biobased Materials, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Rubing Zhang
- CAS
Key Laboratory of Biobased Materials, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Wei Liu
- CAS
Key Laboratory of Biobased Materials, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Yujin Cao
- CAS
Key Laboratory of Biobased Materials, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Mo Xian
- CAS
Key Laboratory of Biobased Materials, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
| | - Huizhou Liu
- CAS
Key Laboratory of Biobased Materials, Qingdao
Institute of Bioenergy and Bioprocess Technology, Chinese Academy
of Sciences, Qingdao 266101, China
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16
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Bezsudnova EY, Popov VO, Boyko KM. Structural insight into the substrate specificity of PLP fold type IV transaminases. Appl Microbiol Biotechnol 2020; 104:2343-2357. [PMID: 31989227 DOI: 10.1007/s00253-020-10369-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/04/2019] [Accepted: 01/09/2020] [Indexed: 01/19/2023]
Abstract
Pyridoxal-5'-phosphate-dependent transaminases of fold type IV (class IV) are promising enzymes for (R)-selective amination of organic compounds. Transaminases of fold type IV exhibit either strict (R)-selectivity or (S)-selectivity that is implemented within geometrically similar active sites of different amino acid compositions. Based on substrate specificity, class IV comprises three large families of transaminases: (S)-selective branched-chain L-amino acid aminotransferases and (R)-selective D-amino acid aminotransferases and (R)-amine:pyruvate transaminases. In this review, we aim to analyze the substrate profiles and correlations between the substrate specificity and organization of the active site in transaminases from these structurally related families. New transaminases with an expanded substrate specificity are also discussed. An analysis of the structural features of substrate binding and comparisons of structural determinants of chiral discrimination between members of the class IV transaminases could be helpful in identifying new biocatalytically relevant enzymes as well as rational protein engineering.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071.
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071.,Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, Moscow, Russian Federation, 123182
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russian Federation, 119071
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17
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Liu L, Wang DH, Chen FF, Zhang ZJ, Chen Q, Xu JH, Wang ZL, Zheng GW. Development of an engineered thermostable amine dehydrogenase for the synthesis of structurally diverse chiral amines. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00071j] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Structurally diverse chiral amines and amino alcohols were synthesized using an engineered thermostable amine dehydrogenase, demonstrating its extensive synthesis potential.
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Dong-Hao Wang
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Fei-Fei Chen
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- P. R. 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
- P. R. China
| | - Zhi-Long Wang
- State Key Laboratory of Microbial Metabolism
- School of Pharmacy
- Shanghai Jiao Tong University
- Shanghai 200240
- P. R. China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering
- Shanghai Collaborative Innovation Center for Biomanufacturing
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
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18
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Sharma A, Gupta G, Ahmad T, Mansoor S, Kaur B. Enzyme Engineering: Current Trends and Future Perspectives. FOOD REVIEWS INTERNATIONAL 2019. [DOI: 10.1080/87559129.2019.1695835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anshula Sharma
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Tawseef Ahmad
- Department of Biotechnology, Punjabi University, Patiala, India
| | | | - Baljinder Kaur
- Department of Biotechnology, Punjabi University, Patiala, India
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19
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Screening and Comparative Characterization of Microorganisms from Iranian Soil Samples Showing ω-Transaminase Activity toward a Plethora of Substrates. Catalysts 2019. [DOI: 10.3390/catal9100874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In this study, soil microorganisms from Iran were screened for ω-transaminase (ω-TA) activity based on growth on minimal media containing (rac)-α-methylbenzylamine (rac-α-MBA) as a sole nitrogen source. Then, for the selection of strains with high enzyme activity, a colorimetric o-xylylendiamine assay was conducted. The most promising strains were identified by 16S rDNA sequencing. Five microorganisms showing high ω-TA activity were subjected to determine optimal conditions for ω-TA activity, including pH, temperature, co-solvent, and the specificity of the ω-TA toward different amine donors and acceptors. Among the five screened microorganisms, Bacillus halotolerans turned out to be the most promising strain: Its cell-free extract showed a highly versatile amino donor spectrum toward aliphatic, aromatic chiral amines and a broad range of pH activity. Transaminase activity also exhibited excellent solvent tolerance, with maximum turnover in the presence of 30% (v/v) DMSO.
