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Jeon H, Pagar AD, Kang H, Giri P, Nadarajan SP, Sarak S, Khobragade TP, Lim S, Patil MD, Lee SG, Yun H. Creation of a ( R)-β-Transaminase by Directed Evolution of d-Amino Acid Aminotransferase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hyunwoo Jeon
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Amol D. Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Hyeona Kang
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Saravanan P. Nadarajan
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Sharad Sarak
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Taresh P. Khobragade
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Seonga Lim
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D. Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali, Punjab 140306, India
| | - Sun-Gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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Neiers F, Gourrat K, Canon F, Schwartz M. Metabolism of Cysteine Conjugates and Production of Flavor Sulfur Compounds by a Carbon-Sulfur Lyase from the Oral Anaerobe Fusobacterium nucleatum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9969-9979. [PMID: 35920882 DOI: 10.1021/acs.jafc.2c01727] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Flavor perception is a key factor in the acceptance or rejection of food. Aroma precursors such as cysteine conjugates are present in various plant-based foods and are metabolized into odorant thiols in the oral cavity. To date, the involved enzymes are unknown, despite previous studies pointing out the likely involvement of carbon-sulfur lyases (C-S lyases) from the oral microbiota. In this study, we show that saliva metabolizes allyl-cysteine into odorant thiol metabolites, with evidence suggesting that microbial pyridoxal phosphate-dependent C-S lyases are involved in the enzymatic process. A phylogenetic analysis of PatB C-S lyase sequences in four oral subspecies of Fusobacterium nucleatum was carried out and led to the identification of several putative targets. FnaPatB1 from F. nucleatum subspecies animalis, a putative C-S lyase, was characterized and showed high activity with a range of cysteine conjugates. Enzymatic and X-ray crystallographic data showed that FnaPatB1 metabolizes cysteine derivatives within a unique active site environment that enables the formation of flavor sulfur compounds. Using an enzymatic screen with a library of pure compounds, we identified several inhibitors able to reduce the C-S lyase activity of FnaPatB1 in vitro, which paves the way for controlling the release of odorant sulfur compounds from their cysteine precursors in the oral cavity.
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Affiliation(s)
- Fabrice Neiers
- Centre for Taste and Feeding Behavior (CSGA), INRAE, CNRS, University of Burgundy-Franche Comté, Institut Agro, F-21000 Dijon, France
| | - Karine Gourrat
- Centre for Taste and Feeding Behavior (CSGA), INRAE, CNRS, University of Burgundy-Franche Comté, Institut Agro, F-21000 Dijon, France
- PROBE Research Infrastructure, Chemosens Facility, F-21000 Dijon, France
| | - Francis Canon
- Centre for Taste and Feeding Behavior (CSGA), INRAE, CNRS, University of Burgundy-Franche Comté, Institut Agro, F-21000 Dijon, France
| | - Mathieu Schwartz
- Centre for Taste and Feeding Behavior (CSGA), INRAE, CNRS, University of Burgundy-Franche Comté, Institut Agro, F-21000 Dijon, France
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3
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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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4
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Ferrandi EE, Bassanini I, Sechi B, Vanoni M, Tessaro D, Guðbergsdóttir SR, Riva S, Peng X, Monti D. Discovery and Characterization of a Novel Thermostable β-Amino Acid Transaminase from a Meiothermus Strain Isolated in an Icelandic Hot Spring. Biotechnol J 2020; 15:e2000125. [PMID: 32893504 DOI: 10.1002/biot.202000125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Indexed: 02/02/2023]
Abstract
A Meiothermus strain capable of using β-phenylalanine for growth is isolated by culture enrichment of samples collected in hot environments and the genome is sequenced showing the presence of 22 putative transaminase (TA) sequences. On the basis of phylogenetic and sequence analysis, a TA termed Ms-TA2 is selected for further studies. The enzyme is successfully produced in Escherichia coli Rosetta(DE3) cells, with 70 mg of pure protein obtained from 1 L culture after purification by affinity chromatography. Ms-TA2 shows high activity toward (S)-β-phenylalanine and other (S)-β-amino acids, as well as a preference for α-ketoglutarate and aromatic aldehydes as amino acceptors. Moreover, Ms-TA2 is shown to be a thermostable enzyme by maintaining about 60% of the starting activity after 3 h incubation at 50 °C and showing a melting temperature of about 73 °C. Finally, a homology-based structural model of Ms-TA2 is built and key active site interactions for substrate and cofactor binding are analyzed.
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Affiliation(s)
- Erica E Ferrandi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy.,Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
| | - Ivan Bassanini
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy.,Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, Milan, 20133, Italy
| | - Barbara Sechi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Marta Vanoni
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Davide Tessaro
- Dipartimento di Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
| | | | - Sergio Riva
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
| | - Daniela Monti
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), CNR, Via Mario Bianco 9, Milan, 20131, Italy
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5
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Kwon S, Lee JH, Kim CM, Ha HJ, Lee SH, Lee CS, Jeon JH, So I, Park HH. Structural insights into the enzyme specificity of a novel ω-transaminase from the thermophilic bacterium Sphaerobacter thermophilus. J Struct Biol 2019; 208:107395. [PMID: 31560999 DOI: 10.1016/j.jsb.2019.09.012] [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: 06/24/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 10/26/2022]
Abstract
Transaminases are pyridoxal 5'-phosphate-dependent enzymes that reversibly catalyze transamination reactions from an amino group donor substrate to an amino group acceptor substrate. ω-Transaminases (ωTAs) utilize compounds with an amino group not at α-carbon position as their amino group donor substrates. Recently, a novel ωTA with broad substrate specificity and high thermostability from the thermophilic bacterium Sphaerobacter thermophilus (St-ωTA) has been reported. Although St-ωTA has been biochemically characterized, little is known about its determinants of substrate specificity. In the present study, we determined the crystal structure of St-ωTA at 1.9 Å resolution to clarify in detail its mechanism of substrate recognition. The structure of St-ωTA revealed that it has a voluminous active site resulting from the unique spatial arrangement of residues comprising its active site. In addition, our molecular docking simulation results suggest that substrate compounds may bind to active site residues via electrostatic interactions or hydrophobic interactions that can be induced by subtle rearrangements of active site residues. On the basis of these structural analyses, we propose a plausible working model of the enzymatic mechanism of St-ωTA. Our results provide profound structural insights into the substrate specificity of St-ωTA and extend the boundaries of knowledge of TAs.
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Affiliation(s)
- Sunghark Kwon
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chang Min Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sung Hoon Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Chang Sup Lee
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ju-Hong Jeon
- Department of Physiology and Biomedical Sciences, Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Insuk So
- Department of Physiology and Biomedical Sciences, Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
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