1
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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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3
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Rimal H, Lee WH, Kim KH, Park H, Oh TJ. Characterization of Two Self-Sufficient Monooxygenases, CYP102A15 and CYP102A170, as Long-Chain Fatty Acid Hydroxylases. J Microbiol Biotechnol 2019; 30:777-784. [PMID: 32482945 PMCID: PMC9728198 DOI: 10.4014/jmb.1911.11048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/07/2020] [Indexed: 12/15/2022]
Abstract
Self-sufficient P450s, due to their fused nature, are the most effective tools for electron transfer to activate C-H bonds. They catalyze the oxygenation of fatty acids at different omega positions. Here, two new, self-sufficient cytochrome P450s, named CYP102A15 and CYP102A170, from polar Bacillus sp. PAMC 25034 and Paenibacillus sp. PAMC 22724, respectively, were cloned and expressed in E. coli. The genes are homologues of CYP102A1 from Bacillus megaterium. They catalyzed the hydroxylation of both saturated and unsaturated fatty acids ranging in length from C12-C20, with a moderately diverse profile compared to other members of the CYP102A subfamily. CYP102A15 exhibited the highest activity toward linoleic acid with Km 15.3 μM, and CYP102A170 showed higher activity toward myristic acid with Km 17.4 μM. CYP10A170 also hydroxylated the Eicosapentaenoic acid at ω-1 position only. Various kinetic parameters of both monooxygenases were also determined.
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Affiliation(s)
- Hemraj Rimal
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 0841, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asan 1460, Republic of Korea
- Genome-based BioIT Convergence Institute, Sunmoon University, Asan 3160, Republic of Korea
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4
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Yang CL, Lin CH, Luo WI, Lee TL, Ramu R, Ng KY, Tsai YF, Wei GT, Yu SSF. Mechanistic Study of the Stereoselective Hydroxylation of [2-2
H1
,3-2
H1
]Butanes Catalyzed by Cytochrome P450 BM3 Variants. Chemistry 2016; 23:2571-2582. [DOI: 10.1002/chem.201603956] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Chung-Ling Yang
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
| | - Cheng-Hung Lin
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Department of Chemistry and Biochemistry; National Chung Cheng University; Chiayi 621 Taiwan
| | - Wen-I Luo
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Tsu-Lin Lee
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
| | - Ravirala Ramu
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Kok Yaoh Ng
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Yi-Fang Tsai
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
| | - Guor-Tzo Wei
- Department of Chemistry and Biochemistry; National Chung Cheng University; Chiayi 621 Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry; Academia Sinica; Taipei 115 Taiwan
- Graduate Institute of Applied Science and Technology; National (Taiwan) University of Science and Technology; Taipei 106 Taiwan
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5
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Hoffmann SM, Danesh-Azari HR, Spandolf C, Weissenborn MJ, Grogan G, Hauer B. Structure-Guided Redesign of CYP153AM.aqfor the Improved Terminal Hydroxylation of Fatty Acids. ChemCatChem 2016. [DOI: 10.1002/cctc.201600680] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sara M. Hoffmann
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Hamid-Reza Danesh-Azari
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Claudia Spandolf
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Gideon Grogan
- York Structural Biology Laboratory; Department of Chemistry; University of York; YO10 5DD York United Kingdom
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
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6
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Brühlmann F, Fourage L, Ullmann C, Haefliger OP, Jeckelmann N, Dubois C, Wahler D. Engineering cytochrome P450 BM3 of Bacillus megaterium for terminal oxidation of palmitic acid. J Biotechnol 2014; 184:17-26. [DOI: 10.1016/j.jbiotec.2014.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/09/2014] [Accepted: 05/04/2014] [Indexed: 01/10/2023]
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7
