1
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Fansher DJ, Besna JN, Pelletier JN. Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation. Faraday Discuss 2024. [PMID: 38993060 DOI: 10.1039/d4fd00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Evolution of P450 BM3 is a topic of extensive research, but screening the various substrate/reaction combinations remains a time-consuming process. Indigo production has the potential to serve as a simple high-throughput method for reaction screening, as bacterial colonies expressing indigo (+) variants can be visually identified via their blue phenotype. Indigo (+) single variants, indigo (-) single variants and a combinatorial library, containing mutations that enable the blue phenotype, were screened for their ability to hydroxylate a panel of 12 aromatic compounds using the 4-aminoantipyrine colorimetric assay. Recombination of indigo (+) single variants to create a multiple-variant library is a particularly useful strategy, as all top performing P450 BM3 variants with high hydroxylation activity were either indigo (+) single variants or contained multiple substitutions. Furthermore, active variants, as determined using the 4-AAP assay, were further characterized and several variants were identified that gave more than 90% conversion with 1,3-dichlorobenzene and predominantly formed 2,6-dichlorophenol; other variants showed significant substrate selectivity. This supports the hypothesis that substitution at positions that enable the indigo (+) phenotype, or hotspot residues, is a general mechanism for increasing aromatic hydroxylation activity. Overall, this research demonstrates that indigo (+) single variants, identified via colorimetric colony-based screening, may be recombined to generate a multiply-substituted variant library containing many variants with high aromatic hydroxylation activity. The combination of colony-based screening and other screening assays greatly accelerates enzyme engineering, as readily-identified indigo (+) single variants can be recombined to create a library of active multiple variants without extensive screening of single variants.
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Affiliation(s)
- Douglas J Fansher
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
| | - Jonathan N Besna
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Joelle N Pelletier
- Chemistry Department, Université de Montréal, Montreal, QC, Canada.
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
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2
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Qiu C, Wang X, Zuo J, Li R, Gao C, Chen X, Liu J, Wei W, Wu J, Hu G, Song W, Xu N, Liu L. Systems engineering Escherichia coli for efficient production p-coumaric acid from glucose. Biotechnol Bioeng 2024; 121:2147-2162. [PMID: 38666765 DOI: 10.1002/bit.28721] [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: 01/30/2024] [Revised: 04/06/2024] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
P-coumaric acid (p-CA), a pant metabolite with antioxidant and anti-inflammatory activity, is extensively utilized in biomedicine, food, and cosmetics industry. In this study, a synthetic pathway (PAL) for p-CA was designed, integrating three enzymes (AtPAL2, AtC4H, AtATR2) into a higher l-phenylalanine-producing strain Escherichia coli PHE05. However, the lower soluble expression and activity of AtC4H in the PAL pathway was a bottleneck for increasing p-CA titers. To overcome this limitation, the soluble expression of AtC4H was enhanced through N-terminal modifications. And an optimal mutant, AtC4HL373T/G211H, which exhibited a 4.3-fold higher kcat/Km value compared to the wild type, was developed. In addition, metabolic engineering strategies were employed to increase the intracellular NADPH pool. Overexpression of ppnk in engineered E. coli PHCA20 led to a 13.9-folds, 1.3-folds, and 29.1% in NADPH content, the NADPH/NADP+ ratio and p-CA titer, respectively. These optimizations significantly enhance p-CA production, in a 5-L fermenter using fed-batch fermentation, the p-CA titer, yield and productivity of engineered strain E. coli PHCA20 were 3.09 g/L, 20.01 mg/g glucose, and 49.05 mg/L/h, respectively. The results presented here provide a novel way to efficiently produce the plant metabolites using an industrial strain.
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Affiliation(s)
- Chong Qiu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiaoge Wang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Jiaojiao Zuo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Runyang Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Jia Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
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3
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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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4
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Bertelmann C, Mock M, Schmid A, Bühler B. Efficiency aspects of regioselective testosterone hydroxylation with highly active CYP450-based whole-cell biocatalysts. Microb Biotechnol 2024; 17:e14378. [PMID: 38018939 PMCID: PMC10832557 DOI: 10.1111/1751-7915.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023] Open
Abstract
Steroid hydroxylations belong to the industrially most relevant reactions catalysed by cytochrome P450 monooxygenases (CYP450s) due to the pharmacological relevance of hydroxylated derivatives. The implementation of respective bioprocesses at an industrial scale still suffers from several limitations commonly found in CYP450 catalysis, that is low turnover rates, enzyme instability, inhibition and toxicity related to the substrate(s) and/or product(s). Recently, we achieved a new level of steroid hydroxylation rates by introducing highly active testosterone-hydroxylating CYP450 BM3 variants together with the hydrophobic outer membrane protein AlkL into Escherichia coli-based whole-cell biocatalysts. However, the activity tended to decrease, which possibly impedes overall productivities and final product titres. In this study, a considerable instability was confirmed and subject to a systematic investigation regarding possible causes. In-depth evaluation of whole-cell biocatalyst kinetics and stability revealed a limitation in substrate availability due to poor testosterone solubility as well as inhibition by the main product 15β-hydroxytestosterone. Instability of CYP450 BM3 variants was disclosed as another critical factor, which is of general significance for CYP450-based biocatalysis. Presented results reveal biocatalyst, reaction and process engineering strategies auguring well for industrial implementation of the developed steroid hydroxylation platform.
