1
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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Suzuki K, Stanfield JK, Omura K, Shisaka Y, Ariyasu S, Kasai C, Aiba Y, Sugimoto H, Shoji O. A Compound I Mimic Reveals the Transient Active Species of a Cytochrome P450 Enzyme: Insight into the Stereoselectivity of P450-Catalysed Oxidations. Angew Chem Int Ed Engl 2023; 62:e202215706. [PMID: 36519803 DOI: 10.1002/anie.202215706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Catching the structure of cytochrome P450 enzymes in flagrante is crucial for the development of P450 biocatalysts, as most structures collected are found trapped in a precatalytic conformation. At the heart of P450 catalysis lies Cpd I, a short-lived, highly reactive intermediate, whose recalcitrant nature has thwarted most attempts at capturing catalytically relevant poses of P450s. We report the crystal structure of P450BM3 mimicking the state in the precise moment preceding epoxidation, which is in perfect agreement with the experimentally observed stereoselectivity. This structure was attained by incorporation of the stable Cpd I mimic oxomolybdenum mesoporphyrin IX into P450BM3 in the presence of styrene. The orientation of styrene to the Mo-oxo species in the crystal structures sheds light onto the dynamics involved in the rotation of styrene to present its vinyl group to Cpd I. This method serves as a powerful tool for predicting and modelling the stereoselectivity of P450 reactions.
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Affiliation(s)
- Kazuto Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Keita Omura
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuma Shisaka
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Chie Kasai
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Hiroshi Sugimoto
- RIKEN SPring-8 Centre, 1-1-1, Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 5, Sanbancho, Chiyoda-ku, Tokyo, 102-0075, Japan
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3
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Omura K, Aiba Y, Suzuki K, Ariyasu S, Sugimoto H, Shoji O. A P450 Harboring Manganese Protoporphyrin IX Generates a Manganese Analogue of Compound I by Activating Dioxygen. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Keita Omura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuto Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroshi Sugimoto
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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4
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Onoda H, Tanaka S, Watanabe Y, Shoji O. Exploring hitherto uninvestigated reactions of the fatty acid peroxygenase CYP152A1: catalase reaction and Compound I formation. Faraday Discuss 2022; 234:304-314. [PMID: 35179151 DOI: 10.1039/d1fd00065a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CYP152A1 (cytochrome P450BSβ) is a fatty acid peroxygenase, which specifically catalyses the oxidation of long-chain fatty acids using hydrogen peroxide as an oxidant. We have found that CYP152A1 possesses catalase activity, which competes with the hydroxylation of long-chain fatty acids, the oxidation of non-native substrates, and haem degradation. Using hydrogen peroxide, Compound I of CYP152A1 could not be observed, due to its swift decomposition via catalase activity, where Compound I reacts with another molecule of hydrogen peroxide to form O2. In contrast, a clear spectral change indicative of Compound I formation was observed when mCPBA was employed as the oxidant. This work presents valuable insights into an important role for the catalase activity of CYP152A1 in avoiding enzyme deactivation when no substrate is available for oxidation.
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Affiliation(s)
- Hiroki Onoda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan. .,Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shota Tanaka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan.
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan.
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0802, Japan.
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5
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Karasawa M, Yonemura K, Stanfield JK, Suzuki K, Shoji O. Ein Designeraußenmembranprotein fördert die Aufnahme von Täuschmolekülen in einen auf Zytochrom P450BM3 beruhenden Ganzzellbiokatalysator. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Masayuki Karasawa
- Department of Chemistry Graduate School of Science Universität Nagoya Furo-cho, Chikusa-ku, Nagoya 464-8602 Japan
| | - Kai Yonemura
- Department of Chemistry Graduate School of Science Universität Nagoya Furo-cho, Chikusa-ku, Nagoya 464-8602 Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry Graduate School of Science Universität Nagoya Furo-cho, Chikusa-ku, Nagoya 464-8602 Japan
| | - Kazuto Suzuki
- Department of Chemistry Graduate School of Science Universität Nagoya Furo-cho, Chikusa-ku, Nagoya 464-8602 Japan
| | - Osami Shoji
- Department of Chemistry Graduate School of Science Universität Nagoya Furo-cho, Chikusa-ku, Nagoya 464-8602 Japan
- Core Research for Evolutional Science and Technology (Japan) Science and Technology Agency 5 Sanbancho Chiyoda-ku, Tokio 102-0075 Japan
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6
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Stanfield JK, Shoji O. The Power of Deception: Using Decoy Molecules to Manipulate P450BM3 Biotransformations. CHEM LETT 2021. [DOI: 10.1246/cl.210584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Joshua Kyle Stanfield
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Aichi 461-8602, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Aichi 461-8602, Japan
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7
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Karasawa M, Yonemura K, Stanfield JK, Suzuki K, Shoji O. Designer Outer Membrane Protein Facilitates Uptake of Decoy Molecules into a Cytochrome P450BM3-Based Whole-Cell Biocatalyst. Angew Chem Int Ed Engl 2021; 61:e202111612. [PMID: 34704327 DOI: 10.1002/anie.202111612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 11/11/2022]
Abstract
We report an OmpF loop deletion mutant, which improves the cellular uptake of external additives into an Escherichia coli whole-cell biocatalyst. Through co-expression of the OmpF mutant with wild-type P450BM3 in the presence of decoy molecules, the yield of the whole-cell biotransformation of benzene could be considerably improved. Notably, with C7AM-Pip-Phe the yield duodecupled from 5.7% to 70%, with 80% phenol selectivity. The benzylic hydroxylation of alkyl- and cycloalkylbenzenes was also examined, and with the aid of decoy molecules, propylbenzene and tetralin were converted to 1-hydroxylated products with 78% yield and 94% ( R ) ee for propylbenzene and 92% yield and 94% ( S ) ee for tetralin. Our results suggest that both the decoy molecule and substrate traverse the artificial channel, synergistically boosting whole-cell bioconversions.