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Controlled oxidation of aliphatic CH bonds in metallo-monooxygenases: Mechanistic insights derived from studies on deuterated and fluorinated hydrocarbons. J Inorg Biochem 2014; 134:118-33. [DOI: 10.1016/j.jinorgbio.2014.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/06/2014] [Accepted: 02/11/2014] [Indexed: 01/01/2023]
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8
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Chiang CH, Ramu R, Tu YJ, Yang CL, Ng KY, Luo WI, Chen CH, Lu YY, Liu CL, Yu SSF. Regioselective Hydroxylation of C12-C15Fatty Acids with Fluorinated Substituents by Cytochrome P450 BM3. Chemistry 2013; 19:13680-91. [DOI: 10.1002/chem.201302402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Indexed: 11/09/2022]
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9
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Babot ED, del Río JC, Kalum L, Martínez AT, Gutiérrez A. Oxyfunctionalization of aliphatic compounds by a recombinant peroxygenase from
Coprinopsis cinerea. Biotechnol Bioeng 2013; 110:2323-32. [DOI: 10.1002/bit.24904] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Esteban D. Babot
- Instituto de Recursos Naturales y Agrobiología de SevillaCSICReina Mercedes 10, E‐41012 SevilleSpain
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de SevillaCSICReina Mercedes 10, E‐41012 SevilleSpain
| | | | | | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de SevillaCSICReina Mercedes 10, E‐41012 SevilleSpain
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10
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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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11
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Gutiérrez A, Babot ED, Ullrich R, Hofrichter M, Martínez AT, del Río JC. Regioselective oxygenation of fatty acids, fatty alcohols and other aliphatic compounds by a basidiomycete heme-thiolate peroxidase. Arch Biochem Biophys 2011; 514:33-43. [DOI: 10.1016/j.abb.2011.08.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 08/04/2011] [Accepted: 08/07/2011] [Indexed: 11/27/2022]
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12
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Wu LL, Yang CL, Lo FC, Chiang CH, Chang CW, Ng KY, Chou HH, Hung HY, Chan SI, Yu SSF. Tuning the regio- and stereoselectivity of C-H activation in n-octanes by cytochrome P450 BM-3 with fluorine substituents: evidence for interactions between a C-F bond and aromatic π systems. Chemistry 2011; 17:4774-87. [PMID: 21400620 DOI: 10.1002/chem.201003631] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Indexed: 11/10/2022]
Abstract
We employed the water-soluble cytochrome P450 BM-3 to study the activity and regiospecificity of oxidation of fluorinated n-octanes. Three mutations, A74G, F87V, and L188Q, were introduced into P450 BM-3 to allow the system to undergo n-octane oxidation. In addition, the alanine at residue 328 was replaced with a phenylalanine to introduce an aromatic residue into the hydrophobic pocket to examine whether or not van der Waals interactions between a C-F substituent in the substrate and the polarizable π system of the phenylalanine may be used to steer the positioning of the substrate within the active-site pocket of the enzyme and control the regioselectivity and stereoselectivity of hydroxylation. Interestingly, not only was the regioselectivity controlled when the fluorine substituent was judiciously positioned in the substrate, but the electron input into the iron-heme group became tightly coupled to the formation of product, essentially without abortive side reactions. Remarkable enhancement of the coupling efficiency between electron input and product formation was observed for a range of fluorinated octanes in the enzyme even without the A328F mutation, presumably because of interactions of the C-F substituent with the π system of the porphyrin macrocycle within the active-site pocket. Evidently, tightening the protein domain containing the heme pocket tunes the distribution of accessible enzyme conformations and the associated protein dynamics that activate the iron porphyrin for substrate hydroxylation to allow the reactions mediated by the high-valent Fe(IV)=O to become kinetically more commensurate with electron transfer from the flavin adenine dinucleotide (FAD)/flavin mononucleotide (FMN) reductase. These observations lend compelling evidence to support significant van der Waals interactions between the CF(2) group and aromatic π systems within the heme pocket when the fluorinated octane substrate is bound.
