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Wei S, Xu G, Zhou J, Ni Y. Structure-Guided Evolution of Cyclohexanone Monooxygenase Toward Bulky Omeprazole Sulfide: Substrate Migration and Stereoselectivity Inversion. Chemphyschem 2024; 25:e202400008. [PMID: 38514394 DOI: 10.1002/cphc.202400008] [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: 01/03/2024] [Revised: 03/06/2024] [Accepted: 03/20/2024] [Indexed: 03/23/2024]
Abstract
Structure-guided engineering of a CHMO from Amycolatopsis methanolica (AmCHMO) was performed for asymmetric sulfoxidation activity and stereoselectivity toward omeprazole sulfide. Initially, combinatorial active-site saturation test (CASTing) and iteratively saturation mutagenesis (ISM) were performed on 5 residues at the "bottleneck" of substrate tunnel, and MT3 was successfully obtained with a specific activity of 46.19 U/g and R-stereoselectivity of 99 % toward OPS. Then, 4 key mutations affecting the stereoselectivity were identified through multiple rounds of ISM on residues at the substrate binding pocket region, resulting MT8 with an inversed stereoselectivity from 99 % (R) to 97 % (S). MT8 has a greatly compromised specific activity of 0.08 U/g. By introducing additional beneficial mutations, MT11 was constructed with significantly increased specific activity of 2.29 U/g and stereoselectivity of 97 % (S). Enlarged substrate tunnel is critical to the expanded substrate spectrum of AmCHMO, while reshaping of substrate binding pocket is important for stereoselective inversion. Based on MD simulation, pre-reaction states of MT3-OPSproR, MT8-OPSproS, and MT11-OPSproS were calculated to be 45.56 %, 17.94 %, and 28.65 % respectively, which further confirm the experimental data on activity and stereoselectivity. Our results pave the way for engineering distinct activity and stereoselectivity of BVMOs toward bulky prazole thioethers.
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Affiliation(s)
- Shiyu Wei
- Institution: School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Address, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Department: Key laboratory of industrial Biotechnology. Institution: Ministry of Education, School of Biotechnology, Address, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Guochao Xu
- Department: Key laboratory of industrial Biotechnology. Institution: Ministry of Education, School of Biotechnology, Address, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jieyu Zhou
- Department: Key laboratory of industrial Biotechnology. Institution: Ministry of Education, School of Biotechnology, Address, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Ye Ni
- Department: Key laboratory of industrial Biotechnology. Institution: Ministry of Education, School of Biotechnology, Address, Jiangnan University, Wuxi, 214122, Jiangsu, China
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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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Cárdenas-Moreno Y, González-Bacerio J, García Arellano H, Del Monte-Martínez A. Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst. Biotechnol Appl Biochem 2023; 70:2108-2135. [PMID: 37753743 DOI: 10.1002/bab.2513] [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: 09/26/2022] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.
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Affiliation(s)
- Yosberto Cárdenas-Moreno
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jorge González-Bacerio
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, Havana, Cuba
| | - Humberto García Arellano
- Department of Environmental Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University, Lerma, Mexico, Mexico
| | - Alberto Del Monte-Martínez
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
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Zhao P, Kong F, Jiang Y, Qin X, Tian X, Cong Z. Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels. J Am Chem Soc 2023; 145:5506-5511. [PMID: 36790023 DOI: 10.1021/jacs.3c00195] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Given prominent physicochemical similarities between H2O2 and water, we report a new strategy for promoting the peroxygenase activity of P450 enzymes by engineering their water tunnels to facilitate H2O2 access to the heme center buried therein. Specifically, the H2O2-driven activities of two native NADH-dependent P450 enzymes (CYP199A4 and CYP153AM.aq) increase significantly (by >183-fold and >15-fold, respectively). Additionally, the amount of H2O2 required for an artificial P450 peroxygenase facilitated by a dual-functional small molecule to obtain the desired product is reduced by 95%-97.5% (with ∼95% coupling efficiency). Structural analysis suggests that mutating the residue at the bottleneck of the water tunnel may open a second pathway for H2O2 to flow to the heme center (in addition to the natural substrate tunnel). This study highlights a promising, generalizable strategy whereby P450 monooxygenases can be modified to adopt peroxygenase activity through H2O2 tunnel engineering, thus broadening the application scope of P450s in synthetic chemistry and synthetic biology.
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Affiliation(s)
- Panxia Zhao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanhui Kong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiangquan Qin
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiaoxia Tian
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shandong Energy Institute, Qingdao, Shandong 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
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Kang BG, Kwon SY, Lee HR, Hwang Y, Youn SY, Oh C, Park JB, Cha SS. Structural and functional characterization of a thermostable secretory phospholipase A 2 from Sciscionella marina and its application in liposome biotransformation. Acta Crystallogr D Struct Biol 2023; 79:188-197. [PMID: 36762864 DOI: 10.1107/s2059798323000384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/14/2023] [Indexed: 02/09/2023] Open
Abstract
Secretory phospholipase A2 (sPLA2), which hydrolyzes the sn-2 acyl bond of lecithin in a Ca2+-dependent manner, is an important enzyme in the oil and oleochemical industries. However, most sPLA2s are not stable under process conditions. Therefore, a thermostable sPLA2 was investigated in this study. A marine bacterial sPLA2 isolated from Sciscionella marina (Sm-sPLA2) was catalytically active even after 5 h of incubation at high temperatures of up to 50°C, which is outstanding compared with a representative bacterial sPLA2 (i.e. sPLA2 from Streptomyces violaceoruber; Sv-sPLA2). Consistent with this, the melting temperature of Sm-sPLA2 was measured to be 7.7°C higher than that of Sv-sPLA2. Furthermore, Sm-sPLA2 exhibited an improved biotransformation performance compared with Sv-sPLA2 in the hydrolysis of soy lecithin to lysolecithin and free fatty acids at 50°C. Structural and mutagenesis studies revealed that the Trp41-mediated anchoring of a Ca2+-binding loop into the rest of the protein body is directly linked to the thermal stability of Sm-sPLA2. This finding provides a novel structural insight into the thermostability of sPLA2 and could be applied to create mutant proteins with enhanced industrial potential.
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Affiliation(s)
- Bu Gyeong Kang
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Seung Yeon Kwon
- Department of Food Science and Biotechnology, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Hyo Ran Lee
- Department of Food Science and Biotechnology, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Yeji Hwang
- Department of Food Science and Biotechnology, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - So Yeon Youn
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Chulhong Oh
- Jeju Marine Research Center, Korea Institute of Ocean Science and Technology, 2670 Iljudong-ro, Gujwa-eup, Jeju 63349, Republic of Korea
| | - Jin Byung Park
- Department of Food Science and Biotechnology, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Sun Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
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