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20
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Zheng X, Cui Y, Li T, Li R, Guo L, Li D, Wu B. Biochemical and structural characterization of a highly active branched-chain amino acid aminotransferase from Pseudomonas sp. for efficient biosynthesis of chiral amino acids. Appl Microbiol Biotechnol 2019; 103:8051-8062. [PMID: 31485690 DOI: 10.1007/s00253-019-10105-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/24/2019] [Accepted: 08/26/2019] [Indexed: 01/11/2023]
Abstract
Aminotransferases (ATs) are important biocatalysts for the synthesis of chiral amines because of their capability of introducing amino group into ketones or keto acids as well as their high enantioselectivity, high regioselectivity. Among all ATs, branched-chain amino acid aminotransferase (BCAT) can use branched-chain amino acids (BCAAs) as substrate, including L-valine, L-leucine, and L-isoleucine, with α-ketoglutarate to form the corresponding α-keto acids and L-glutamate. Alternatively, BCATs have been used for the biosynthesis of unnatural amino acids, such as L-tert-leucine and L-norvaline. In the present study, the BCAT from Pseudomonas sp. (PsBCAT) was cloned and expressed in Escherichia coli for biochemical and structural analyses. The optimal reaction temperature and pH of PsBCAT were 40 °C and 8.5, respectively. PsBCAT exhibited a comparatively broader substrate spectrum and showed remarkably high activity with bulked aliphatic L-amino acids (kcat up to 220 s-1). Additionally, PsBCAT had activities with aromatic L-amino acids, L-histidine, L-lysine, and L-threonine. This substrate promiscuity is unique for the BCAT family and could prove useful in industrial applications. To analyze the catalytic mechanism of PsBCAT with the broad substrate spectrum, the crystal structure of PsBCAT was also determined. Based on the determined crystal structure, we found some differences in the organization of the substrate binding cavity, which may influence the substrate specificity of the enzyme. Finally, conjugated with the ornithine aminotransferase (OrnAT) to shift the reaction equilibrium towards the product formation, the coupled system was applied to the asymmetric synthesis of L-tert-leucine and L-norvaline. In summary, the structural and functional characteristics of PsBCAT were analyzed in detail, and this information will be conducive to industrial production of enantiopure chiral amino acids by aminotransferase.
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Affiliation(s)
- Xinxin Zheng
- College of Life Sciences and Technology, Xinjiang University, Urumqi, Xinjiang, 830046, People's Republic of China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Tao Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Lu Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Defeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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21
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Marchenkova MA, Konarev PV, Rakitina TV, Timofeev VI, Boikova AS, Dyakova YA, Ilina KB, Korzhenevskiy DA, Yu Nikolaeva A, Pisarevsky YV, Kovalchuk MV. Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium Thermobaculum terrenum by small-angle X-ray scattering. J Biomol Struct Dyn 2019; 38:2939-2944. [PMID: 31347457 DOI: 10.1080/07391102.2019.1649195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The pre-crystallization solution of the transaminase from Thermobaculum terrenum (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric composition of the protein were observed after the addition of the precipitant. Comparison of the observed oligomers with the crystal structure of TaTT (PDB ID 6GKR) shows that dodecamers may act as building blocks in the growth of transaminase single crystals. Correlating of these results to the similar X-ray studies of other proteins suggests that SAXS may be a valuable tool for searching optimum crystallization conditions. AbbreviationSAXSsmall-angle X-ray scatteringTatransaminaseTaTTtransaminase from Thermobaculum terrenumPLPpyridoxal-5'-phosphateR-PEAR-(þ)-1-phenylethylamineBCATbranched-chain amino acid aminotransferaseDAATD-aminoacid aminotransferaseR-TAR-amine:pyruvate transaminaseCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Margarita A Marchenkova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Petr V Konarev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Tatiana V Rakitina
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,Shemyakin - Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Hormonal Regulation Proteins, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Anastasiia S Boikova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yulia A Dyakova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | | | - Alena Yu Nikolaeva
- National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Yurii V Pisarevsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Moscow, Russian Federation.,National Research Centre 'Kurchatov Institute', Moscow, Russian Federation.,St. Petersburg State University, St. Petersburg, Russian Federation
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22
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Palacio CM, Rozeboom HJ, Lanfranchi E, Meng Q, Otzen M, Janssen DB. Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism. FEBS J 2019; 286:4086-4102. [PMID: 31162815 DOI: 10.1111/febs.14950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/29/2019] [Accepted: 06/01/2019] [Indexed: 01/31/2023]
Abstract
The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).
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Affiliation(s)
- Cyntia M Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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23
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Narancic T, Almahboub SA, O’Connor KE. Unnatural amino acids: production and biotechnological potential. World J Microbiol Biotechnol 2019; 35:67. [DOI: 10.1007/s11274-019-2642-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
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24
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Zeifman YS, Boyko KM, Nikolaeva AY, Timofeev VI, Rakitina TV, Popov VO, Bezsudnova EY. Functional characterization of PLP fold type IV transaminase with a mixed type of activity from Haliangium ochraceum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:575-585. [PMID: 30902765 DOI: 10.1016/j.bbapap.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/01/2019] [Accepted: 03/16/2019] [Indexed: 12/11/2022]
Abstract
Pyridoxal-5'-phosphate (PLP)-dependent transaminases are industrially important enzymes catalyzing the stereoselective amination of ketones and keto acids. Transaminases of PLP fold type IV are characterized by (R)- or (S)-stereoselective transfer of amino groups, depending on the substrate profile of the enzyme. PLP fold type IV transaminases include branched-chain amino acid transaminases (BCATs), D-amino acid transaminases and (R)-amine:pyruvate transaminases. Recently, transaminases with a mixed type of activity were identified and characterized. Here, we report biochemical and structural characterization of a transaminase from myxobacterium Haliangium ochraceum (Hoch3033), which is active towards keto analogs of branched-chain amino acids (specific substrates for BCATs) and (R)-(+)-α-methylbenzylamine (specific substrate for (R)-amine:pyruvate transaminases). The enzyme is characterized by an alkaline pH optimum (pH 10.0-10.5) and a tolerance to high salt concentrations (up to 2 M NaCl). The structure of Hoch3033 was determined at 2.35 Å resolution. The overall fold of the enzyme was similar to those of known enzymes of PLP fold type IV. The mixed type of activity of Hoch3033 was implemented within the BCAT-like active site. However, in the active site of Hoch3033, we observed substitutions of specificity-determining residues that are important for substrate binding in canonical BCATs. We suggest that these changes result in the loss of activity towards α-ketoglutarate and increase the affinity towards (R)-(+)-α-methylbenzylamine. These results complement our knowledge of the catalytic diversity of transaminases and indicate the need for further research to understand the structural basis of substrate specificity in these enzymes.
