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Costanzo A, Fata F, Freda I, De Sciscio ML, Gugole E, Bulfaro G, Di Renzo M, Barbizzi L, Exertier C, Parisi G, D'Abramo M, Vallone B, Savino C, Montemiglio LC. Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP. Structure 2024:S0969-2126(24)00223-5. [PMID: 38971159 DOI: 10.1016/j.str.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/08/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
OleP is a bacterial cytochrome P450 involved in oleandomycin biosynthesis as it catalyzes regioselective epoxidation on macrolide intermediates. OleP has recently been reported to convert lithocholic acid (LCA) into murideoxycholic acid through a highly regioselective reaction and to unspecifically hydroxylate testosterone (TES). Since LCA and TES mainly differ by the substituent group at the C17, here we used X-ray crystallography, equilibrium binding assays, and molecular dynamics simulations to investigate the molecular basis of the diverse reactivity observed with the two steroids. We found that the differences in the structure of TES and LCA affect the capability of these molecules to directly form hydrogen bonds with N-terminal residues of OleP internal helix I. The establishment of these contacts, by promoting the bending of helix I, fosters an efficient trigger of the open-to-closed structural transition that occurs upon substrate binding to OleP and contributes to the selectivity of the subsequent monooxygenation reaction.
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Affiliation(s)
- Antonella Costanzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Francesca Fata
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Ida Freda
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Elena Gugole
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giovanni Bulfaro
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Matteo Di Renzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Luca Barbizzi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giacomo Parisi
- Department of Basic and Applied Sciences for Engineering (SBAI), Sapienza, University of Rome, Via Antonio Scarpa, 16, 00161 Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
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2
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Suzuki K, Stanfield JK, Omura K, Shisaka Y, Ariyasu S, Kasai C, Aiba Y, Sugimoto H, Shoji O. A Compound I Mimic Reveals the Transient Active Species of a Cytochrome P450 Enzyme: Insight into the Stereoselectivity of P450-Catalysed Oxidations. Angew Chem Int Ed Engl 2023; 62:e202215706. [PMID: 36519803 DOI: 10.1002/anie.202215706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Catching the structure of cytochrome P450 enzymes in flagrante is crucial for the development of P450 biocatalysts, as most structures collected are found trapped in a precatalytic conformation. At the heart of P450 catalysis lies Cpd I, a short-lived, highly reactive intermediate, whose recalcitrant nature has thwarted most attempts at capturing catalytically relevant poses of P450s. We report the crystal structure of P450BM3 mimicking the state in the precise moment preceding epoxidation, which is in perfect agreement with the experimentally observed stereoselectivity. This structure was attained by incorporation of the stable Cpd I mimic oxomolybdenum mesoporphyrin IX into P450BM3 in the presence of styrene. The orientation of styrene to the Mo-oxo species in the crystal structures sheds light onto the dynamics involved in the rotation of styrene to present its vinyl group to Cpd I. This method serves as a powerful tool for predicting and modelling the stereoselectivity of P450 reactions.
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Affiliation(s)
- Kazuto Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Keita Omura
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuma Shisaka
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinya Ariyasu
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Chie Kasai
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Hiroshi Sugimoto
- RIKEN SPring-8 Centre, 1-1-1, Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 5, Sanbancho, Chiyoda-ku, Tokyo, 102-0075, Japan
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3
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Werck-Reichhart D. Promiscuity, a Driver of Plant Cytochrome P450 Evolution? Biomolecules 2023; 13:biom13020394. [PMID: 36830762 PMCID: PMC9953472 DOI: 10.3390/biom13020394] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Plant cytochrome P450 monooxygenases were long considered to be highly substrate-specific, regioselective and stereoselective enzymes, in this respect differing from their animal counterparts. The functional data that have recently accumulated clearly counter this initial dogma. Highly promiscuous P450 enzymes have now been reported, mainly in terpenoid pathways with functions in plant adaptation, but also some very versatile xenobiotic/herbicide metabolizers. An overlap and predictable interference between endogenous and herbicide metabolism are starting to emerge. Both substrate preference and permissiveness vary between plant P450 families, with high promiscuity seemingly favoring retention of gene duplicates and evolutionary blooms. Yet significant promiscuity can also be observed in the families under high negative selection and with essential functions, usually enhanced after gene duplication. The strategies so far implemented, to systematically explore P450 catalytic capacity, are described and discussed.