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Affiliation(s)
- Li-Lan Wu
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
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13
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Abstract
The cytochromes P450 (P450s) are a superfamily of oxidative haemoproteins that are capable of catalysing a vast range of oxidative transformations, including the oxidation of unactivated alkanes, often with high stereo- and regio-selectivity. Fatty acid hydroxylation by P450s is widespread across both bacteria and higher organisms, with the sites of oxidation and specificity of oxidation varying from system to system. Several key examples are discussed in the present article, with the focus on P450(BioI) (CYP107H1), a biosynthetic P450 found in the biotin operon of Bacillus subtilis. The biosynthetic function of P450(BioI) is the formation of pimelic acid, a biotin precursor, via a multiple-step oxidative cleavage of long-chain fatty acids. P450(BioI) is a member of an important subgroup of P450s that accept their substrates not free in solution, but rather presented by a separate carrier protein. Structural characterization of the P450(BioI)-ACP (acyl-carrier protein) complex has recently been performed, which has revealed the basis for the oxidation of the centre of the fatty acid chain. The P450(BioI)-ACP structure is the first such P450-carrier protein complex to be characterized structurally, with important implications for other biosynthetically intriguing P450-carrier protein complexes.
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14
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Branco RJ, Seifert A, Budde M, Urlacher VB, Ramos MJ, Pleiss J. Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium. Proteins 2008; 73:597-607. [DOI: 10.1002/prot.22083] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Chowdhary PK, Alemseghed M, Haines DC. Cloning, expression and characterization of a fast self-sufficient P450: CYP102A5 from Bacillus cereus. Arch Biochem Biophys 2007; 468:32-43. [DOI: 10.1016/j.abb.2007.09.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 09/10/2007] [Accepted: 09/13/2007] [Indexed: 11/27/2022]
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16
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Cryle MJ, De Voss JJ. Is the ferric hydroperoxy species responsible for sulfur oxidation in cytochrome p450s? Angew Chem Int Ed Engl 2007; 45:8221-3. [PMID: 17111450 DOI: 10.1002/anie.200603411] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Max J Cryle
- Department of Chemistry, School of Molecular and Microbial Sciences, University of Queensland, St. Lucia Brisbane 4072, Australia
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17
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Facile determination of the absolute stereochemistry of hydroxy fatty acids by GC: application to the analysis of fatty acid oxidation by a P450BM3 mutant. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.01.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Cryle MJ, Matovic NJ, De Voss JJ. The stereochemistry of fatty acid hydroxylation by cytochrome P450BM3. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2006.10.136] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Is the Ferric Hydroperoxy Species Responsible for Sulfur Oxidation in Cytochrome P450s? Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200603411] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Budde M, Morr M, Schmid RD, Urlacher VB. Selective Hydroxylation of Highly Branched Fatty Acids and their Derivatives by CYP102A1 from Bacillus megaterium. Chembiochem 2006; 7:789-94. [PMID: 16566047 DOI: 10.1002/cbic.200500444] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Highly branched fatty acids, the main components of the preen-gland waxes of the domestic goose and the Muscovy duck, and their derivatives are promising chiral precursors for the synthesis of macrolide antibiotics. The key step in the utilisation of these compounds is their regioselective hydroxylation, which cannot be achieved in a classical chemical approach. Three P450 monooxygenases, CYP102A1, CYP102A2 and CYP102A3, demonstrating high turnover numbers in the hydroxylation of iso and anteiso fatty acids (>400 min(-1)), were tested for their activity towards these substrates. CYP102A1 from Bacillus megaterium and its A74G F87V L188Q triple mutant hydroxylate a variety of these substrates with high activity and regioselectivity. In all cases, the triple mutant showed much higher activities than the wild-type enzyme. The binding constants, determined for wild-type CYP102A1 and the triple mutant with tetramethylnonanol as substrate, were >200 microM and approximately 23 microM, respectively. Data derived from binding analysis support the differences in activity found for the wild-type CYP102A1 and the triple mutant. Surprisingly, CYP102A2 and CYP102A3 from Bacillus subtilis did not show any activity. Substrate binding spectra, recorded to investigate substrate accessibility to the enzyme's active sites, revealed that the substrates either could not access the active site of the Bacillus subtilis monooxygenases, or did not come into proximity with the heme.