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Affiliation(s)
- Yulia S Zeifman
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation.
| | - Konstantin M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Alena Yu Nikolaeva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Vladimir I Timofeev
- Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation; FSRC «Crystallography and Photonics» RAS, Leninskiy Prospekt 59, 119333 Moscow, Russian Federation
| | - Tatiana V Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation; Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, 117997 Moscow, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation; Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova sqr 1, 123182 Moscow, Russian Federation
| | - Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russian Federation
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25
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Kwon S, Park HH. Crystal structure of the apo form of a β-transaminase from Mesorhizobium sp. strain LUK. Protein Sci 2019; 28:964-970. [PMID: 30805955 DOI: 10.1002/pro.3594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 11/10/2022]
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent β-transaminases (βTAs) reversibly catalyze transamination reactions by recognizing amino groups linked to the β-carbon atoms of their substrates. Although several βTA structures have been determined as holo forms containing PLP, little is known about the effect of PLP on the conversion of the apo structure to the holo structure. We determined the crystal structure of the apo form of a βTA from Mesorhizobium sp. strain LUK at 2.2 Å resolution to elucidate how PLP affects the βTA structure. The structure revealed three major disordered regions near the active site. Structural comparison with the holo form also showed that the disordered regions in the apo form are ordered and partially adopt secondary structures in the holo form. These findings suggest that PLP incorporation into the active site contributes to the structural stability of the active site architecture, thereby forming the complete active site. Our results provide novel structural insights into the role of PLP in terms of active site formation.
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Affiliation(s)
- Sunghark Kwon
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun H Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
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26
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Cong X, Li X, Li S. Crystal structure of the aromatic-amino-acid aminotransferase from Streptococcus mutans. Acta Crystallogr F Struct Biol Commun 2019; 75:141-146. [PMID: 30713166 PMCID: PMC6360443 DOI: 10.1107/s2053230x18018472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 12/31/2018] [Indexed: 11/10/2022] Open
Abstract
Streptococcus mutans, a facultatively aerobic and Gram-positive bacterium, is the primary causative agent of dental caries and contributes to the multispecies biofilm known as dental plaque. In this study, the aromatic-amino-acid aminotransferase from Streptococcus mutans (SmAroAT) was recombinantly expressed in Escherichia coli. An effective purification protocol was established. The recombinant protein was crystallized using the hanging-drop vapor-diffusion method with PEG 3350 as the primary precipitant. The crystal structure of SmAroAT was solved at 2.2 Å resolution by the molecular-replacement method. Structural analysis indicated that the proteins of the aromatic-amino-acid aminotransferase family have conserved structural elements that might play a role in substrate binding. These results may help in obtaining a better understanding of the catabolism and biosynthesis of aromatic amino acids.
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Affiliation(s)
- Xuzhen Cong
- Central Laboratory, Capital Medical University, Beijing 100069, People’s Republic of China
- Shandong Mental Health Center, Jinan, Shandong 250014, People’s Republic of China
| | - Xiaolu Li
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing 100005, People’s Republic of China
| | - Shentao Li
- Central Laboratory, Capital Medical University, Beijing 100069, People’s Republic of China
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27
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Kim G, Jeon H, Khobragade TP, Patil MD, Sung S, Yoon S, Won Y, Sarak S, Yun H. Glutamate as an Efficient Amine Donor for the Synthesis of Chiral β‐ and γ‐Amino Acids Using Transaminase. ChemCatChem 2019. [DOI: 10.1002/cctc.201802048] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Geon‐Hee Kim
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Hyunwoo Jeon
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Taresh P. Khobragade
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Mahesh D. Patil
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Sihyong Sung
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Sanghan Yoon
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Yumi Won
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Sharad Sarak
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
| | - Hyungdon Yun
- Department of Systems BiotechnologyKonkuk University 120 Neungdong-ro Gwangjin-gu, Seoul 05029 Korea
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Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines. Appl Environ Microbiol 2019; 85:AEM.02404-18. [PMID: 30413473 PMCID: PMC6328768 DOI: 10.1128/aem.02404-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 11/04/2018] [Indexed: 12/31/2022] Open
Abstract
Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways. Amination of bulky ketones, particularly in (R) configuration, is an attractive chemical conversion; however, known ω-transaminases (ω-TAs) show insufficient levels of performance. By applying two screening methods, we discovered 10 amine transaminases from the class III ω-TA family that were 38% to 76% identical to homologues. We present examples of such enzymes preferring bulky ketones over keto acids and aldehydes with stringent (S) selectivity. We also report representatives from the class III ω-TAs capable of converting (R) and (S) amines and bulky ketones and one that can convert amines with longer alkyl substituents. The preference for bulky ketones was associated with the presence of a hairpin region proximal to the conserved Arg414 and residues conforming and close to it. The outward orientation of Arg414 additionally favored the conversion of (R) amines. This configuration was also found to favor the utilization of putrescine as an amine donor, so that class III ω-TAs with Arg414 in outward orientation may participate in vivo in the catabolism of putrescine. The positioning of the conserved Ser231 also contributes to the preference for amines with longer alkyl substituents. Optimal temperatures for activity ranged from 45 to 65°C, and a few enzymes retained ≥50% of their activity in water-soluble solvents (up to 50% [vol/vol]). Hence, our results will pave the way to design, in the future, new class III ω-TAs converting bulky ketones and (R) amines for the production of high-value products and to screen for those converting putrescine. IMPORTANCE Amine transaminases of the class III ω-TAs are key enzymes for modification of chemical building blocks, but finding those capable of converting bulky ketones and (R) amines is still challenging. Here, by an extensive analysis of the substrate spectra of 10 class III ω-TAs, we identified a number of residues playing a role in determining the access and positioning of bulky ketones, bulky amines, and (R)- and (S) amines, as well as of environmentally relevant polyamines, particularly putrescine. The results presented can significantly expand future opportunities for designing (R)-specific class III ω-TAs to convert valuable bulky ketones and amines, as well as for deepening the knowledge into the polyamine catabolic pathways.
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Kim GH, Jeon H, Khobragade TP, Patil MD, Sung S, Yoon S, Won Y, Choi IS, Yun H. Enzymatic synthesis of sitagliptin intermediate using a novel ω-transaminase. Enzyme Microb Technol 2019; 120:52-60. [DOI: 10.1016/j.enzmictec.2018.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/17/2018] [Accepted: 10/05/2018] [Indexed: 01/10/2023]
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30
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Characterization of ELP-fused ω-Transaminase and Its Application for the Biosynthesis of β-Amino Acid. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0268-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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31
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Diaminopelargonic acid transaminase from Psychrobacter cryohalolentis is active towards (S)-(-)-1-phenylethylamine, aldehydes and α-diketones. Appl Microbiol Biotechnol 2018; 102:9621-9633. [DOI: 10.1007/s00253-018-9310-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/09/2018] [Accepted: 08/07/2018] [Indexed: 11/25/2022]
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32
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Buß O, Voss M, Delavault A, Gorenflo P, Syldatk C, Bornscheuer U, Rudat J. β-Phenylalanine Ester Synthesis from Stable β-Keto Ester Substrate Using Engineered ω-Transaminases. Molecules 2018; 23:molecules23051211. [PMID: 29783679 PMCID: PMC6100204 DOI: 10.3390/molecules23051211] [Citation(s) in RCA: 11] [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: 04/16/2018] [Revised: 05/12/2018] [Accepted: 05/15/2018] [Indexed: 11/16/2022] Open
Abstract
The successful synthesis of chiral amines from ketones using ω-transaminases has been shown in many cases in the last two decades. In contrast, the amination of β-keto acids is a special and relatively new challenge, as they decompose easily in aqueous solution. To avoid this, transamination of the more stable β-keto esters would be an interesting alternative. For this reason, ω-transaminases were tested in this study, which enabled the transamination of the β-keto ester substrate ethyl benzoylacetate. Therefore, a ω-transaminase library was screened using a coloring o-xylylenediamine assay. The ω-transaminase mutants 3FCR_4M and ATA117 11Rd show great potential for further engineering experiments aiming at the synthesis of chiral (S)- and (R)-β-phenylalanine esters. This alternative approach resulted in the conversion of 32% and 13% for the (S)- and (R)-enantiomer, respectively. Furthermore, the (S)-β-phenylalanine ethyl ester was isolated by performing a semi-preparative synthesis.
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Affiliation(s)
- Oliver Buß
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany.
| | - Moritz Voss
- Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - André Delavault
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany.
| | - Pascal Gorenflo
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany.
| | - Christoph Syldatk
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany.
| | - Uwe Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany.
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One-pot, two-step transaminase and transketolase synthesis of l-gluco-heptulose from l-arabinose. Enzyme Microb Technol 2018; 116:16-22. [PMID: 29887012 DOI: 10.1016/j.enzmictec.2018.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/21/2018] [Accepted: 05/10/2018] [Indexed: 11/23/2022]
Abstract
The use of biocatalysis for the synthesis of high value added chemical building blocks derived from biomass is becoming an increasingly important application for future sustainable technologies. The synthesis of a higher value chemical from l-arabinose, the predominant monosaccharide obtained from sugar beet pulp, is demonstrated here via a transketolase and transaminase coupled reaction. Thermostable transketolases derived from Deinococcus geothermalis and Deinococcus radiodurans catalysed the synthesis of l-gluco-heptulose from l-arabinose and β-hydroxypyruvate at elevated temperatures with high conversions. β-Hydroxypyruvate, a commercially expensive compound used in the transketolase reaction, was generated in situ from l-serine and α-ketoglutaric acid via a thermostable transaminase, also from Deinococcus geothermalis. The two steps were investigated and implemented in a one-pot system for the sustainable and efficient production of l-gluco-heptulose.