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Affiliation(s)
- Danièle Werck-Reichhart
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67000 Strasbourg, France
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4
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De Sciscio ML, Nardi AN, Parisi G, Bulfaro G, Costanzo A, Gugole E, Exertier C, Freda I, Savino C, Vallone B, Montemiglio LC, D’Abramo M. Effect of Salts on the Conformational Dynamics of the Cytochrome P450 OleP. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020832. [PMID: 36677890 PMCID: PMC9867029 DOI: 10.3390/molecules28020832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Cytochrome P450 OleP catalytic activity is strongly influenced by its structural dynamic conformational behavior. Here, we combine equilibrium-binding experiments with all-atom molecular dynamics simulations to clarify how different environments affect OleP conformational equilibrium between the open and the closed-catalytic competent-forms. Our data clearly show that at high-ionic strength conditions, the closed form is favored, and, very interestingly, different mechanisms, depending on the chemistry of the cations, can be used to rationalize such an effect.
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Affiliation(s)
- Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | | | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, IIT, 00185 Rome, Italy
| | - Giovanni Bulfaro
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Antonella Costanzo
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Elena Gugole
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
| | - Marco D’Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
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Montemiglio LC, Gugole E, Freda I, Exertier C, D’Auria L, Chen CG, Nardi AN, Cerutti G, Parisi G, D’Abramo M, Savino C, Vallone B. Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics. Biomolecules 2021; 12:biom12010055. [PMID: 35053203 PMCID: PMC8774231 DOI: 10.3390/biom12010055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 12/16/2022] Open
Abstract
Substrate binding to the cytochrome P450 OleP is coupled to a large open-to-closed transition that remodels the active site, minimizing its exposure to the external solvent. When the aglycone substrate binds, a small empty cavity is formed between the I and G helices, the BC loop, and the substrate itself, where solvent molecules accumulate mediating substrate-enzyme interactions. Herein, we analyzed the role of this cavity in substrate binding to OleP by producing three mutants (E89Y, G92W, and S240Y) to decrease its volume. The crystal structures of the OleP mutants in the closed state bound to the aglycone 6DEB showed that G92W and S240Y occupied the cavity, providing additional contact points with the substrate. Conversely, mutation E89Y induces a flipped-out conformation of this amino acid side chain, that points towards the bulk, increasing the empty volume. Equilibrium titrations and molecular dynamic simulations indicate that the presence of a bulky residue within the cavity impacts the binding properties of the enzyme, perturbing the conformational space explored by the complexes. Our data highlight the relevance of this region in OleP substrate binding and suggest that it represents a key substrate-protein contact site to consider in the perspective of redirecting its activity towards alternative compounds.
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Affiliation(s)
- Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
| | - Elena Gugole
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
| | - Lucia D’Auria
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Cheng Giuseppe Chen
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Alessandro Nicola Nardi
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Gabriele Cerutti
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, IIT, 00185 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
- Correspondence: (C.S.); (B.V.); Tel.: +39-06-49910548 (C.S. & B.V.)
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
- Correspondence: (C.S.); (B.V.); Tel.: +39-06-49910548 (C.S. & B.V.)