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Affiliation(s)
| | - Magdalena Mock
- Department of Solar MaterialsLeipzigGermany
- Present address:
Department of Mechanical Engineering and Material SciencesGeorg Agricola University of Applied SciencesBochumGermany
| | | | - Bruno Bühler
- Department of Solar MaterialsLeipzigGermany
- Department of Microbial BiotechnologyHelmholtz Centre for Environmental Research GmbH–UFZLeipzigGermany
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5
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Harwood LA, Xiong Z, Christensen KE, Wang R, Wong LL, Robertson J. Selective P450 BM3 Hydroxylation of Cyclobutylamine and Bicyclo[1.1.1]pentylamine Derivatives: Underpinning Synthetic Chemistry for Drug Discovery. J Am Chem Soc 2023; 145:27767-27773. [PMID: 38051939 PMCID: PMC10740007 DOI: 10.1021/jacs.3c10542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Achieving single-step syntheses of a set of related compounds divergently and selectively from a common starting material affords substantial efficiency gains when compared with preparing those same compounds by multiple individual syntheses. In order for this approach to be realized, complementary reagent systems must be available; here, a panel of engineered P450BM3 enzymes is shown to fulfill this remit in the selective C-H hydroxylation of cyclobutylamine derivatives at chemically unactivated sites. The oxidations can proceed with high regioselectivity and stereoselectivity, producing valuable bifunctional intermediates for synthesis and applications in fragment-based drug discovery. The process also applies to bicyclo[1.1.1]pentyl (BCP) amine derivatives to achieve the first direct enantioselective functionalization of the bridging methylenes and open a short and efficient route to chiral BCP bioisosteres for medicinal chemistry. The combination of substrate, enzyme, and reaction engineering provides a powerful general platform for small-molecule elaboration and diversification.
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Affiliation(s)
- Lucy A. Harwood
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ziyue Xiong
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
| | - Kirsten E. Christensen
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ruiyao Wang
- Wisdom
Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool
University, Suzhou Industrial
Park, Suzhou, Jiangsu, 215123, P. R. China
| | - Luet L. Wong
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K.
| | - Jeremy Robertson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
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6
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Akter J, Stockdale TP, Child SA, Lee JHZ, De Voss JJ, Bell SG. Selective carbon-hydrogen bond hydroxylation using an engineered cytochrome P450 peroxygenase. J Inorg Biochem 2023; 244:112209. [PMID: 37080140 DOI: 10.1016/j.jinorgbio.2023.112209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
The cytochrome P450 enzyme CYP102A1 (P450BM3) is a versatile monooxygenase enzyme which has been adapted and engineered for multiple applications in chemical synthesis. Mutation of threonine 268 to glutamate (Thr268Glu) converted the heme domain of this enzyme into a H2O2 utilizing peroxygenase. This variant displayed significantly increased peroxide driven hydroxylation activity towards the saturated linear fatty acids tested (undecanoic through to hexadecenoic acid) when compared to the wild-type heme domain. The product distributions arising from fatty acid oxidation using this peroxygenase variant were broadly similar to those obtained with the wild-type monooxygenase holoenzyme, with oxidation occurring predominantly at the ω-1 through to ω-3 positions. 10-Undecenoic acid was regioselectively hydroxylated at the allylic ω-2 carbon by the Thr268Glu peroxygenase. The effect of isotopic substitution were measured using [9,9,10,10-d4]-dodecanoic acid. The kinetic isotope effect for both the monooxygenase and peroxygenase systems ranged between 7.9 and 9.5, with that of the peroxygenase enzyme being marginally lower. This highlights that carbon‑hydrogen bond abstraction is important in the mechanism of both the monooxygenase and peroxygenase systems. This would infer that the ferryl-oxo radical cation intermediate, compound I, is the likely reactive intermediate in both systems. The peroxygenase variant offers the possibility of simpler cytochrome P450 systems for selective oxidations. To demonstrate this we used this system to oxidize tetradecanoic acid using light driven generation of H2O2 by a flavin.
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Affiliation(s)
- Jinia Akter
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia
| | - Tegan P Stockdale
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Stella A Child
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia
| | - Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia.
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide 5005, Australia.
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7
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Chen J, Dong S, Fang W, Jiang Y, Chen Z, Qin X, Wang C, Zhou H, Jin L, Feng Y, Wang B, Cong Z. Regiodivergent and Enantioselective Hydroxylation of C-H bonds by Synergistic Use of Protein Engineering and Exogenous Dual-Functional Small Molecules. Angew Chem Int Ed Engl 2023; 62:e202215088. [PMID: 36417593 DOI: 10.1002/anie.202215088] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
It is a great challenge to optionally access diverse hydroxylation products from a given substrate bearing multiple reaction sites of sp3 and sp2 C-H bonds. Herein, we report the highly selective divergent hydroxylation of alkylbenzenes by an engineered P450 peroxygenase driven by a dual-functional small molecule (DFSM). Using combinations of various P450BM3 variants with DFSMs enabled access to more than half of all possible hydroxylated products from each substrate with excellent regioselectivity (up to >99 %), enantioselectivity (up to >99 % ee), and high total turnover numbers (up to 80963). Crystal structure analysis, molecular dynamic simulations, and theoretical calculations revealed that synergistic effects between exogenous DFSMs and the protein environment controlled regio- and enantioselectivity. This work has implications for exogenous-molecule-modulated enzymatic regiodivergent and enantioselective hydroxylation with potential applications in synthetic chemistry.