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34
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Zhou S, Wang S, Wang J, Nian Y, Peng P, Soloshonok VA, Liu H. Configurationally Stable (S
)- and (R
)-α-Methylproline-Derived Ligands for the Direct Chemical Resolution of Free Unprotected β3
-Amino Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shengbin Zhou
- University of Chinese Academy of Sciences; No.19A Yuquan Road 100049 Beijing China
- CAS Key Laboratory of Receptor Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 Zuchongzhi Road 201203 Shanghai China
| | - Shuni Wang
- University of Chinese Academy of Sciences; No.19A Yuquan Road 100049 Beijing China
- CAS Key Laboratory of Receptor Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 Zuchongzhi Road 201203 Shanghai China
| | - Jiang Wang
- University of Chinese Academy of Sciences; No.19A Yuquan Road 100049 Beijing China
- CAS Key Laboratory of Receptor Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 Zuchongzhi Road 201203 Shanghai China
| | - Yong Nian
- University of Chinese Academy of Sciences; No.19A Yuquan Road 100049 Beijing China
- CAS Key Laboratory of Receptor Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 Zuchongzhi Road 201203 Shanghai China
| | - Panfeng Peng
- University of Chinese Academy of Sciences; No.19A Yuquan Road 100049 Beijing China
- CAS Key Laboratory of Receptor Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 Zuchongzhi Road 201203 Shanghai China
| | - Vadim A. Soloshonok
- Department of Organic Chemistry I; Faculty of Chemistry; University of the Basque Country UPV/EHU; Paseo Manuel Lardizábal 3 20018 San Sebastián Spain
- IKERBASQUE - Basque Foundation for Science; Maria Diaz de Haro 3 48013 Bilbao Spain
| | - Hong Liu
- University of Chinese Academy of Sciences; No.19A Yuquan Road 100049 Beijing China
- CAS Key Laboratory of Receptor Research; Shanghai Institute of Materia Medica; Chinese Academy of Sciences; 555 Zuchongzhi Road 201203 Shanghai China
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35
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Contente ML, Planchestainer M, Molinari F, Paradisi F. Stereoelectronic effects in the reaction of aromatic substrates catalysed by Halomonas elongata transaminase and its mutants. Org Biomol Chem 2018; 14:9306-9311. [PMID: 27722400 DOI: 10.1039/c6ob01629d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A transaminase from Halomonas elongata and four mutants generated by an in silico-based design were recombinantly produced in E. coli, purified and applied to the amination of mono-substituted aromatic carbonyl-derivatives. While benzaldehyde derivatives were excellent substrates, only NO2-acetophenones were transformed into the (S)-amine with a high enantioselectivity. The different behaviour of wild-type and mutated transaminases was assessed by in silico substrate binding mode studies.
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Affiliation(s)
- Martina Letizia Contente
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland and Department of Food Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
| | | | - Francesco Molinari
- Department of Food Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
| | - Francesca Paradisi
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland and School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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36
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Bezsudnova EY, Boyko KM, Popov VO. Properties of Bacterial and Archaeal Branched-Chain Amino Acid Aminotransferases. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523060 DOI: 10.1134/s0006297917130028] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Branched-chain amino acid aminotransferases (BCATs) catalyze reversible stereoselective transamination of branched-chain amino acids (BCAAs) L-leucine, L-isoleucine, and L-valine. BCATs are the key enzymes of BCAA metabolism in all organisms. The catalysis proceeds through the ping-pong mechanism with the assistance of the cofactor pyridoxal 5'-phosphate (PLP). BCATs differ from other (S)-selective transaminases (TAs) in 3D-structure and organization of the PLP-binding domain. Unlike other (S)-selective TAs, BCATs belong to the PLP fold type IV and are characterized by the proton transfer on the re-face of PLP, in contrast to the si-specificity of proton transfer in fold type I (S)-selective TAs. Moreover, BCATs are the only (S)-selective enzymes within fold type IV TAs. Dual substrate recognition in BCATs is implemented via the "lock and key" mechanism without side-chain rearrangements of the active site residues. Another feature of the active site organization in BCATs is the binding of the substrate α-COOH group on the P-side of the active site near the PLP phosphate group. Close localization of two charged groups seems to increase the effectiveness of external aldimine formation in BCAT catalysis. In this review, the structure-function features and the substrate specificity of bacterial and archaeal BCATs are analyzed. These BCATs differ from eukaryotic ones in the wide substrate specificity, optimal temperature, and reactivity toward pyruvate as the second substrate. The prospects of biotechnological application of BCATs in stereoselective synthesis are discussed.