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Affiliation(s)
- Michael Budde
- Institute for Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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21
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Urlacher VB, Makhsumkhanov A, Schmid RD. Biotransformation of β-ionone by engineered cytochrome P450 BM-3. Appl Microbiol Biotechnol 2006; 70:53-9. [PMID: 16001257 DOI: 10.1007/s00253-005-0028-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Revised: 05/12/2005] [Accepted: 05/19/2005] [Indexed: 10/25/2022]
Abstract
Wild-type cytochrome P450 monooxygenase from Bacillus megaterium (P450 BM-3) has a low hydroxylation activity for beta-ionone (<1 min(-1)). Substitution of phenylalanine by valine at position 87 led to a more than 100-fold increase in beta-ionone hydroxylation activity (115 min(-1)). Enzyme activity could be further increased by both site-directed and random mutagenesis. The mutant R47L Y51F F87V, designed by site-directed mutagenesis, and the mutant A74E F87V P386S, obtained after two rounds of error-prone polymerase chain reaction, exhibited an increase in activity of up to 300-fold compared to the wild-type enzyme. The triple mutant R47 LY51F F87V exhibited moderate enantioselectivity, forming (R)-4-hydroxy-beta-ionone with an optical purity of 39%. All mutants regioselectively converted beta-ionone into 4-hydroxy-beta-ionone. The regioselectivity is determined amongst others by the absolute configuration of the substrate.
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Affiliation(s)
- Vlada B Urlacher
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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22
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Cryle MJ, Espinoza RD, Smith SJ, Matovic NJ, De Voss JJ. Are branched chain fatty acids the natural substrates for P450BM3? Chem Commun (Camb) 2006:2353-5. [PMID: 16733577 DOI: 10.1039/b601202g] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Branched chain fatty acids are substrates for cytochrome P450(BM3) (CYP102) from Bacillus megaterium; oxidation of C15 and C17 iso and anteiso fatty acids by P450(BM3) leads to the formation of hydroxylated products that possess high levels of regiochemical and stereochemical purity.
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Affiliation(s)
- Max J Cryle
- Department of Chemistry, University of Queensland, St. Lucia, Brisbane, Australia 4072
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23
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Maurer S, Kühnel K, Kaysser L, Eiben S, Schmid R, Urlacher V. Catalytic Hydroxylation in Biphasic Systems using CYP102A1 Mutants. Adv Synth Catal 2005. [DOI: 10.1002/adsc.200505044] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Cryle MJ, Ortiz de Montellano PR, De Voss JJ. Cyclopropyl containing fatty acids as mechanistic probes for cytochromes P450. J Org Chem 2005; 70:2455-69. [PMID: 15787531 DOI: 10.1021/jo047985d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] The mechanism of aliphatic hydroxylation by cytochromes P450 has been the subject of intense debate with several proposed mechanistic alternatives. Various cyclopropyl containing compounds (radical clocks), which can produce both unrearranged and ring opened products upon oxidation, have been key tools in these investigations. In this study, we introduce several cyclopropyl containing fatty acids 1a-4a with which to probe the mechanism of P450s capable of fatty acid hydroxylation. The probes are shown to be capable of distinguishing radical from cationic intermediates due to the rapid equilibration of isomeric cyclopropyl cations. Ring opening of a radical intermediate in an oxidative transformation is expected to yield a single rearranged alcohol, whereas a cation isomerizes prior to ring opening, leading to two isomeric homoallylic alcohols. Oxidation of these probes by P450(BM3) and P450(BioI) gives results consistent with a radical but not a cationic intermediate in fatty acid hydroxylation by these enzymes. Quantitation of the unrearranged and ring opened products gives remarkably homogeneous rates for oxygen rebound of (2-3) x 10(10) s(-1). The effects of introduction of a cyclopropane ring into a fatty acid upon the regiochemistry of hydroxylation are discussed.
