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Cheng F, Sun KX, Gong XX, Peng W, Zhang HY, Liang XH, Xue YP, Zheng YG. Development of growth selection system and pocket engineering of d-amino acid oxidase to enhance selective deamination activity toward d-phosphinothricin. Biotechnol Bioeng 2024; 121:2893-2906. [PMID: 38822747 DOI: 10.1002/bit.28763] [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: 12/10/2023] [Revised: 03/31/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
D-amino acid oxidase (DAAO)-catalyzed selective oxidative deamination is a very promising process for synthesizing l-amino acids including l-phosphinothricin (l-PPT, a high-efficiency and broad-spectrum herbicide). However, the wild-type DAAO's low activity toward unnatural substrates like d-phosphinothricin (d-PPT) hampers its application. Herein, a DAAO from Caenorhabditis elegans (CeDAAO) was screened and engineered to improve the catalytic potential on d-PPT. First, we designed a novel growth selection system, taking into account the intricate relationship between the growth of Escherichia coli (E. coli) and the catalytic mechanism of DAAO. The developed system was used for high-throughput screening of gene libraries, resulting in the discovery of a variant (M6) with significantly increased catalytic activity against d-PPT. The variant displays different catalytic properties on substrates with varying hydrophobicity and hydrophilicity. Analysis using Alphafold2 modeling and molecular dynamic simulations showed that the reason for the enhanced activity was the substrate-binding pocket with enlarged size and suitable charge distribution. Further QM/MM calculations revealed that the crucial factor for enhancing activity lies in reducing the initial energy barrier of the reductive half reaction. Finally, a comprehensive binding-model index to predict the enhanced activity of DAAO toward d-PPT, and an enzymatic deracemization approach was developed, enabling the efficient synthesis of l-PPT with remarkable efficiency.
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Affiliation(s)
- Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ke-Xiang Sun
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Xiao-Xiao Gong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Wei Peng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Hua-Yue Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Xi-Hang Liang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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Li Q, Wang H, Zhang W, Wang W, Ren X, Wu M, Shi G. Structure-Guided Evolution Modulate Alcohol Oxidase to Improve Ethanol Oxidation Performance. Appl Biochem Biotechnol 2024; 196:1948-1965. [PMID: 37453026 DOI: 10.1007/s12010-023-04626-3] [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] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
A high ethanol usage of alcohol oxidase (AOX) was required in industry. In this study, a "expand substrate pocket" strategy achieved a high activity AOX from Hansenula polymorpha (H. polymorpha) by Phe to Val residue (F/V) site-directed mutation to enlarge ethanol channel. Although H. Polymorpha AOX (HpAOX) possessed respectively 71.3% and 76.1% similarity with AOX (PpAOX) from Pichia pastoris (P. pastoris) in DNA and protein sequences, their active site structures including catalytic site and substrate channel were similar according to computer-aided analysis. After 3D structure analysis, Phe99 residue of their substrate channels was the most important residue to impact enzyme activity because of its large aromatic side chains. F99V mutation of HpAOX (HpAOXF99V) was designed and executed based on the enzyme catalytic mechanism and molecular computation in order to allow more larger size ethanol into active site. The highest enzyme activity of the fourth strains of HpAOXF99V mutant strain exhibited 12.06-folds increase than that of the host GS115 strain. Furthermore, kinetic studies indicated that the HpAOXF99V significantly promoted catalytic efficiency of ethanol than HpAOX, including Km, Vmax, kcat and kcat/Km. We also provided a new insight that the cofactor FAD irritated both active AOX octamer biosynthesis production and enzyme-catalysed ability due to help enzyme assembly and redox potential.
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Affiliation(s)
- Qian Li
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Haiou Wang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China.
| | - Wenxiao Zhang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Wenxuan Wang
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Xiaoyu Ren
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Mengyao Wu
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Guoqing Shi
- School of Chemistry and Biological Engineering, Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, China
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Li A, Ting W, Yang K, Zhang X, Yin D, Qin Y, Zhang L. Engineering a Carbonyl Reductase as a Potential Tool for the Synthesis of Chiral α‐Tetralinols. ChemCatChem 2021. [DOI: 10.1002/cctc.202100890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aipeng Li
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an P. R. China
| | - Wang Ting
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an P. R. China
| | - Ke Yang
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an P. R. China
| | - Xuanshuo Zhang
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an P. R. China
| | - Dongming Yin
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an P. R. China
| | - Yong Qin
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an P. R. China
- State Key Laboratory of Coal Conversion Institute of Coal Chemistry Chinese Academy of Sciences 030001 Taiyuan P. R. China
| | - Lianbing Zhang
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an P. R. China
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Li A, Wang T, Tian Q, Yang X, Yin D, Qin Y, Zhang L. Single-Point Mutant Inverts the Stereoselectivity of a Carbonyl Reductase toward β-Ketoesters with Enhanced Activity. Chemistry 2021; 27:6283-6294. [PMID: 33475219 DOI: 10.1002/chem.202005195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Indexed: 01/06/2023]
Abstract
Enzyme stereoselectivity control is still a major challenge. To gain insight into the molecular basis of enzyme stereo-recognition and expand the source of antiPrelog carbonyl reductase toward β-ketoesters, rational enzyme design aiming at stereoselectivity inversion was performed. The designed variant Q139G switched the enzyme stereoselectivity toward β-ketoesters from Prelog to antiPrelog, providing corresponding alcohols in high enantiomeric purity (89.1-99.1 % ee). More importantly, the well-known trade-off between stereoselectivity and activity was not found. Q139G exhibited higher catalytic activity than the wildtype enzyme, the enhancement of the catalytic efficiency (kcat /Km ) varied from 1.1- to 27.1-fold. Interestingly, the mutant Q139G did not lead to reversed stereoselectivity toward aromatic ketones. Analysis of enzyme-substrate complexes showed that the structural flexibility of β-ketoesters and a newly formed cave together facilitated the formation of the antiPrelog-preferred conformation. In contrast, the relatively large and rigid structure of the aromatic ketones prevents them from forming the antiPrelog-preferred conformation.
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Affiliation(s)
- Aipeng Li
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Ting Wang
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Qing Tian
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Xiaohong Yang
- Department of Chemistry, University of California, One Shields Avenue, Davis, California, 95616, United States
| | - Dongming Yin
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
| | - Yong Qin
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Lianbing Zhang
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China.,Research & Development Institute in Shenzhen, Northwestern Polytechnical University, 518057, Shenzhen, China
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Li A, Li X, Pang W, Tian Q, Wang T, Zhang L. Fine-tuning of the substrate binding mode to enhance the catalytic efficiency of an ortho-haloacetophenone-specific carbonyl reductase. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02335f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fine-tuning of the substrate binding mode was successfully applied for enhancing the catalytic efficiency of an ortho-haloacetophenone-specific carbonyl reductase.
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Affiliation(s)
- Aipeng Li
- Research & Development Institute in Shenzhen
- Northwestern Polytechnical University
- 518057 Shenzhen
- China
- School of Life Sciences
| | - Xue Li
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Wei Pang
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Qing Tian
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Ting Wang
- School of Life Sciences
- Northwestern Polytechnical University
- 710072 Xi'an
- China
| | - Lianbing Zhang
- Research & Development Institute in Shenzhen
- Northwestern Polytechnical University
- 518057 Shenzhen
- China
- School of Life Sciences
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