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Affiliation(s)
- E Yu Bezsudnova
- Bach Institute of Biochemistry, The Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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37
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Buß O, Buchholz PCF, Gräff M, Klausmann P, Rudat J, Pleiss J. The ω-transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space. Proteins 2018; 86:566-580. [PMID: 29423963 DOI: 10.1002/prot.25477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 01/02/2023]
Abstract
The ω-Transaminase Engineering Database (oTAED) was established as a publicly accessible resource on sequences and structures of the biotechnologically relevant ω-transaminases (ω-TAs) from Fold types I and IV. The oTAED integrates sequence and structure data, provides a classification based on fold type and sequence similarity, and applies a standard numbering scheme to identify equivalent positions in homologous proteins. The oTAED includes 67 210 proteins (114 655 sequences) which are divided into 169 homologous families based on global sequence similarity. The 44 and 39 highly conserved positions which were identified in Fold type I and IV, respectively, include the known catalytic residues and a large fraction of glycines and prolines in loop regions, which might have a role in protein folding and stability. However, for most of the conserved positions the function is still unknown. Literature information on positions that mediate substrate specificity and stereoselectivity was systematically examined. The standard numbering schemes revealed that many positions which have been described in different enzymes are structurally equivalent. For some positions, multiple functional roles have been suggested based on experimental data in different enzymes. The proposed standard numbering schemes for Fold type I and IV ω-TAs assist with analysis of literature data, facilitate annotation of ω-TAs, support prediction of promising mutation sites, and enable navigation in ω-TA sequence space. Thus, it is a useful tool for enzyme engineering and the selection of novel ω-TA candidates with desired biochemical properties.
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Affiliation(s)
- Oliver Buß
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Engler-Bunte-Ring 3, Karlsruhe, 76131, Germany
| | - Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany
| | - Maike Gräff
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany
| | - Peter Klausmann
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Engler-Bunte-Ring 3, Karlsruhe, 76131, Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Engler-Bunte-Ring 3, Karlsruhe, 76131, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany
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38
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Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
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Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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Buchholz PCF, Fademrecht S, Pleiss J. Percolation in protein sequence space. PLoS One 2017; 12:e0189646. [PMID: 29261740 PMCID: PMC5738032 DOI: 10.1371/journal.pone.0189646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023] Open
Abstract
The currently known protein sequences are not distributed equally in sequence space, but cluster into families. Analyzing the cluster size distribution gives a glimpse of the large and unknown extant protein sequence space, which has been explored during evolution. For six protein superfamilies with different fold and function, the cluster size distributions followed a power law with slopes between 2.4 and 3.3, which represent upper limits to the cluster distribution of extant sequences. The power law distribution of cluster sizes is in accordance with percolation theory and strongly supports connectedness of extant sequence space. Percolation of extant sequence space has three major consequences: (1) It transforms our view of sequence space as a highly connected network where each sequence has multiple neighbors, and each pair of sequences is connected by many different paths. A high degree of connectedness is a necessary condition of efficient evolution, because it overcomes the possible blockage by sign epistasis and reciprocal sign epistasis. (2) The Fisher exponent is an indicator of connectedness and saturation of sequence space of each protein superfamily. (3) All clusters are expected to be connected by extant sequences that become apparent as a higher portion of extant sequence space becomes known. Being linked to biochemically distinct homologous families, bridging sequences are promising enzyme candidates for applications in biotechnology because they are expected to have substrate ambiguity or catalytic promiscuity.
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Affiliation(s)
- Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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40
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Buß O, Muller D, Jager S, Rudat J, Rabe KS. Improvement in the Thermostability of a β-Amino Acid Converting ω-Transaminase by Using FoldX. Chembiochem 2017; 19:379-387. [PMID: 29120530 DOI: 10.1002/cbic.201700467] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 12/19/2022]
Abstract
ω-Transaminases (ω-TAs) are important biocatalysts for the synthesis of active, chiral pharmaceutical ingredients containing amino groups, such as β-amino acids, which are important in peptidomimetics and as building blocks for drugs. However, the application of ω-TAs is limited by the availability and stability of enzymes with high conversion rates. One strategy for the synthesis and optical resolution of β-phenylalanine and other important aromatic β-amino acids is biotransformation by utilizing an ω-transaminase from Variovorax paradoxus. We designed variants of this ω-TA to gain higher process stability on the basis of predictions calculated by using the FoldX software. We herein report the first thermostabilization of a nonthermostable S-selective ω-TA by FoldX-guided site-directed mutagenesis. The melting point (Tm ) of our best-performing mutant was increased to 59.3 °C, an increase of 4.0 °C relative to the Tm value of the wild-type enzyme, whereas the mutant fully retained its specific activity.