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Affiliation(s)
- Jie Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Shandong Energy Institute, 266101, Qingdao, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Shandong Energy Institute, 266101, Qingdao, China
| | - Wenhan Fang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, 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, 266101, Qingdao, China.,Shandong Energy Institute, 266101, Qingdao, China
| | - Zhifeng Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, China.,Hubei Key Laboratory of Natural Products Research and Development, Key Laboratory of Functional Yeast, China National Light Industry, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, 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, 266101, Qingdao, China.,Department of Chemistry, Yanbian University, 133002, Yanji, China
| | - Cong Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, China
| | - Haifeng Zhou
- Hubei Key Laboratory of Natural Products Research and Development, Key Laboratory of Functional Yeast, China National Light Industry, College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, China
| | - Longyi Jin
- Department of Chemistry, Yanbian University, 133002, Yanji, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101, Qingdao, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Shandong Energy Institute, 266101, Qingdao, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, 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, 266101, Qingdao, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Shandong Energy Institute, 266101, Qingdao, China
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8
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Meng S, Ji Y, Zhu L, Dhoke GV, Davari MD, Schwaneberg U. The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s. Biotechnol Adv 2022; 61:108051. [DOI: 10.1016/j.biotechadv.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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9
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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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10
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Li RJ, Tian K, Li X, Gaikaiwari AR, Li Z. Engineering P450 Monooxygenases for Highly Regioselective and Active p-Hydroxylation of m-Alkylphenols. ACS Catal 2022. [DOI: 10.1021/acscatal.1c06011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ren-Jie Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Kaiyuan Tian
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Xirui Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Anand Raghavendra Gaikaiwari
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
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11
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Rousseau O, Ebert MCCJC, Quaglia D, Fendri A, Parisien AH, Besna JN, Iyathurai S, Pelletier JN. Indigo Formation and Rapid NADPH Consumption Provide Robust Prediction of Raspberry Ketone Synthesis by Engineered Cytochrome P450 BM3. ChemCatChem 2019. [DOI: 10.1002/cctc.201901974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Rousseau
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Maximilian C. C. J. C. Ebert
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Daniela Quaglia
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Ali Fendri
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
| | - Adem H. Parisien
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Jonathan N. Besna
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Saathanan Iyathurai
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
| | - Joelle N. Pelletier
- Department of ChemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- Center for Green Chemistry and Catalysis (CGCC)Université de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
- PROTEOThe Québec Network for Research on Protein Function Engineering and Applications Québec QC−G1V 0A6 Canada
- Department of BiochemistryUniversité de Montréal 2900 Édouard-Montpetit Montréal QC H3T 1J4 Canada
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12
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Chen J, Kong F, Ma N, Zhao P, Liu C, Wang X, Cong Z. Peroxide-Driven Hydroxylation of Small Alkanes Catalyzed by an Artificial P450BM3 Peroxygenase System. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02507] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jie Chen
- 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
| | - Nana Ma
- 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
| | - 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
| | - Chuanfei Liu
- 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
| | - Xiling Wang
- 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
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13
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Li Y, Wong LL. Multi‐Functional Oxidase Activity of CYP102A1 (P450BM3) in the Oxidation of Quinolines and Tetrahydroquinolines. Angew Chem Int Ed Engl 2019; 58:9551-9555. [DOI: 10.1002/anie.201904157] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Yushu Li
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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14
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Li Y, Wong LL. Multi‐Functional Oxidase Activity of CYP102A1 (P450BM3) in the Oxidation of Quinolines and Tetrahydroquinolines. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yushu Li
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Luet L. Wong
- Department of ChemistryUniversity of OxfordInorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
- Oxford Suzhou Centre for Advanced Research Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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15
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Dezvarei S, Shoji O, Watanabe Y, Bell SG. The effect of decoy molecules on the activity of the P450Bm3 holoenzyme and a heme domain peroxygenase variant. CATAL COMMUN 2019. [DOI: 10.1016/j.catcom.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Selective hydroxylation of 1,8- and 1,4-cineole using bacterial P450 variants. Arch Biochem Biophys 2019; 663:54-63. [DOI: 10.1016/j.abb.2018.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/24/2018] [Accepted: 12/21/2018] [Indexed: 01/10/2023]
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17
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Lu N, Meng F, Xu W, Tang L, Xu Y. Molecular simulation study of CYP2B6 polymorphism with and without psoralen. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1513646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Nan Lu
- School of Pharmaceutical Engineering, and Key Laboratory of Structure-Based Drug Design & Discovery, Shenyang Pharmaceutical University, Shenyang, People’s Republic of China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, People’s Republic of China
| | - Weiren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, People’s Republic of China
| | - Lida Tang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, People’s Republic of China
| | - Youjun Xu
- School of Pharmaceutical Engineering, and Key Laboratory of Structure-Based Drug Design & Discovery, Shenyang Pharmaceutical University, Shenyang, People’s Republic of China
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18
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Syntrivanis LD, Wong LL, Robertson J. Hydroxylation of Eleuthoside Synthetic Intermediates by P450BM3
(CYP102A1). European J Org Chem 2018. [DOI: 10.1002/ejoc.201801206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | - Luet Lok Wong
- Department of Chemistry; Inorganic Chemistry Laboratory; University of Oxford; South Parks Road 3QR Oxford, OX1 UK
| | - Jeremy Robertson
- Department of Chemistry; Chemistry Research Laboratory; University of Oxford; Mansfield Road 3TA (UK) Oxford, OX1
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19
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Weingartner AM, Sauer DF, Dhoke GV, Davari MD, Ruff AJ, Schwaneberg U. A hydroquinone-specific screening system for directed P450 evolution. Appl Microbiol Biotechnol 2018; 102:9657-9667. [PMID: 30191291 PMCID: PMC6208966 DOI: 10.1007/s00253-018-9328-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 11/24/2022]
Abstract
The direct hydroxylation of benzene to hydroquinone (HQ) under mild reaction conditions is a challenging task for chemical catalysts. Cytochrome P450 (CYP) monooxygenases are known to catalyze the oxidation of a variety of aromatic compounds with atmospheric dioxygen. Protein engineering campaigns led to the identification of novel P450 variants, which yielded improvements in respect to activity, specificity, and stability. An effective screening strategy is crucial for the identification of improved enzymes with desired characteristics in large mutant libraries. Here, we report a first screening system designed for screening of P450 variants capable to produce hydroquinones. The hydroquinone quantification assay is based on the interaction of 4-nitrophenylacetonitrile (NpCN) with hydroquinones under alkaline conditions. In the 96-well plate format, a low detection limit (5 μM) and a broad linear detection range (5 to 250 μM) were obtained. The NpCN assay can be used for the quantification of dihydroxylated aromatic compounds such as hydroquinones, catechols, and benzoquinones. We chose the hydroxylation of pseudocumene by P450 BM3 as a target reaction and screened for improved trimethylhydroquinone (TMHQ) formation. The new P450 BM3 variant AW2 (R47Q, Y51F, I401M, A330P) was identified by screening a saturation mutagenesis library of amino acid position A330 with the NpCN assay. In summary, a 70-fold improved TMHQ formation was achieved with P450 BM3 AW2 when compared to the wild type (WT) and a 1.8-fold improved TMHQ formation compared to the recently reported P450 BM3 M3 (R47S, Y51W, A330F, I401M).
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Affiliation(s)
| | - Daniel F Sauer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Gaurao V Dhoke
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Anna Joëlle Ruff
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.
