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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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Li Y, Zhang R, Xu Y. Structure-based mechanisms: On the way to apply alcohol dehydrogenases/reductases to organic-aqueous systems. Int J Biol Macromol 2020; 168:412-427. [PMID: 33316337 DOI: 10.1016/j.ijbiomac.2020.12.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022]
Abstract
Alcohol dehydrogenases/reductases catalyze enantioselective syntheses of versatile chiral compounds relying on direct hydride transfer from cofactor to substrates, or to an intermediate and then to substrates. Since most of the substrates catalyzed by alcohol dehydrogenases/reductases are insoluble in aqueous solutions, increasing interest has been turning to organic-aqueous systems. However, alcohol dehydrogenases/reductases are normally instable in organic solvents, leading to the unsatisfied enantioselective synthesis efficiency. The behaviors of these enzymes in organic solvents at an atomic level are unclear, thus it is of great importance to understand its structure-based mechanisms in organic-aqueous systems to improve their relative stability. Here, we summarized the accessible structures of alcohol dehydrogenases/reductases in Protein Data Bank crystallized in organic-aqueous systems, and compared the structures of alcohol dehydrogenases/reductases which have different tolerance towards organic solvents. By understanding the catalytic behaviors and mechanisms of these enzymes in organic-aqueous systems, the efficient enantioselective syntheses mediated by alcohol dehydrogenases/reductases and further challenges are also discussed through solvent engineering and enzyme-immobilization in the last decade.
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Affiliation(s)
- Yaohui Li
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; Department of Biological Science, Columbia University, New York, NY 10025, United States
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
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3
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Ferrario V, Hansen N, Pleiss J. Interpretation of cytochrome P450 monooxygenase kinetics by modeling of thermodynamic activity. J Inorg Biochem 2018. [DOI: 10.1016/j.jinorgbio.2018.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Ritter C, Nett N, Acevedo‐Rocha CG, Lonsdale R, Kräling K, Dempwolff F, Hoebenreich S, Graumann PL, Reetz MT, Meggers E. Bioorthogonale enzymatische Aktivierung maskierter Verbindungen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Cornelia Ritter
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Nathalie Nett
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Carlos G. Acevedo‐Rocha
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland)
- LOEWE‐Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans‐Meerwein‐Straße, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
| | - Richard Lonsdale
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland)
| | - Katja Kräling
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Felix Dempwolff
- LOEWE‐Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans‐Meerwein‐Straße, 35043 Marburg (Deutschland)
| | - Sabrina Hoebenreich
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
| | - Peter L. Graumann
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- LOEWE‐Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans‐Meerwein‐Straße, 35043 Marburg (Deutschland)
| | - Manfred T. Reetz
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland)
| | - Eric Meggers
- Fachbereich Chemie, Philipps‐Universität Marburg, Hans‐Meerwein‐Straße 4, 35043 Marburg (Deutschland)
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China)
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Ritter C, Nett N, Acevedo-Rocha CG, Lonsdale R, Kräling K, Dempwolff F, Hoebenreich S, Graumann PL, Reetz MT, Meggers E. Bioorthogonal Enzymatic Activation of Caged Compounds. Angew Chem Int Ed Engl 2015; 54:13440-3. [PMID: 26356324 DOI: 10.1002/anie.201506739] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/14/2015] [Indexed: 11/06/2022]
Abstract
Engineered cytochrome P450 monooxygenase variants are reported as highly active and selective catalysts for the bioorthogonal uncaging of propargylic and benzylic ether protected substrates, including uncaging in living E. coli. observed selectivity is supported by induced-fit docking and molecular dynamics simulations. This proof-of-principle study points towards the utility of bioorthogonal enzyme/protecting group pairs for applications in the life sciences.
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Affiliation(s)
- Cornelia Ritter
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Nathalie Nett
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Carlos G Acevedo-Rocha
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany).,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).,LOEWE Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, 35043 Marburg (Germany).,Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043 Marburg (Germany)
| | - Richard Lonsdale
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany).,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)
| | - Katja Kräling
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Felix Dempwolff
- LOEWE Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, 35043 Marburg (Germany)
| | - Sabrina Hoebenreich
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany)
| | - Peter L Graumann
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany).,LOEWE Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Hans-Meerwein-Straße, 35043 Marburg (Germany)
| | - Manfred T Reetz
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany). .,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
| | - Eric Meggers
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg (Germany). .,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P. R. China).
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Abstract
P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.
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Affiliation(s)
- Christopher J C Whitehouse
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
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