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Affiliation(s)
- Max J Cryle
- Department of Chemistry, University of Queensland, St. Lucia, Brisbane, Australia 4072
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Lentz O, Urlacher V, Schmid RD. Substrate specificity of native and mutated cytochrome P450 (CYP102A3) from Bacillus subtilis. J Biotechnol 2004; 108:41-9. [PMID: 14741768 DOI: 10.1016/j.jbiotec.2003.11.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Within the Bacillus subtilis genome sequencing project, two monooxygenases (CYP102A2 and CYP102A3) were discovered which revealed a similarity of 76% to the well-known cytochrome P450 BM-3 (CYP102A1) of Bacillus megaterium. All enzymes are natural fusion proteins consisting of a heme domain and a reductase domain. We here report the cloning, expression and characterization of B. subtilis enzyme CYP102A3. The substrate specificity of this enzyme is similar to that of B. megaterium CYP102A1, which hydroxylates medium-chain fatty acids in subterminal positions. A double mutant was prepared that hydroxylates a number of other substrates, which do not bear any resemblance to the natural substrate of this enzyme family.
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Affiliation(s)
- Oliver Lentz
- Institut für Technische Biochemie, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany
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26
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Cryle MJ, Matovic NJ, De Voss JJ. Products of cytochrome P450(BioI) (CYP107H1)-catalyzed oxidation of fatty acids. Org Lett 2003; 5:3341-4. [PMID: 12943422 DOI: 10.1021/ol035254e] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Oxidation of tetradecanoic and hexadecanoic acids by cytochrome P450(BioI) (CYP107H1) produces mainly the 11-, 12-, and 13-hydroxy C(14) fatty acids and the 11- to 15-hydroxy C(16) fatty acids, respectively. In contrast to previous reports, terminal hydroxylation is not observed. The enantiospecificity of fatty acid hydroxylation by P450(BioI) was also determined, and the enzyme was shown to be moderately selective for production of the (R)-alcohols.
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Affiliation(s)
- Max J Cryle
- Department of Chemistry, University of Queensland, St. Lucia, Brisbane 4072, Australia
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27
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Rock DA, Perkins BNS, Wahlstrom J, Jones JP. A method for determining two substrates binding in the same active site of cytochrome P450BM3: an explanation of high energy omega product formation. Arch Biochem Biophys 2003; 416:9-16. [PMID: 12859976 DOI: 10.1016/s0003-9861(03)00228-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A number of enzymes from the cytochrome P450 family show atypical (non-Michaelis-Menten) kinetic behavior resulting from substrate activation, inhibition, partial inhibition, biphasic saturation, or autoactivation. Herein, we provide a technique that can identify multiple substrate occupancy in the same active site of a P450 as a result of an altered kinetic profile. Using an isotope effect on product ratios confirms that the enzyme-substrate (ES) complex responsible for omega hydroxylation of palmitic acid (palmitate) is in rapid equilibrium with the ES complex that leads to omega-1 hydroxylation of palmitate. Co-incubation of a second substrate, lauric acid (laurate), results in a change in the ratio of omega to omega-1 hydroxylated palmitate. Furthermore, an isotope effect on palmitate is observed when deuterated laurate is co-incubated with non-deuterated palmitate. These results are only consistent with both substrates being in the same active site simultaneously. This mode of binding explains how the F87A mutant of P450BM3 is able to produce the omega alcohol, a product that arises from the high-energy primary radical.