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Affiliation(s)
- Masayuki Karasawa
- Nagoya University: Nagoya Daigaku, Chemistry, Science & Agricultural Building SA601, Furo-cho, Chikusa-ku, 464-8602, Nagoya-shi, JAPAN
| | - Kai Yonemura
- Nagoya University: Nagoya Daigaku, Chemistry, Science & Agricultural Building SA601, Furo-cho, Chikusa-ku, 464-8602, Nagoya-shi, JAPAN
| | - Joshua Kyle Stanfield
- Nagoya University: Nagoya Daigaku, Chemistry, Science & Agricultural Building SA601, Furo-cho, Chikusa-ku, 464-8602, Nagoya-shi, JAPAN
| | - Kazuto Suzuki
- Nagoya University: Nagoya Daigaku, Chemistry, Science & Agricultural Building SA601, Furo-cho, Chikusa-ku, 464-8602, Nagoya-shi, JAPAN
| | - Osami Shoji
- Nagoya University, Graduate School of Science, Furo, Chikusa,, 464-8602, Nagoya, JAPAN
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8
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Zhao P, Chen J, Ma N, Chen J, Qin X, Liu C, Yao F, Yao L, Jin L, Cong Z. Enabling highly ( R)-enantioselective epoxidation of styrene by engineering unique non-natural P450 peroxygenases. Chem Sci 2021; 12:6307-6314. [PMID: 34084428 PMCID: PMC8115292 DOI: 10.1039/d1sc00317h] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Unlike the excellent (S)-enantioselective epoxidation of styrene performed by natural styrene monooxygenases (ee > 99%), the (R)-enantioselective epoxidation of styrene has not yet achieved a comparable efficiency using natural or engineered oxidative enzymes. This report describes the H2O2-dependent (R)-enantioselective epoxidation of unfunctionalized styrene and its derivatives by site-mutated variants of a unique non-natural P450BM3 peroxygenase, working in tandem with a dual-functional small molecule (DFSM). The observed (R)-enantiomeric excess (ee) of styrene epoxidation is up to 99% with a turnover number (TON) of 918 by the best enantioselective mutant F87A/T268I/L181Q, while the best active mutant F87A/T268I/V78A/A184L (with 98% ee) gave a catalytic TON of 4350, representing the best activity of a P450 peroxygenase towards styrene epoxidation to date. Following this approach, a set of styrene derivatives, such as o-, m-, p-chlorostyrenes and fluorostyrenes, could also be epoxidized with modest to very good TONs (362–3480) and high (R)-enantioselectivities (95–99% ee). The semi-preparative scale synthesis of (R)-styrene oxide performed at 0 °C with high conversion, maintaining enantioselectivity, and moderate isolated yields, further suggests the potential application of the current P450 enzymatic system in styrene epoxidation. This study indicates that the synergistic use of protein engineering and an exogenous DFSM constitutes an efficient strategy to control the enantioselectivity of styrene epoxidation, thus substantially expanding the chemical scope of P450 enzymes as useful bio-oxidative catalysts. H2O2-dependent epoxidation of unfunctionalized styrenes is achieved with high (R)-enantioselectivity and moderate to excellent TONs by combining site-mutated variants of cytochrome P450BM3 monooxygenase and a dual-functional small molecule (DFSM).![]()
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Affiliation(s)
- Panxia Zhao
- CAS Key Laboratory of Biofuels, 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
| | - Jie Chen
- CAS Key Laboratory of Biofuels, 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
| | - Nana Ma
- CAS Key Laboratory of Biofuels, 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
| | - Jingfei Chen
- CAS Key Laboratory of Biofuels, 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, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong 266101 China .,Department of Chemistry, Yanbian University Yanji Jilin 133002 China
| | - Chuanfei Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong 266101 China
| | - Fuquan Yao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong 266101 China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong 266101 China
| | - Longyi Jin
- Department of Chemistry, Yanbian University Yanji Jilin 133002 China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels, 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
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