1
|
Lin RD, Xing X, Yu Y, Li WD, Chang DD, Tao FY, Wang N. Theoretical Analysis of Selectivity Differences in Ketoreductases toward Aldehyde and Ketone Carbonyl Groups. J Chem Inf Model 2024; 64:3400-3410. [PMID: 38537611 DOI: 10.1021/acs.jcim.3c01996] [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: 04/23/2024]
Abstract
Lactobacillus kefir alcohol dehydrogenase (LkADH) and ketoreductase from Chryseobacterium sp. CA49 (ChKRED12) exhibit different chemoselectivity and stereoselectivity toward a substrate with both keto and aldehyde carbonyl groups. LkADH selectively reduces the keto carbonyl group while retaining the aldehyde carbonyl group, producing optically pure R-alcohols. In contrast, ChKRED12 selectively reduces the aldehyde group and exhibits low reactivity toward ketone carbonyls. This study investigated the structural basis for these differences and the role of specific residues in the active site. Molecular dynamics (MD) simulations and quantum chemical calculations were used to investigate the interactions between the substrate and the enzymes and the essential cause of this phenomenon. The present study has revealed that LkADH and ChKRED12 exhibit significant differences in the structure of their respective active pockets, which is a crucial determinant of their distinct chemoselectivity toward the same substrate. Moreover, residues N89, N113, and E144 within LkADH as well as Q151 and D190 within ChKRED12 have been identified as key contributors to substrate stabilization within the active pocket through electrostatic interactions and van der Waals forces, followed by hydride transfer utilizing the coenzyme NADPH. Furthermore, the enantioselectivity mechanism of LkADH has been elucidated using quantum chemical methods. Overall, these findings not only provide fundamental insights into the underlying reasons for the observed differences in selectivity but also offer a detailed mechanistic understanding of the catalytic reaction.
Collapse
Affiliation(s)
- Ru-De Lin
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Xiu Xing
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Yuan Yu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Wen-Dian Li
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, China Tobacco Sichuan Industrial Co., Ltd., Chengdu 610066, China
- Sichuan Sanlian New Material Co., Ltd., Chengdu 610041, China
| | - Dan-Dan Chang
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, China Tobacco Sichuan Industrial Co., Ltd., Chengdu 610066, China
- Sichuan Sanlian New Material Co., Ltd., Chengdu 610041, China
| | - Fei-Yan Tao
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, China Tobacco Sichuan Industrial Co., Ltd., Chengdu 610066, China
- Sichuan Sanlian New Material Co., Ltd., Chengdu 610041, China
| | - Na Wang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| |
Collapse
|
2
|
Wang D, Zheng P, Chen P, Dan Wu. Engineering an α-L-rhamnosidase from Aspergillus niger for efficient conversion of rutin substrate. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
3
|
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
| |
Collapse
|
4
|
Wang T, Yang K, Tian Q, Han R, Zhang X, Li A, Zhang L. Acetoacetyl-CoA reductase PhaB as an excellent anti-Prelog biocatalyst for the synthesis of chiral β-hydroxyl ester and the molecular basis of its catalytic performance. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|