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Pardhe BD, Paudel L, Han SR, Oh TJ. Genomic insight into O-demethylation of 4-methoxybenzoate by a two-component system from Amycolatopsis magusensis KCCM40447. Heliyon 2024; 10:e25083. [PMID: 38317971 PMCID: PMC10838780 DOI: 10.1016/j.heliyon.2024.e25083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Cytochrome P450 monooxygenases perform a multitude of roles, including the generation of hydroxylated aromatic compounds that might be utilized by microorganisms for their survival. WGS data of Amycolatopsis magusensis KCCM40447 revealed a complete circular genome of 9,099,986 base pairs and functionally assigned 8601 protein-encoding genes. Genomic analysis confirmed that the gene for 4-methoxybenzoate monoxygenase (CYP199A35) was conserved in close proximity to the gene for 4-hydroxybenzoate transporter (PcaK). The co-localized genes encoding CYP199A35, and ferredoxin-NAD(P) reductase (Mbr) represent a two-component system for electron transfer. CYP199A35 was specific for O-demethylation of para O-methyl substituted benzoic acid derivatives, 4-methoxybenzoate (4 MB), and 4-methoxycinnamic acid (4MCA) using the native redox partner (Mbr); two-component system and non-physiological redox partners (Pdr/Pdx); three-component system. The catalytic efficiency for O-demethylation of 4 MB using Mbr and Pdr/Pdx was 0.02 ± 0.006 min-1 μM-1 and 0.07 ± 0.02 min-1 μM-1 respectively. Further, sequence annotation and function prediction by RAST and KEEG analysis revealed a complete catabolic pathway for the utilization of 4 MB by strain KCCM40447, which was also proved experimentally.
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Affiliation(s)
- Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, Republic of Korea
| | - Lakshan Paudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-based BioIT Convergence Institute, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sun Moon University, Asan, Republic of Korea
- Genome-based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan, Republic of Korea
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Chao RR, Lau ICK, Coleman T, Churchman LR, Child SA, Lee JHZ, Bruning JB, De Voss JJ, Bell SG. The stereoselective oxidation of para-substituted benzenes by a cytochrome P450 biocatalyst. Chemistry 2021; 27:14765-14777. [PMID: 34350662 DOI: 10.1002/chem.202102757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Indexed: 11/10/2022]
Abstract
The serine 244 to aspartate (S244D) variant of the cytochrome P450 enzyme CYP199A4 was used to expand its substrate range beyond benzoic acids. Substrates, in which the carboxylate group of the benzoic acid moiety is replaced, were oxidised with high activity by the S244D mutant (product formation rates > 60 nmol.(nmol-CYP) -1 .min -1 ) and with total turnover numbers of up to 20,000. Ethyl α-hydroxylation was more rapid than methyl oxidation, styrene epoxidation and S -oxidation. The S244D mutant catalysed the ethyl hydroxylation, epoxidation and sulfoxidation reactions with an excess of one stereoisomer (in some instances up to >98%). The crystal structure of 4-methoxybenzoic acid-bound CYP199A4 S244D showed that the active site architecture and the substrate orientation were similar to that of the WT enzyme. Overall, this work demonstrates that CYP199A4 can catalyse the stereospecific hydroxylation, epoxidation or sulfoxidation of substituted benzene substrates under mild conditions resulting in more sustainable transformations using this heme monooxygenase enzyme.
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Affiliation(s)
- Rebecca R Chao
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Ian C-K Lau
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Tom Coleman
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Luke R Churchman
- The University of Queensland, School of Chemistry and Molecular Biosciences, AUSTRALIA
| | - Stella A Child
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Joel H Z Lee
- The University of Adelaide, The Department of Chemistry, AUSTRALIA
| | - John B Bruning
- The University of Adelaide, School of Biological Sciences, AUSTRALIA
| | - James J De Voss
- The University of Queensland, School of Chemistry and Molecular Biosciences, AUSTRALIA
| | - Stephen Graham Bell
- University of Adelaide, School of Chemistry & Physics, North Terrace, 5005, Adelaide, AUSTRALIA
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Podgorski MN, Coleman T, Chao RR, De Voss JJ, Bruning JB, Bell SG. Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions. J Inorg Biochem 2019; 203:110913. [PMID: 31759265 DOI: 10.1016/j.jinorgbio.2019.110913] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/26/2019] [Accepted: 11/07/2019] [Indexed: 01/03/2023]
Abstract
The cytochrome P450 metalloenzyme (CYP) CYP199A4 from Rhodopseudomonas palustris HaA2 catalyzes the highly efficient oxidation of para-substituted benzoic acids. Here we determined crystal structures of CYP199A4, and the binding and turnover parameters, with different meta-substituted benzoic acids in order to establish which criteria are important for efficient catalysis. When compared to the para isomers, the meta-substituted benzoic acids were less efficiently oxidized. For example, 3-formylbenzoic acid was oxidized with lower activity than the equivalent para isomer and 3-methoxybenzoic acid did not undergo O-demethylation by CYP199A4. The structural data highlighted that the meta-substituted benzoic acids bound in the enzyme active site in a modified position with incomplete loss of the distal water ligand of the heme moiety. However, for both sets of isomers the meta- or para-substituent pointed towards, and was in close proximity, to the heme iron. The absence of oxidation activity with 3-methoxybenzoic acid was assigned to the observation that the CH bonds of this molecule point away from the heme iron. In contrast, in the para isomer they are in an ideal location for abstraction. These findings were confirmed by using the bulkier 3-ethoxybenzoic acid as a substrate which removed the water ligand and reoriented the meta-substituent so that the methylene hydrogens pointed towards the heme, enabling more efficient oxidation. Overall we show relatively small changes in substrate structure and position in the active site can have a dramatic effect on the activity.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Rebecca R Chao
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, Qld 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.
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4
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Lanfranchi E, Trajković M, Barta K, de Vries JG, Janssen DB. Exploring the Selective Demethylation of Aryl Methyl Ethers with a
Pseudomonas
Rieske Monooxygenase. Chembiochem 2018; 20:118-125. [DOI: 10.1002/cbic.201800594] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Elisa Lanfranchi
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
- Present address: School of Food and Nutritional Science SciencesUniversity College Cork College Road Cork T12 YN60 Republic of Ireland
| | - Miloš Trajković
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
| | - Katalin Barta
- Synthetic Organic ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
| | - Johannes G. de Vries
- Synthetic Organic ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
- Leibniz-Institut für Katalyse e.V. Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Dick B. Janssen
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
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Bowen AM, Johnson EOD, Mercuri F, Hoskins NJ, Qiao R, McCullagh JSO, Lovett JE, Bell SG, Zhou W, Timmel CR, Wong LL, Harmer JR. A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy. J Am Chem Soc 2018; 140:2514-2527. [PMID: 29266939 DOI: 10.1021/jacs.7b11056] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C-H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe2S2] cluster-binding loop and the α3 helix and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe2S2] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity.
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Affiliation(s)
- Alice M Bowen
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Eachan O D Johnson
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Francesco Mercuri
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) Via P. Gobetti 101, 40129 Bologna, Italy
| | - Nicola J Hoskins
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Ruihong Qiao
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Janet E Lovett
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Weihong Zhou
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - Christiane R Timmel
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Luet Lok Wong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Jeffrey R Harmer
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
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