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6
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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7
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Grobe S, Badenhorst CPS, Bayer T, Hamnevik E, Wu S, Grathwol CW, Link A, Koban S, Brundiek H, Großjohann B, Bornscheuer UT. Modifikation der Regioselektivität einer P450‐Monooxygenase ermöglicht die Synthese von Ursodeoxycholsäure durch die 7β‐Hydroxylierung von Lithocholsäure. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sascha Grobe
- Abteilung für Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald Felix Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Christoffel P. S. Badenhorst
- Abteilung für Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald Felix Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Thomas Bayer
- Abteilung für Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald Felix Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Emil Hamnevik
- Abteilung für Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald Felix Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Shuke Wu
- Abteilung für Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald Felix Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Christoph W. Grathwol
- Institut für Pharmazie Universität Greifswald Friedrich-Ludwig-Jahn-Str. 17 17487 Greifswald Deutschland
| | - Andreas Link
- Institut für Pharmazie Universität Greifswald Friedrich-Ludwig-Jahn-Str. 17 17487 Greifswald Deutschland
| | - Sven Koban
- Enzymicals AG Walther-Rathenau-Str. 49 17487 Greifswald Deutschland
| | - Henrike Brundiek
- Enzymicals AG Walther-Rathenau-Str. 49 17487 Greifswald Deutschland
| | - Beatrice Großjohann
- HERBRAND PharmaChemicals GmbH, Betriebsstätte Anklam An der Redoute 1 17390 Murchin Deutschland
| | - Uwe T. Bornscheuer
- Abteilung für Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald Felix Hausdorff-Str. 4 17487 Greifswald Deutschland
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8
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Grobe S, Badenhorst CPS, Bayer T, Hamnevik E, Wu S, Grathwol CW, Link A, Koban S, Brundiek H, Großjohann B, Bornscheuer UT. Engineering Regioselectivity of a P450 Monooxygenase Enables the Synthesis of Ursodeoxycholic Acid via 7β-Hydroxylation of Lithocholic Acid. Angew Chem Int Ed Engl 2021; 60:753-757. [PMID: 33085147 PMCID: PMC7839452 DOI: 10.1002/anie.202012675] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Indexed: 12/11/2022]
Abstract
We engineered the cytochrome P450 monooxygenase CYP107D1 (OleP) from Streptomyces antibioticus for the stereo- and regioselective 7β-hydroxylation of lithocholic acid (LCA) to yield ursodeoxycholic acid (UDCA). OleP was previously shown to hydroxylate testosterone at the 7β-position but LCA is exclusively hydroxylated at the 6β-position, forming murideoxycholic acid (MDCA). Structural and 3DM analysis, and molecular docking were used to identify amino acid residues F84, S240, and V291 as specificity-determining residues. Alanine scanning identified S240A as a UDCA-producing variant. A synthetic "small but smart" library based on these positions was screened using a colorimetric assay for UDCA. We identified a nearly perfectly regio- and stereoselective triple mutant (F84Q/S240A/V291G) that produces 10-fold higher levels of UDCA than the S240A variant. This biocatalyst opens up new possibilities for the environmentally friendly synthesis of UDCA from the biological waste product LCA.
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Affiliation(s)
- Sascha Grobe
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryUniversity of GreifswaldFelix Hausdorff-Str. 417487GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryUniversity of GreifswaldFelix Hausdorff-Str. 417487GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryUniversity of GreifswaldFelix Hausdorff-Str. 417487GreifswaldGermany
| | - Emil Hamnevik
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryUniversity of GreifswaldFelix Hausdorff-Str. 417487GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryUniversity of GreifswaldFelix Hausdorff-Str. 417487GreifswaldGermany
| | - Christoph W. Grathwol
- Institute of PharmacyUniversity of GreifswaldFriedrich-Ludwig-Jahn-Str. 1717487GreifswaldGermany
| | - Andreas Link
- Institute of PharmacyUniversity of GreifswaldFriedrich-Ludwig-Jahn-Str. 1717487GreifswaldGermany
| | - Sven Koban
- Enzymicals AGWalther-Rathenau-Str. 4917487GreifswaldGermany
| | | | - Beatrice Großjohann