- DWI - Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52074, Aachen, Germany.
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20
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Geronimo I, Denning CA, Heidary DK, Glazer EC, Payne CM. Molecular Determinants of Substrate Affinity and Enzyme Activity of a Cytochrome P450 BM3 Variant. Biophys J 2018; 115:1251-1263. [PMID: 30224054 DOI: 10.1016/j.bpj.2018.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/29/2022] Open
Abstract
Cytochrome P450BM3 catalyzes the hydroxylation and/or epoxidation of fatty acids, fatty amides, and alcohols. Protein engineering has produced P450BM3 variants capable of accepting drug molecules normally metabolized by human P450 enzymes. The enhanced substrate promiscuity has been attributed to the greater flexibility of the lid of the substrate channel. However, it is not well understood how structurally different and highly polar drug molecules can stably bind in the active site nor how the activity and coupling efficiency of the enzyme may be affected by the lack of enzyme-substrate complementarity. To address these important aspects of non-native small molecule binding, this study investigated the binding of drug molecules with different size, charge, polar surface area, and human P450 affinity on the promiscuous R47L/F87V/L188Q/E267V/F81I pentuple mutant of P450BM3. Binding free energy data and energy decomposition analysis showed that pentuple mutant P450BM3 stably binds (i.e., negative ΔGb°) a broad range of substrate and inhibitor types because dispersion interactions with active site residues overcome unfavorable repulsive and electrostatic effects. Molecular dynamics simulations revealed that 1) acidic substrates tend to disrupt the heme propionate A-K69 salt bridge, which may reduce heme oxidizing ability, and 2) the lack of complementarity leads to high substrate mobility and water density in the active site, which may lead to uncoupling. These factors must be considered in future developments of P450BM3 as a biocatalyst in the large-scale production of drug metabolites.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | | | - David K Heidary
- Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky.
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21
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Efficient hydroxylation of cycloalkanes by co-addition of decoy molecules to variants of the cytochrome P450 CYP102A1. J Inorg Biochem 2018. [DOI: 10.1016/j.jinorgbio.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Li Y, Qin B, Li X, Tang J, Chen Y, Zhou L, You S. Selective Oxidations of Cyperenoic Acid by Slightly Reshaping the Binding Pocket of Cytochrome P450 BM3. ChemCatChem 2018. [DOI: 10.1002/cctc.201701088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuxin Li
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Bin Qin
- Wuya College of Innovation; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Xiaoqin Li
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Jun Tang
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Yu Chen
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Lina Zhou
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Song You
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
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23
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Stereoselective hydroxylation of isophorone by variants of the cytochromes P450 CYP102A1 and CYP101A1. Enzyme Microb Technol 2018; 111:29-37. [PMID: 29421034 DOI: 10.1016/j.enzmictec.2018.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 11/23/2022]
Abstract
The stereoselective oxidation of hydrocarbons is an area of research where enzyme biocatalysis can make a substantial impact. The cyclic ketone isophorone was stereoselectively hydroxylated (≥95%) by wild-type CYP102A1 to form (R)-4-hydroxyisophorone, an important chiral synthon and flavour and fragrance compound. CYP102A1 variants were also selective for 4-hydroxyisophorone formation and the product formation rate increased over the wild-type enzyme by up to 285-fold, with the best mutants being R47L/Y51F/I401P and A74G/F87V/L188Q. The latter variant, which contained mutations in the distal substrate binding pocket, was marginally less selective. Combining perfluorodecanoic acid decoy molecules with the rate accelerating variant R47L/Y51F/I401P engendered further improvement with the purified enzymes. However when the decoy molecules were used with A74G/F87V/L188Q the amount of product generated by the enzyme was reduced. Addition of decoy molecules to whole-cell turnovers did not improve the productivity of these CYP102A1 systems. WT CYP101A1 formed significant levels of 7-hydroxyisophorone as a minor product alongside 4-hydroxyisophorone. However the F87W/Y96F/L244A/V247L CYP101A1 mutant was ≥98% selective for (R)-4-hydroxyisophorone. A comparison of the two enzyme systems using whole-cell oxidation reactions showed that the best CYP101A1 variant was able to generate more product. We also characterised that the further oxidation metabolite 4-ketoisophorone was produced and then subsequently reduced to levodione by an endogenous Escherichia coli ene reductase.
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24
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Dennig A, Weingartner AM, Kardashliev T, Müller CA, Tassano E, Schürmann M, Ruff AJ, Schwaneberg U. An Enzymatic Route to α-Tocopherol Synthons: Aromatic Hydroxylation of Pseudocumene and Mesitylene with P450 BM3. Chemistry 2017; 23:17981-17991. [PMID: 28990705 DOI: 10.1002/chem.201703647] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Indexed: 02/06/2023]
Abstract
Aromatic hydroxylation of pseudocumene (1 a) and mesitylene (1 b) with P450 BM3 yields key phenolic building blocks for α-tocopherol synthesis. The P450 BM3 wild-type (WT) catalyzed selective aromatic hydroxylation of 1 b (94 %), whereas 1 a was hydroxylated to a large extent on benzylic positions (46-64 %). Site-saturation mutagenesis generated a new P450 BM3 mutant, herein named "variant M3" (R47S, Y51W, A330F, I401M), with significantly increased coupling efficiency (3- to 8-fold) and activity (75- to 230-fold) for the conversion of 1 a and 1 b. Additional π-π interactions introduced by mutation A330F improved not only productivity and coupling efficiency, but also selectivity toward aromatic hydroxylation of 1 a (61 to 75 %). Under continuous nicotinamide adenine dinucleotide phosphate recycling, the novel P450 BM3 variant M3 was able to produce the key tocopherol precursor trimethylhydroquinone (3 a; 35 % selectivity; 0.18 mg mL-1 ) directly from 1 a. In the case of 1 b, overoxidation leads to dearomatization and the formation of a valuable p-quinol synthon that can directly serve as an educt for the synthesis of 3 a. Detailed product pattern analysis, substrate docking, and mechanistic considerations support the hypothesis that 1 a binds in an inverted orientation in the active site of P450 BM3 WT, relative to P450 BM3 variant M3, to allow this change in chemoselectivity. This study provides an enzymatic route to key phenolic synthons for α-tocopherols and the first catalytic and mechanistic insights into direct aromatic hydroxylation and dearomatization of trimethylbenzenes with O2 .