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Affiliation(s)
- Dan A Rock
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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28
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Weil K, Gruber P, Heckel F, Harmsen D, Schreier P. Selective (R)-3-hydroxylation of FA by Stenotrophomonas maltophilia. Lipids 2002; 37:317-23. [PMID: 11942484 DOI: 10.1007/s11745-002-0897-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Soil samples were screened for microorganisms selectively transforming FA. One of the isolated strains was identified as the bacterium Stenotrophomonas maltophilia by its phenotypic features and genotypic characterization by sequencing the ribosomal RNA gene. Using linoleic acid as substrate resulted in the formation of two major compounds. After liquid chromatographic isolation and separation, their structures were elucidated by HPLC-tandem MS, GC-MS, and NMR techniques to be 3-hydroxy-Z6-dodecenoic acid and 3-hydroxy-Z5,Z8-tetradecadienoic acid. In additional experiments, other FA, such as a-linolenic, oleic, palmitoleic, myristoleic, and cis-vaccenic acids, were converted to 3-hydroxylated metabolites of shorter chain lengths as well. Determination of the enantiomeric composition revealed highly enriched (R)-hydroxylation (88-98% enantiomeric excess).
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Affiliation(s)
- Kerstin Weil
- Lehrstuhl für Lebensmittelchemie, Universität Würzburg, Germany
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29
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Weil K, Humpf HU, Schwab W, Schreier P. Absolute configuration of 3-hydroxy acids formed by Stenotrophomonas maltophilia: application of multidimensional gas chromatography and circular dichroism spectroscopy. Chirality 2002; 14:51-8. [PMID: 11748801 DOI: 10.1002/chir.10029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The soil bacterium Stenotrophomonas maltophilia was found to transform various long-chain fatty acids selectively into 3-hydroxy fatty acids of shorter chain length. Their chiral evaluation was performed by multidimensional gas chromatography (MDGC) on modified cyclodextrin phase comparing the enantiodistribution of 1,3-diol formed without loss of stereochemical information from a representative microbial product with those of synthetic (3RS)- and (3S)-1,3-diols. Enantiomeric excesses of 84-98% (R) were determined for the microbially produced 3-hydroxy acids. In addition, the CD exciton chirality method was applied to determine their absolute configuration. Derivatization with 9-anthryldiazomethane and 2-naphthoylimidazole led to the required bichromophoric structures. Their CD spectra displayed a positive first Cotton effect around 254 nm and a negative second Cotton effect around 237 nm, which confirmed the (R)-configuration of the bacterial products.
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Affiliation(s)
- Kerstin Weil
- Universität Würzburg, Lehrstuhl für Lebensmittelchemie, Am Hubland, D-97074 Würzburg, Germany
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30
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Li QS, Ogawa J, Schmid RD, Shimizu S. Residue size at position 87 of cytochrome P450 BM-3 determines its stereoselectivity in propylbenzene and 3-chlorostyrene oxidation. FEBS Lett 2001; 508:249-52. [PMID: 11718725 DOI: 10.1016/s0014-5793(01)03074-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We report here oxidation of propylbenzene and 3-chlorostyrene by wild-type cytochrome P450 BM-3 with high turnover (479 nmol 1-phenyl-1-propanol/min/nmol P450 and 300 nmol 3-chlorostyrene oxide/min/nmol P450). Furthermore, the residue size at position 87 of P450 BM-3 was found to play critical roles in determining stereoselectivity in oxidation of propylbenzene and 3-chlorostyrene. Replacement of Phe87 with Val, Ala and Gly resulted in decreases in optical purity of produced (R)-(+)-1-phenyl-1-propanol from 90.0 to 37.4, 26.0 and -15.6% e.e., respectively, and in increases in those of produced (R)-(+)-3-chlorostyrene oxide from -61.0 to -38.0, 67.0 and 94.6% e.e., respectively.
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Affiliation(s)
- Q S Li
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University, Japan
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31
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Lentz O, Li QS, Schwaneberg U, Lutz-Wahl S, Fischer P, Schmid RD. Modification of the fatty acid specificity of cytochrome P450 BM-3 from Bacillus megaterium by directed evolution: a validated assay. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1381-1177(01)00015-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Hoch U, Falck JR, de Montellano PRO. Molecular Basis for the ω-Regiospecificity of the CYP4A2 and CYP4A3 Fatty Acid Hydroxylases. J Biol Chem 2000. [DOI: 10.1016/s0021-9258(19)61465-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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