- HERBRAND PharmaChemicals GmbH, Betriebsstätte AnklamAn der Redoute 117390MurchinGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryUniversity of GreifswaldFelix Hausdorff-Str. 417487GreifswaldGermany
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9
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Parisi G, Freda I, Exertier C, Cecchetti C, Gugole E, Cerutti G, D’Auria L, Macone A, Vallone B, Savino C, Montemiglio LC. Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate. Biomolecules 2020; 10:biom10101411. [PMID: 33036250 PMCID: PMC7600006 DOI: 10.3390/biom10101411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 11/22/2022] Open
Abstract
The cytochrome P450 OleP catalyzes the epoxidation of aliphatic carbons on both the aglycone 8.8a-deoxyoleandolide (DEO) and the monoglycosylated L-olivosyl-8.8a-deoxyoleandolide (L-O-DEO) intermediates of oleandomycin biosynthesis. We investigated the substrate versatility of the enzyme. X-ray and equilibrium binding data show that the aglycone DEO loosely fits the OleP active site, triggering the closure that prepares it for catalysis only on a minor population of enzyme. The open-to-closed state transition allows solvent molecules to accumulate in a cavity that forms upon closure, mediating protein–substrate interactions. In silico docking of the monoglycosylated L-O-DEO in the closed OleP–DEO structure shows that the L-olivosyl moiety can be hosted in the same cavity, replacing solvent molecules and directly contacting structural elements involved in the transition. X-ray structures of aglycone-bound OleP in the presence of L-rhamnose confirm the cavity as a potential site for sugar binding. All considered, we propose L-O-DEO as the optimal substrate of OleP, the L-olivosyl moiety possibly representing the molecular wedge that triggers a more efficient structural response upon substrate binding, favoring and stabilizing the enzyme closure before catalysis. OleP substrate versatility is supported by structural solvent molecules that compensate for the absence of a glycosyl unit when the aglycone is bound.
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Affiliation(s)
- Giacomo Parisi
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Current affiliation: Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161 Rome, Italy
| | - Ida Freda
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
| | - Cécile Exertier
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
| | - Cristina Cecchetti
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Current affiliation: Department of Life Sciences Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Elena Gugole
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
| | - Gabriele Cerutti
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Current affiliation: Zuckerman Mind Brain Behavior Institute, Columbia University, 3227 Broadway, New York, NY 10027, USA
| | - Lucia D’Auria
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (L.D.); (A.M.)
| | - Alberto Macone
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (L.D.); (A.M.)
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
- Correspondence: (C.S.); (L.C.M.)
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
- Correspondence: (C.S.); (L.C.M.)
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10
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Grobe S, Wszołek A, Brundiek H, Fekete M, Bornscheuer UT. Highly selective bile acid hydroxylation by the multifunctional bacterial P450 monooxygenase CYP107D1 (OleP). Biotechnol Lett 2020; 42:819-824. [PMID: 31974648 PMCID: PMC7101289 DOI: 10.1007/s10529-020-02813-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Regio- and stereoselective hydroxylation of lithocholic acid (LCA) using CYP107D1 (OleP), a cytochrome P450 monooxygenase from the oleandomycin synthesis pathway of Streptomyces antibioticus. RESULTS Co-expression of CYP107D1 from S. antibioticus and the reductase/ferredoxin system PdR/PdX from Pseudomonas putida was performed in Escherichia coli whole cells. In vivo hydroxylation of LCA exclusively yielded the 6β-OH product murideoxycholic acid (MDCA). In resting cells, 19.5% of LCA was converted to MDCA within 24 h, resulting in a space time yield of 0.04 mmol L-1 h-1. NMR spectroscopy confirmed the identity of MDCA as the sole product. CONCLUSIONS The multifunctional P450 monooxygenase CYP107D1 (OleP) can hydroxylate LCA, forming MDCA as the only product.
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Affiliation(s)
- Sascha Grobe
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | | | | | | | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany.