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Affiliation(s)
- Alexander Dennig
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | | | - Tsvetan Kardashliev
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | | | - Erika Tassano
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Martin Schürmann
- DSM Ahead R&D BV/DSM Innovative Synthesis, Post address: P.O. Box 1066, 6160 BB, Geleen, The Netherlands
| | - Anna Joëlle Ruff
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.,DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52074, Aachen, Germany
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25
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Panneerselvam S, Shehzad A, Mueller-Dieckmann J, Wilmanns M, Bocola M, Davari MD, Schwaneberg U. Crystallographic insights into a cobalt (III) sepulchrate based alternative cofactor system of P450 BM3 monooxygenase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:134-140. [PMID: 28739446 DOI: 10.1016/j.bbapap.2017.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022]
Abstract
P450 BM3 is a multi-domain heme-containing soluble bacterial monooxygenase. P450 BM3 and variants are known to oxidize structurally diverse substrates. Crystal structures of individual domains of P450 BM3 are available. However, the spatial organization of the full-length protein is unknown. In this study, crystal structures of the P450 BM3 M7 heme domain variant with and without cobalt (III) sepulchrate are reported. Cobalt (III) sepulchrate acts as an electron shuttle in an alternative cofactor system employing zinc dust as the electron source. The crystal structure shows a binding site for the mediator cobalt (III) sepulchrate at the entrance of the substrate access channel. The mediator occupies an unusual position which is far from the active site and distinct from the binding of the natural redox partner (FAD/NADPH binding domain).
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Affiliation(s)
| | - Aamir Shehzad
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | | | - Matthias Wilmanns
- European Molecular Biology Laboratory-Hamburg, c/o DESY, Hamburg, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52056 Aachen, Germany.
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26
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Munday SD, Dezvarei S, Lau IC, Bell SG. Examination of Selectivity in the Oxidation of
ortho
‐ and
meta
‐Disubstituted Benzenes by CYP102A1 (P450 Bm3) Variants. ChemCatChem 2017. [DOI: 10.1002/cctc.201700116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel D. Munday
- Department of Chemistry University of Adelaide Adelaide. SA 5005 Australia
| | | | - Ian C.‐K. Lau
- Department of Chemistry University of Adelaide Adelaide. SA 5005 Australia
| | - Stephen G. Bell
- Department of Chemistry University of Adelaide Adelaide. SA 5005 Australia
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27
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Shoji O, Watanabe Y. Monooxygenation of Nonnative Substrates Catalyzed by Bacterial Cytochrome P450s Facilitated by Decoy Molecules. CHEM LETT 2017. [DOI: 10.1246/cl.160963] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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O'Hanlon JA, Ren X, Morris M, Wong LL, Robertson J. Hydroxylation of anilides by engineered cytochrome P450BM3. Org Biomol Chem 2017; 15:8780-8787. [DOI: 10.1039/c7ob02236k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cytochrome P450BM3mutants achieve selectivepara-hydroxylation of substitutedN-sulfonylanilines under mild conditions.
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Affiliation(s)
- Jack A. O'Hanlon
- Department of Chemistry
- University of Oxford
- Chemistry Research laboratory
- Oxford
- UK
| | - Xinkun Ren
- Department of Chemistry
- University of Oxford
- Inorganic Chemistry Laboratory
- Oxford
- UK
| | - Melloney Morris
- Syngenta UK
- Jealott's Hill International Research Centre
- Bracknell
- UK
| | - Luet Lok Wong
- Department of Chemistry
- University of Oxford
- Inorganic Chemistry Laboratory
- Oxford
- UK
| | - Jeremy Robertson
- Department of Chemistry
- University of Oxford
- Chemistry Research laboratory
- Oxford
- UK
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29
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An engineered outer membrane pore enables an efficient oxygenation of aromatics and terpenes. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Ren X, O’Hanlon JA, Morris M, Robertson J, Wong LL. Synthesis of Imidazolidin-4-ones via a Cytochrome P450-Catalyzed Intramolecular C–H Amination. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xinkun Ren
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Jack A. O’Hanlon
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield
Road, Oxford OX1 3TA, United Kingdom
| | - Melloney Morris
- Syngenta
UK, Jealott’s Hill International Research Centre, Bracknell RG42 6EY, United Kingdom
| | - Jeremy Robertson
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield
Road, Oxford OX1 3TA, United Kingdom
| | - Luet Lok Wong
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
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31
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Hall EA, Sarkar MR, Lee JHZ, Munday SD, Bell SG. Improving the Monooxygenase Activity and the Regio- and Stereoselectivity of Terpenoid Hydroxylation Using Ester Directing Groups. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01882] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emma A. Hall
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Md. Raihan Sarkar
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Joel H. Z. Lee
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Samuel D. Munday
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen G. Bell
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
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32
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Munday SD, Dezvarei S, Bell SG. Increasing the Activity and Efficiency of Stereoselective Oxidations by using Decoy Molecules in Combination with Rate-Enhancing Variants of P450Bm3. ChemCatChem 2016. [DOI: 10.1002/cctc.201600551] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Samuel D. Munday
- Department of Chemistry; University of Adelaide; SA 5005 Australia
| | | | - Stephen G. Bell
- Department of Chemistry; University of Adelaide; SA 5005 Australia
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33
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Munday SD, Shoji O, Watanabe Y, Wong LL, Bell SG. Improved oxidation of aromatic and aliphatic hydrocarbons using rate enhancing variants of P450Bm3 in combination with decoy molecules. Chem Commun (Camb) 2016; 52:1036-9. [PMID: 26593228 DOI: 10.1039/c5cc09247g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Enzyme performance can be improved using decoy molecules or engineered variants to accelerate the activity without affecting selectivity. Here we combine a rate accelerator variant of cytochrome P450Bm3 with decoy molecules to enhance the oxidation activity of a range of small organic molecules. This combined approach offers superior biocatalytic efficiency without modifying the product distribution.