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Affiliation(s)
- Oliver Buß
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Delphine Muller
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Sven Jager
- Computational Biology, Technische Universität Darmstadt, Schnittspahnstrasse 2, 64287, Darmstadt, Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, Section II: Technical Biology, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces I, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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Kelly SA, Pohle S, Wharry S, Mix S, Allen CCR, Moody TS, Gilmore BF. Application of ω-Transaminases in the Pharmaceutical Industry. Chem Rev 2017; 118:349-367. [PMID: 29251912 DOI: 10.1021/acs.chemrev.7b00437] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chiral amines are valuable building blocks for the pharmaceutical industry. ω-TAms have emerged as an exciting option for their synthesis, offering a potential "green alternative" to overcome the drawbacks associated with conventional chemical methods. In this review, we explore the application of ω-TAms for pharmaceutical production. We discuss the diverse array of reactions available involving ω-TAms and process considerations of their use in both kinetic resolution and asymmetric synthesis. With the aid of specific drug intermediates and APIs, we chart the development of ω-TAms using protein engineering and their contribution to elegant one-pot cascades with other enzymes, including carbonyl reductases (CREDs), hydrolases and monoamine oxidases (MAOs), providing a comprehensive overview of their uses, beginning with initial applications through to the present day.
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Affiliation(s)
- Stephen A Kelly
- School of Pharmacy, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
| | - Stefan Pohle
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Scott Wharry
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Stefan Mix
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
| | - Thomas S Moody
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate, Athlone, Co. Roscommon, Ireland
| | - Brendan F Gilmore
- School of Pharmacy, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
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42
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Slabu I, Galman JL, Lloyd RC, Turner NJ. Discovery, Engineering, and Synthetic Application of Transaminase Biocatalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02686] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Iustina Slabu
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - James L. Galman
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Richard C. Lloyd
- Dr.
Reddy’s Laboratories, Chirotech Technology Centre, CB4 0PE Cambridge, United Kingdom
| | - Nicholas J. Turner
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
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43
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Rodríguez-Hinestroza RA, López C, López-Santín J, Kane C, Dolors Benaiges M, Tzedakis T. HLADH-catalyzed synthesis of β-amino acids, assisted by continuous electrochemical regeneration of NAD + in a filter press microreactor. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2016.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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44
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Mathew S, Nadarajan SP, Sundaramoorthy U, Jeon H, Chung T, Yun H. Biotransformation of β-keto nitriles to chiral (S)-β-amino acids using nitrilase and ω-transaminase. Biotechnol Lett 2016; 39:535-543. [DOI: 10.1007/s10529-016-2271-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/08/2016] [Indexed: 11/28/2022]
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45
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Rapheeha OKL, Roux-van der Merwe MP, Badenhorst J, Chhiba V, Bode ML, Mathiba K, Brady D. Hydrolysis of nitriles by soil bacteria: variation with soil origin. J Appl Microbiol 2016; 122:686-697. [PMID: 27930842 DOI: 10.1111/jam.13367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/09/2016] [Accepted: 11/28/2016] [Indexed: 12/01/2022]
Abstract
AIMS The aim of this study was to explore bacterial soil diversity for nitrile biocatalysts, in particular, those for hydrolysis of β-substituted nitriles, to the corresponding carboxamides and acids that may be incorporated into peptidomimetics. To achieve this, we needed to compare the efficiency of isolation methods and determine the influence of land use and geographical origin of the soil sample. METHODS AND RESULTS Nitrile-utilizing bacteria were isolated from various soil environments across a 1000 km long transect of South Africa, including agricultural soil, a gold mine tailing dam and uncultivated soil. The substrate profile of these isolates was determined through element-limited growth studies on seven different aliphatic or aromatic nitriles. A subset of these organisms expressing broad substrate ranges was evaluated for their ability to hydrolyse β-substituted nitriles (3-amino-3-phenylpropionitrile and 3-hydroxy-4-phenoxybutyronitrile) and the active organisms were found to be Rhodococcus erythropolis from uncultivated soil and Rhodococcus rhodochrous from agricultural soils. CONCLUSIONS The capacity for hydrolysis of β-substituted nitriles appears to reside almost exclusively in Rhodococci. Land use has a much greater effect on the biocatalysis substrate profile than geographical location. SIGNIFICANCE AND IMPACT OF THE STUDY Enzymes are typically substrate specific in their catalytic reactions, and this means that a wide diversity of enzymes is required to provide a comprehensive biocatalysis toolbox. This paper shows that the microbial diversity of nitrile hydrolysis activity can be targeted according to land utilization. Nitrile biocatalysis is a green chemical method for the enzymatic production of amides and carboxylic acids that has industrial applications, such as in the synthesis of acrylamide and nicotinamide. The biocatalysts discovered in this study may be applied to the synthesis of peptidomimetics which are an important class of therapeutic compounds.