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11
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Fürst MJLJ, Fiorentini F, Fraaije MW. Beyond active site residues: overall structural dynamics control catalysis in flavin-containing and heme-containing monooxygenases. Curr Opin Struct Biol 2019; 59:29-37. [DOI: 10.1016/j.sbi.2019.01.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 12/31/2022]
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12
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He F, Mori T, Morita I, Nakamura H, Alblova M, Hoshino S, Awakawa T, Abe I. Molecular basis for the P450-catalyzed C–N bond formation in indolactam biosynthesis. Nat Chem Biol 2019; 15:1206-1213. [DOI: 10.1038/s41589-019-0380-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022]
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13
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Guengerich FP, Wilkey CJ, Phan TTN. Human cytochrome P450 enzymes bind drugs and other substrates mainly through conformational-selection modes. J Biol Chem 2019; 294:10928-10941. [PMID: 31147443 DOI: 10.1074/jbc.ra119.009305] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/29/2019] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) enzymes are major catalysts involved in the oxidations of most drugs, steroids, carcinogens, fat-soluble vitamins, and natural products. The binding of substrates to some of the 57 human P450s and other mammalian P450s is more complex than a two-state system and has been proposed to involve mechanisms such as multiple ligand occupancy, induced-fit, and conformational-selection. Here, we used kinetic analysis of binding with multiple concentrations of substrates and computational modeling of these data to discern possible binding modes of several human P450s. We observed that P450 2D6 binds its ligand rolapitant in a mechanism involving conformational-selection. P450 4A11 bound the substrate lauric acid via conformational-selection, as did P450 2C8 with palmitic acid. Binding of the steroid progesterone to P450 21A2 was also best described by a conformational-selection model. Hexyl isonicotinate binding to P450 2E1 could be described by either a conformational-selection or an induced-fit model. Simulation of the binding of the ligands midazolam, bromocriptine, testosterone, and ketoconazole to P450 3A4 was consistent with an induced-fit or a conformational-selection model, but the concentration dependence of binding rates for varying both P450 3A4 and midazolam concentrations revealed discordance in the parameters, indicative of conformational-selection. Binding of the P450s 2C8, 2D6, 3A4, 4A11, and 21A2 was best described by conformational-selection, and P450 2E1 appeared to fit either mode. These findings highlight the complexity of human P450-substrate interactions and that conformational-selection is a dominant feature of many of these interactions.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
| | - Clayton J Wilkey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Thanh T N Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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14
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Guengerich FP, Wilkey CJ, Glass SM, Reddish MJ. Conformational selection dominates binding of steroids to human cytochrome P450 17A1. J Biol Chem 2019; 294:10028-10041. [PMID: 31072872 DOI: 10.1074/jbc.ra119.008860] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/06/2019] [Indexed: 12/17/2022] Open
Abstract
Cytochrome P450 (P450, CYP) enzymes are the major catalysts involved in the oxidation of steroids as well as many other compounds. Their versatility has been explained in part by flexibility of the proteins and complexity of the binding mechanisms. However, whether these proteins bind their substrates via induced fit or conformational selection is not understood. P450 17A1 has a major role in steroidogenesis, catalyzing the two-step oxidations of progesterone and pregnenolone to androstenedione and dehydroepiandrosterone, respectively, via 17α-hydroxy (OH) intermediates. We examined the interaction of P450 17A1 with its steroid substrates by analyzing progress curves (UV-visible spectroscopy), revealing that the rates of binding of any of these substrates decreased with increasing substrate concentration, a hallmark of conformational selection. Further, when the concentration of 17α-OH pregnenolone was held constant and the P450 concentration increased, the binding rate increased, and such opposite patterns are also diagnostic of conformational selection. Kinetic simulation modeling was also more consistent with conformational selection than with an induced-fit mechanism. Cytochrome b 5 partially enhances P450 17A1 lyase activity by altering the P450 17A1 conformation but did not measurably alter the binding of 17α-OH pregnenolone or 17α-OH progesterone, as judged by the apparent Kd and binding kinetics. The P450 17A1 inhibitor abiraterone also bound to P450 17A1 in a multistep manner, and modeling indicated that the selective inhibition of the two P450 17A1 steps by the drug orteronel can be rationalized only by a multiple-conformation model. In conclusion, P450 17A1 binds its steroid substrates via conformational selection.
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Affiliation(s)
- F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Clayton J Wilkey
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Sarah M Glass
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Michael J Reddish
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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