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Affiliation(s)
- Samuel D Munday
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Luet-Lok Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
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Gricman Ł, Weissenborn MJ, Hoffmann SM, Borlinghaus N, Hauer B, Pleiss J. Redox Partner Interaction Sites in Cytochrome P450 Monooxygenases:In SilicoAnalysis and Experimental Validation. ChemistrySelect 2016. [DOI: 10.1002/slct.201600369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sara M. Hoffmann
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Niels Borlinghaus
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
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35
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Zhao F, Bai P, Liu T, Li D, Zhang X, Lu W, Yuan Y. Optimization of a cytochrome P450 oxidation system for enhancing protopanaxadiol production inSaccharomyces cerevisiae. Biotechnol Bioeng 2016; 113:1787-95. [DOI: 10.1002/bit.25934] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/21/2015] [Accepted: 01/07/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Fanglong Zhao
- School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 PR China
| | - Peng Bai
- School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 PR China
- Key Laboratory of System Bioengineering (Tianjin University); Ministry of Education; Tianjin PR China
| | - Ting Liu
- School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 PR China
| | - Dashuai Li
- School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 PR China
| | - Xiangmei Zhang
- School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 PR China
| | - Wenyu Lu
- School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 PR China
- Key Laboratory of System Bioengineering (Tianjin University); Ministry of Education; Tianjin PR China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin PR China
| | - Yingjin Yuan
- School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 PR China
- Key Laboratory of System Bioengineering (Tianjin University); Ministry of Education; Tianjin PR China
- SynBio Research Platform; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin PR China
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36
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Munday SD, Maddigan NK, Young RJ, Bell SG. Characterisation of two self-sufficient CYP102 family monooxygenases from Ktedonobacter racemifer DSM44963 which have new fatty acid alcohol product profiles. Biochim Biophys Acta Gen Subj 2016; 1860:1149-62. [PMID: 26825771 DOI: 10.1016/j.bbagen.2016.01.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 11/26/2022]
Abstract
BACKGROUND Two self-sufficient CYP102 family encoding genes (Krac_0936 and Krac_9955) from the bacterium Ktedonobacter racemifer DSM44963, which possesses one of the largest bacterial genomes, have been identified. METHODS Phylogenetic analysis of both the encoded cytochrome P450 enzymes, Krac0936 and Krac9955. Both enzymes were produced and their turnovers with fatty acid substrates assessed in vitro and using a whole-cell oxidation system. RESULTS Krac0936 hydroxylated straight chain, saturated fatty acids predominantly at the ω-1 and ω-2 positions using NADPH as the cofactor. Krac0936 was less active towards shorter unsaturated fatty acids but longer unsaturated acids were efficiently oxidised. cis,cis-9,12-Octadecadienoic and pentadecanoic acids were the most active substrates tested with Krac0936. Unusually Krac9955 showed very low levels of NAD(P)H oxidation activity though coupling of the reducing equivalents to product formation was high. The product distribution of tridecanoic, tetradecanoic and pentadecanoic acid oxidation by Krac9955 favoured oxidation at the ω-4, ω-5 and ω-6 positions, respectively. CONCLUSION Krac0936 and Krac9955 are self-sufficient P450 monooxygenases. Krac0936 has a preference for pentadecanoic acid over other straight chain fatty acids and showed little or no activity with dodecanoic or octadecanoic acids. Krac9955 preferably oxidised shorter fatty acids compared to Krac0936 with tridecanoic having the highest levels of product formation. Unlike Krac0936 and P450Bm3, Krac9995 showed lower activities with unsaturated fatty acids. GENERAL SIGNIFICANCE In this study of two of the CYP enzymes from K. racemifer we have shown that this bacterium from the Chloroflexi phylum contains genes which encode new proteins with novel activity.
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Affiliation(s)
- Samuel D Munday
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | | | - Rosemary J Young
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
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37
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Dennig A, Busto E, Kroutil W, Faber K. Biocatalytic One-Pot Synthesis of l-Tyrosine Derivatives from Monosubstituted Benzenes, Pyruvate, and Ammonia. ACS Catal 2015. [DOI: 10.1021/acscatal.5b02129] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Dennig
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
| | - Eduardo Busto
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
| | - Wolfgang Kroutil
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
| | - Kurt Faber
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
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38
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Lim JB, Barker KA, Eller KA, Jiang L, Molina V, Saifee JF, Sikes HD. Insights into electron leakage in the reaction cycle of cytochrome P450 BM3 revealed by kinetic modeling and mutagenesis. Protein Sci 2015; 24:1874-83. [PMID: 26311413 DOI: 10.1002/pro.2793] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 08/20/2015] [Accepted: 08/23/2015] [Indexed: 11/08/2022]
Abstract
As a single polypeptide, cytochrome P450 BM3 fuses oxidase and reductase domains and couples each domain's function to perform catalysis with exceptional activity upon binding of substrate for hydroxylation. Mutations introduced into the enzyme to change its substrate specificity often decrease coupling efficiency between the two domains, resulting in unproductive consumption of cofactors and formation of water and/or reactive species. This phenomenon can correlate with leakage, in which P450 BM3 uses electrons from NADPH to reduce oxygen to water and/or reactive species even without bound substrate. The physical basis for leakage is not yet well understood in this particular member of the cytochrome P450 family. To clarify the relationship between leakage and coupling, we used simulations to illustrate how different combinations of kinetic parameters related to substrate-free consumption of NADPH and substrate hydroxylation can lead to either minimal effects on coupling or a dramatic decrease in coupling as a result of leakage. We explored leakage in P450 BM3 by introducing leakage-enhancing mutations and combining these mutations to assess whether doing so increases leakage further. The variants in this study provide evidence that while a transition to high spin may be vital for coupled hydroxylation, it is not required for enhanced leakage; substrate binding and the consequent shift in spin state are not necessary as a redox switch for catalytic oxidation of NADPH. Additionally, the variants in this study suggest a tradeoff between leakage and stability and thus evolvability, as the mutations we investigated were far more deleterious than other mutations that have been used to change substrate specificity.