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Affiliation(s)
- O K L Rapheeha
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa
| | - M P Roux-van der Merwe
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa
| | - J Badenhorst
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa
| | - V Chhiba
- CSIR Biosciences, Pretoria, South Africa.,Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - M L Bode
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - K Mathiba
- CSIR Biosciences, Pretoria, South Africa
| | - D Brady
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa.,CSIR Biosciences, Pretoria, South Africa.,Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
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46
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Dold SM, Cai L, Rudat J. One-step purification and immobilization of a β-amino acid aminotransferase using magnetic (M-PVA) beads. Eng Life Sci 2016. [DOI: 10.1002/elsc.201600042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Sarah-Marie Dold
- Institute of Process Engineering in Life Sciences Section II: Technical Biology; , Karlsruhe Institute of Technology; Karlsruhe Germany
| | - Liyin Cai
- Institute of Process Engineering in Life Sciences Section II: Technical Biology; , Karlsruhe Institute of Technology; Karlsruhe Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences Section II: Technical Biology; , Karlsruhe Institute of Technology; Karlsruhe Germany
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Bezsudnova EY, Stekhanova TN, Suplatov DA, Mardanov AV, Ravin NV, Popov VO. Experimental and computational studies on the unusual substrate specificity of branched-chain amino acid aminotransferase from Thermoproteus uzoniensis. Arch Biochem Biophys 2016; 607:27-36. [PMID: 27523731 DOI: 10.1016/j.abb.2016.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 01/26/2023]
Abstract
PLP-Dependent fold-type IV branched-chain amino acid aminotransferases (BCATs) from archaea have so far been poorly characterized. A new BCAT from the hyperthermophilic archaeon Thermoproteus uzoniensis (TUZN1299) has been studied. TUZN1299 was found to be highly active toward branched-chain amino acids (BCAAs), positively charged amino acids, l-methionine, l-threonine, l-homoserine, l-glutamine, as well as toward 2-oxobutyrate and keto analogs of BCAAs, whereas l-glutamate and α-ketoglutarate were not converted in the overall reaction. According to stopped-flow experiments, the enzyme showed the highest specificity to BCAAs and their keto analogs. In order to explain the molecular mechanism of the unusual specificity of TUZN1299, bioinformatic analysis was implemented to identify the subfamily-specific positions in the aminotransferase class IV superfamily of enzymes. The role of the selected residues in binding of various ligands in the active site was further studied using molecular modeling. The results indicate that Glu188 forms a novel binding site for positively charged and polar side-chains of amino acids. Lack of accommodation for α-ketoglutarate and l-glutamate is due to the unique orientation and chemical properties of residues 102-106 in the loop forming the A-pocket. The likely functional roles of TUZN1299 in cellular metabolism - in the synthesis and degradation of BCAAs - are discussed.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation.
| | - Tatiana N Stekhanova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation
| | - Dmitry A Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskiye Gory 1-73, Moscow, 119992, Russian Federation
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation
| | - Vladimir O Popov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, 119071, Moscow, Russian Federation; NBICS Center, National Research Centre "Kurchatov Institute", Akad. Kurchatova Sqr 1, 123182, Moscow, Russian Federation
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48
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Characterization of aromatic aminotransferases from Ephedra sinica Stapf. Amino Acids 2016; 48:1209-20. [DOI: 10.1007/s00726-015-2156-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/13/2015] [Indexed: 01/12/2023]
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49
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Buß O, Jager S, Dold SM, Zimmermann S, Hamacher K, Schmitz K, Rudat J. Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters. PLoS One 2016; 11:e0146104. [PMID: 26730596 PMCID: PMC4711668 DOI: 10.1371/journal.pone.0146104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/14/2015] [Indexed: 01/15/2023] Open
Abstract
β-keto esters are used as precursors for the synthesis of β-amino acids, which are building blocks for some classes of pharmaceuticals. Here we describe the comparison of screening procedures for hydrolases to be used for the hydrolysis of β-keto esters, the first step in the preparation of β-amino acids. Two of the tested high throughput screening (HTS) assays depend on coupled enzymatic reactions which detect the alcohol released during ester hydrolysis by luminescence or absorption. The third assay detects the pH shift due to acid formation using an indicator dye. To choose the most efficient approach for screening, we assessed these assays with different statistical methods—namely, the classical Z’-factor, standardized mean difference (SSMD), the Kolmogorov-Smirnov-test, and t-statistics. This revealed that all three assays are suitable for HTS, the pH assay performing best. Based on our data we discuss the explanatory power of different statistical measures. Finally, we successfully employed the pH assay to identify a very fast hydrolase in an enzyme-substrate screening.
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Affiliation(s)
- O. Buß
- Karlsruhe Institute of Technology, Technical Biology, Karlsruhe, Germany
- * E-mail: (OB); (SJ)
| | - S. Jager
- Technische Universität Darmstadt, Computational Biology and Simulation, Darmstadt, Germany
- * E-mail: (OB); (SJ)
| | - S. -M. Dold
- Karlsruhe Institute of Technology, Technical Biology, Karlsruhe, Germany
| | - S. Zimmermann
- Karlsruhe Institute of Technology, Biomolecular Separation Engineering, Karlsruhe, Germany
| | - K. Hamacher
- Technische Universität Darmstadt, Computational Biology and Simulation, Darmstadt, Germany
| | - K. Schmitz
- Technische Universität Darmstadt, Biological Chemistry, Darmstadt, Germany
| | - J. Rudat
- Karlsruhe Institute of Technology, Technical Biology, Karlsruhe, Germany
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50
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Whole-cell biocatalytic production of variously substituted β-aryl- and β-heteroaryl-β-amino acids. J Biotechnol 2016; 217:12-21. [DOI: 10.1016/j.jbiotec.2015.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/23/2015] [Accepted: 10/12/2015] [Indexed: 01/28/2023]
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