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Guan ZB, Deng XT, Zhang ZH, Xu GC, Cheng WL, Liao XR, Cai YJ. Engineering Glucosamine-6-Phosphate Synthase to Achieve Efficient One-Step Biosynthesis of Glucosamine. ACS Chem Biol 2024; 19:1237-1242. [PMID: 38723147 DOI: 10.1021/acschembio.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
As an important functional monosaccharide, glucosamine (GlcN) is widely used in fields such as medicine, food nutrition, and health care. Here, we report a distinct GlcN biosynthesis method that utilizes engineered Bacillus subtilis glucosamine-6-phosphate synthase (BsGlmS) to convert D-fructose to directly generate GlcN. The best variant obtained by using a combinatorial active-site saturation test/iterative saturation mutagenesis (CAST/ISM) strategy was a quadruple mutant S596D/V597G/S347H/G299Q (BsGlmS-BK19), which has a catalytic activity 1736-fold that of the wild type toward D-fructose. Upon using mutant BK19 as a whole-cell catalyst, D-fructose was converted into GlcN with 65.32% conversion in 6 h, whereas the wild type only attained a conversion rate of 0.31% under the same conditions. Molecular docking and molecular dynamics simulations were implemented to provide insights into the mechanism underlying the enhanced activity of BK19. Importantly, the BsGlmS-BK19 variant specifically catalyzes D-fructose without the need for phosphorylated substrates, representing a significant advancement in GlcN biosynthesis.
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Affiliation(s)
- Zheng-Bing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xue-Ting Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zi-Hao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guo-Chao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wan-Li Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Xiang-Ru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yu-Jie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
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Ni ZF, Xu P, Zong MH, Lou WY. Structure-guided protein engineering of ammonia lyase for efficient synthesis of sterically bulky unnatural amino acids. BIORESOUR BIOPROCESS 2021; 8:103. [PMID: 38650190 PMCID: PMC10992142 DOI: 10.1186/s40643-021-00456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/08/2021] [Indexed: 11/10/2022] Open
Abstract
Enzymatic asymmetric amination addition is seen as a promising approach for synthesizing amine derivatives, especially unnatural amino acids, which are valuable precursors to fine chemicals and drugs. Despite the broad substrate spectrum of methylaspartate lyase (MAL), some bulky substrates, such as caffeic acid, cannot be effectively accepted. Herein, we report a group of variants structurally derived from Escherichia coli O157:H7 MAL (EcMAL). A combined mutagenesis strategy was used to simultaneously redesign the key residues of the entrance tunnel and binding pocket to explore the possibility of accepting bulky substrates with potential application to chiral drug synthesis. Libraries of residues capable of lining the active center of EcMAL were then constructed and screened by an effective activity solid-phase color screening method using tyrosinase as a cascade catalyst system. Activity assays and molecular dynamics studies of the resultant variants showed that the substrate specificity of EcMAL was modified by adjusting the polarity of the binding pocket and the degree of flexibility of the entrance tunnel. Compared to M3, the optimal variant M8 was obtained with a 15-fold increase in catalytic activity. This structure-based protein engineering of EcMAL can be used to open new application directions or to develop practical multi-enzymatic processes for the production of various useful compounds.
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Affiliation(s)
- Zi-Fu Ni
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Pei Xu
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Min-Hua Zong
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Wen-Yong Lou
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China.
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Reetz MT, Garcia-Borràs M. The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions. J Am Chem Soc 2021; 143:14939-14950. [PMID: 34491742 PMCID: PMC8461649 DOI: 10.1021/jacs.1c04551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Indexed: 02/07/2023]
Abstract
Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
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Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Marc Garcia-Borràs
- Institute
of Computational Chemistry and Catalysis (IQCC) and Departament de
Química, Universitat de Girona, Carrer Maria Aurèlia Capmany
69, 17003 Girona, Spain
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De Raffele D, Martí S, Moliner V. A QM/MM study on the origin of retro-aldolase activity of a catalytic antibody. Chem Commun (Camb) 2021; 57:5306-5309. [PMID: 33912877 DOI: 10.1039/d1cc01081f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The retro-aldolase mechanism of methodol catalysed by the catalytic antibody 33F12 is described based on the exploration of the free energy landscape obtained with QM/MM methods. The amino acids involved in the reaction have been identified, as well as their specific role played in the active site and in the flexibility of the loops. Finally, the comparison with a de novo enzyme RA95.5-8F provides a deeper understanding of catalytic differences between such different protein scaffolds.
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Affiliation(s)
- Daria De Raffele
- Departament de Química Física i Analítica, Universitat Jaume I, Castellón 12071, Spain.
| | - Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, Castellón 12071, Spain.
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, Castellón 12071, Spain.
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5
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Li W, Sun W, Li C. Engineered microorganisms and enzymes for efficiently synthesizing plant natural products. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Bunzel HA, Anderson JLR, Mulholland AJ. Designing better enzymes: Insights from directed evolution. Curr Opin Struct Biol 2021; 67:212-218. [PMID: 33517098 DOI: 10.1016/j.sbi.2020.12.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/03/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
De novo enzymes can be created by computational design and directed evolution. Here, we review recent insights into the origins of catalytic power in evolved designer enzymes to pinpoint opportunities for next-generation designs: Evolution precisely organizes active sites, introduces catalytic H-bonding networks, invokes electrostatic catalysis, and creates dynamical networks embedding the active site in a reactive protein scaffold. Such insights foster our fundamental knowledge of enzyme catalysis and fuel the future design of tailor-made enzymes.
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Affiliation(s)
- H Adrian Bunzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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Osuna S. The challenge of predicting distal active site mutations in computational enzyme design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1502] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Girona Spain
- ICREA Barcelona Spain
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