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Affiliation(s)
- Joseph B Lim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Kimberly A Barker
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Kristen A Eller
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Linda Jiang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Veronica Molina
- Department of Chemical Engineering, Polytechnic University of Puerto Rico, San Juan, 00918, Puerto Rico
| | | | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
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39
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Ren X, Yorke JA, Taylor E, Zhang T, Zhou W, Wong LL. Drug Oxidation by Cytochrome P450BM3 : Metabolite Synthesis and Discovering New P450 Reaction Types. Chemistry 2015; 21:15039-47. [PMID: 26311271 DOI: 10.1002/chem.201502020] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Indexed: 11/06/2022]
Abstract
There is intense interest in late-stage catalytic C-H bond functionalization as an integral part of synthesis. Effective catalysts must have a broad substrate range and tolerate diverse functional groups. Drug molecules provide a good test of these attributes of a catalyst. A library of P450BM3 mutants developed from four base mutants with high activity for hydrocarbon oxidation produced human metabolites of a panel of drugs that included neutral (chlorzoxazone, testosterone), cationic (amitriptyline, lidocaine) and anionic (diclofenac, naproxen) compounds. No single mutant was active for all the tested drugs but multiple variants in the library showed high activity with each compound. The high conversions enabled full product characterization that led to the discovery of the new P450 reaction type of oxidative decarboxylation of an α-hydroxy carboxylic acid and the formation a protected imine from an amine, offering a novel route to α-functionalization of amines. The substrate range and varied product profiles suggest that this library of enzymes is a good basis for developing late-stage C-H activation catalysts.
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Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK)
| | - Jake A Yorke
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK)
| | - Emily Taylor
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK)
| | - Ting Zhang
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071 (P. R. China)
| | - Weihong Zhou
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071 (P. R. China).
| | - Luet Lok Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd., Oxford OX1 3QR (UK).
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40
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Ko S, Yang YH, Choi KY, Kim BG. rational design and directed evolution of CYP102A1 (BM3) for regio-specific hydroxylation of isoflavone. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0718-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Zhang A, Zhang T, Hall EA, Hutchinson S, Cryle MJ, Wong LL, Zhou W, Bell SG. The crystal structure of the versatile cytochrome P450 enzyme CYP109B1 from Bacillus subtilis. MOLECULAR BIOSYSTEMS 2015; 11:869-81. [PMID: 25587700 DOI: 10.1039/c4mb00665h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The crystal structure of the versatile CYP109B1 enzyme from Bacillus subtilis has been solved at 1.8 Å resolution. This is the first structure of an enzyme from this CYP family, whose members are prevalent across diverse species of bacteria. In the crystal structure the enzyme has an open conformation with an access channel leading from the heme to the surface. The substrate-free structure reveals the location of the key residues in the active site that are responsible for binding the substrate in the correct orientation for regioselective oxidation. Importantly, there are significant differences among these residues in members of the CYP109 and closely related CYP106 families and these likely account for the variations in substrate binding and oxidation profiles observed with these enzymes. A whole-cell oxidation biosystem was developed, which contains CYP109B1 and a phthalate family oxygenase reductase (PFOR), from Pseudomonas putida KT24440, as the electron transfer partner. This electron transfer system is able to support CYP109B1 activity resulting in the regioselective hydroxylation of both α- and β-ionone in vivo and in vitro. The PFOR is therefore a versatile electron transfer partner that is able to support the activity of CYP enzymes from other bacterium. The crystal structure of CYP109B1 has a positively charged proximal face and this explains why it can interact with PFOR and adrenodoxin which are predominantly negatively charged around their [2Fe-2S] clusters.
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Affiliation(s)
- Aili Zhang
- College of Life Sciences, Nankai University, Tianjin 300071, China.
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42
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Hall EA, Bell SG. The efficient and selective biocatalytic oxidation of norisoprenoid and aromatic substrates by CYP101B1 from Novosphingobium aromaticivorans DSM12444. RSC Adv 2015. [DOI: 10.1039/c4ra14010a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CYP101B1 fromNovosphingobium aromaticivoransoxidises ionone derivatives and phenylcyclohexane with high activity and regioselectivity.
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Affiliation(s)
- Emma A. Hall
- School of Chemistry and Physics
- University of Adelaide
- Australia
| | - Stephen G. Bell
- School of Chemistry and Physics
- University of Adelaide
- Australia
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43
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Catalano J, Sadre-Bazzaz K, Amodeo GA, Tong L, McDermott A. Structural evidence: a single charged residue affects substrate binding in cytochrome P450 BM-3. Biochemistry 2013; 52:6807-15. [PMID: 23829560 PMCID: PMC5945292 DOI: 10.1021/bi4000645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 BM-3 is a bacterial enzyme with sequence similarity to mammalian P450s that catalyzes the hydroxylation of fatty acids with high efficiency. Enzyme-substrate binding and dynamics has been an important topic of study for cytochromes P450 because most of the crystal structures of substrate-bound structures show the complex in an inactive state. We have determined a new crystal structure for cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG), which unexpectedly showed a direct bidentate ion pair between NPG and arginine 47 (R47). We further explored the role of R47, the only charged residue in the binding pocket in cytochrome P450 BM-3, through mutagenesis and crystallographic studies. The mutations of R47 to glutamine (R47Q), glutamic acid (R47E), and lysine (R47K) were designed to investigate the role of its charge in binding and catalysis. The oppositely charged R47E mutation had the greatest effect on activity and binding. The crystal structure of R47E BMP shows that the glutamic acid side chain is blocking the entrance to the binding pocket, accounting for NPG's low binding affinity and charge repulsion. For R47Q and R47K BM-3, the mutations caused only a slight change in kcat and a large change in Km and Kd, which suggests that R47 mostly is involved in binding and that our crystal structure, 4KPA , represents an initial binding step in the P450 cycle.
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Affiliation(s)
- Jaclyn Catalano
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Kianoush Sadre-Bazzaz
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Gabriele A. Amodeo
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Liang Tong
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Ann McDermott
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
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44
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Butler CF, Peet C, Mason AE, Voice MW, Leys D, Munro AW. Key mutations alter the cytochrome P450 BM3 conformational landscape and remove inherent substrate bias. J Biol Chem 2013; 288:25387-25399. [PMID: 23828198 DOI: 10.1074/jbc.m113.479717] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s) have enormous potential in the production of oxychemicals, due to their unparalleled regio- and stereoselectivity. The Bacillus megaterium P450 BM3 enzyme is a key model system, with several mutants (many distant from the active site) reported to alter substrate selectivity. It has the highest reported monooxygenase activity of the P450 enzymes, and this catalytic efficiency has inspired protein engineering to enable its exploitation for biotechnologically relevant oxidations with structurally diverse substrates. However, a structural rationale is lacking to explain how these mutations have such effects in the absence of direct change to the active site architecture. Here, we provide the first crystal structures of BM3 mutants in complex with a human drug substrate, the proton pump inhibitor omeprazole. Supported by solution data, these structures reveal how mutation alters the conformational landscape and decreases the free energy barrier for transition to the substrate-bound state. Our data point to the importance of such "gatekeeper" mutations in enabling major changes in substrate recognition. We further demonstrate that these mutants catalyze the same 5-hydroxylation reaction as performed by human CYP2C19, the major human omeprazole-metabolizing P450 enzyme.
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Affiliation(s)
- Christopher F Butler
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Caroline Peet
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - Amy E Mason
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Andrew W Munro
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and.
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45
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Dennig A, Lülsdorf N, Liu H, Schwaneberg U. Regioselective o-hydroxylation of monosubstituted benzenes by P450 BM3. Angew Chem Int Ed Engl 2013; 52:8459-62. [PMID: 23818430 DOI: 10.1002/anie.201303986] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Alexander Dennig
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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46
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Dennig A, Lülsdorf N, Liu H, Schwaneberg U. Regioselektiveo-Hydroxylierung monosubstituierter Benzole mit P450 BM3. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303986] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Ji Y, Mao G, Wang Y, Bartlam M. Structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases. Front Microbiol 2013; 4:58. [PMID: 23519435 PMCID: PMC3604635 DOI: 10.3389/fmicb.2013.00058] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/28/2013] [Indexed: 11/13/2022] Open
Abstract
Environmental microbes utilize four degradation pathways for the oxidation of n-alkanes. Although the enzymes degrading n-alkanes in different microbes may vary, enzymes functioning in the first step in the aerobic degradation of alkanes all belong to the alkane hydroxylases. Alkane hydroxylases are a class of enzymes that insert oxygen atoms derived from molecular oxygen into different sites of the alkane terminus (or termini) depending on the type of enzymes. In this review, we summarize the different types of alkane hydroxylases, their degrading steps, and compare typical enzymes from various classes with regard to their three-dimensional structures, in order to provide insights into how the enzymes mediate their different roles in the degradation of n-alkanes and what determines their different substrate ranges. Through the above analyzes, the degrading mechanisms of enzymes can be elucidated and molecular biological methods can be utilized to expand their catalytic roles in the petrochemical industry or in bioremediation of oil-contaminated environments.
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Affiliation(s)
- Yurui Ji
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
| | - Guannan Mao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai UniversityTianjin, China
- College of Life Sciences, Nankai UniversityTianjin, China
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48
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Bell SG, French L, Rees NH, Cheng SS, Preston G, Wong LL. A phthalate family oxygenase reductase supports terpene alcohol oxidation by CYP238A1 fromPseudomonas putidaKT2440. Biotechnol Appl Biochem 2013; 60:9-17. [DOI: 10.1002/bab.1084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 12/18/2012] [Indexed: 01/09/2023]
Affiliation(s)
| | - Laura French
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
| | - Nicholas Huw Rees
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
| | - Sophia Shuyi Cheng
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
| | - Gail Preston
- Department of Plant Sciences; University of Oxford; Oxford; UK
| | - Luet-Lok Wong
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
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49
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Kawakami N, Shoji O, Watanabe Y. Direct hydroxylation of primary carbons in small alkanes by wild-type cytochrome P450BM3 containing perfluorocarboxylic acids as decoy molecules. Chem Sci 2013. [DOI: 10.1039/c3sc50378j] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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50
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Sideri A, Goyal A, Di Nardo G, Tsotsou GE, Gilardi G. Hydroxylation of non-substituted polycyclic aromatic hydrocarbons by cytochrome P450 BM3 engineered by directed evolution. J Inorg Biochem 2012; 120:1-7. [PMID: 23262457 DOI: 10.1016/j.jinorgbio.2012.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/20/2012] [Accepted: 11/26/2012] [Indexed: 11/18/2022]
Abstract
Chrysene and pyrene are known toxic compounds recalcitrant to biodegradation. Here directed evolution allowed us to identify two new mutants of cytochrome P450 BM3 that are able to hydroxylate both compounds. Random mutagenesis has been used to generate libraries of mutants of P450 BM3 active toward polycyclic aromatic hydrocarbons (PAHs) PAHs. After two rounds of error-prone PCR and backcross with parental DNA, three mutants were identified for improved activity toward pyrene and for the first time a new activity toward chrysene in comparison to the wild type enzyme. The mutants show higher affinity and coupling efficiency for chrysene with faster rates of product formation compared to the wild type. Furthermore, the mutants are able to hydroxylate chrysene in different positions, producing four metabolites, 1-, 3-, 4-, and 6-hydroxychrysene, and to hydroxylate pyrene to 1-hydroxypyrene. The majority of the mutation sites are found to be far from the active site, demonstrating the power of directed evolution in identifying mutations difficult to predict with a rational design approach. The different product profiles obtained for the different P450 BM3 mutants indicate that substrate orientation in the catalytic pocket of the protein can be modified by protein engineering. The mutants can be used for metabolic engineering for safe and cost-effective sustainable production of hydroxylated PAHs for industrial purposes as well as for the assessment of their carcinogenic activity in mammals.
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Affiliation(s)
- Anastasia Sideri
- Department of Life Sciences and Systems Biology, University of Torino via Accademia Albertina 13, 10123, Torino, Italy
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