1
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Jones BS, Ross CM, Foley G, Pozhydaieva N, Sharratt JW, Kress N, Seibt LS, Thomson RES, Gumulya Y, Hayes MA, Gillam EMJ, Flitsch SL. Engineering Biocatalysts for the C-H Activation of Fatty Acids by Ancestral Sequence Reconstruction. Angew Chem Int Ed Engl 2024; 63:e202314869. [PMID: 38163289 DOI: 10.1002/anie.202314869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids, but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the subterminal positions of fatty acids. Herein we show that ancestral sequence reconstruction (ASR) is an effective tool to explore the sequence-activity landscape of a family of multidomain, self-sufficient P450 monooxygenases. We resurrected 11 catalytically active CYP116B ancestors, each with a unique regioselectivity fingerprint that varied from subterminal in the older ancestors to mid-chain in the lineage leading to the extant, P450-TT. In lineages leading to extant enzymes in thermophiles, thermostability increased from ancestral to extant forms, as expected if thermophily had arisen de novo. Our studies show that ASR can be applied to multidomain enzymes to develop active, self-sufficient monooxygenases as regioselective biocatalysts for fatty acid hydroxylation.
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Affiliation(s)
- Bethan S Jones
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Connie M Ross
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Nadiia Pozhydaieva
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Joseph W Sharratt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Nico Kress
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Lisa S Seibt
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, 4072, Australia
| | - Sabine L Flitsch
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, UK
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2
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Zhou TP, Feng J, Wang Y, Li S, Wang B. Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS AU 2024; 4:1591-1604. [PMID: 38665654 PMCID: PMC11040706 DOI: 10.1021/jacsau.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (-)-naseseazine C (2) through intramolecular C-N bond formation and intermolecular C-C coupling. A thorough understanding of its catalytic mechanism is crucial for the engineering or design of P450-catalyzed C-N dimerization reactions. By employing MD simulations, QM/MM calculations, and enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that the most favorable pathway entails the transfer of a hydrogen atom from N7-H to Cpd I. Subsequently, there is a conformational change in the substrate radical, shifting it from the Re-face to the Si-face of N7 in Substrate 1. The Si-face conformation of Substrate 1 is stabilized by the protein environment and the π-π stacking interaction between the indole ring and heme porphyrin. The subsequent intermolecular C3-C6' bond formation between Substrate 1 radical and Substrate 2 occurs via a radical attack mechanism. The conformational switch of the Substrate 1 radical not only lowers the barrier of the intermolecular C3-C6' bond formation but also yields the correct stereoselectivity observed in experiments. In addition, we evaluated the reactivity of the ferric-superoxide species, showing it is not reactive enough to initiate the hydrogen atom abstraction from the indole NH group of the substrate. Our simulation provides a comprehensive mechanistic insight into how the P450 enzyme precisely controls both the intramolecular C-N cyclization and intermolecular C-C coupling. The current findings align with the available experimental data, emphasizing the pivotal role of substrate dynamics in governing P450 catalysis.
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Affiliation(s)
- Tai-Ping Zhou
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianqiang Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yongchao Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shengying Li
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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3
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Famulari A, Correddu D, Di Nardo G, Gilardi G, Mitrikas G, Chiesa M, García-Rubio I. Heme Spin Distribution in the Substrate-Free and Inhibited Novel CYP116B5hd: A Multifrequency Hyperfine Sublevel Correlation (HYSCORE) Study. Molecules 2024; 29:518. [PMID: 38276601 PMCID: PMC10819608 DOI: 10.3390/molecules29020518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.
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Affiliation(s)
- Antonino Famulari
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Danilo Correddu
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, 15341 Athens, Greece;
| | - Mario Chiesa
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Inés García-Rubio
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
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4
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Lu J, Liu Y, Zhang R, Hu Z, Xue K, Dong B. Biochar inoculated with Pseudomonas putida alleviates its inhibitory effect on biodegradation pathways in phenanthrene-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132550. [PMID: 37729712 DOI: 10.1016/j.jhazmat.2023.132550] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Controversial results are reported whereby biodegradation of polycyclic aromatic hydrocarbons (PAHs) can be promoted or inhibited by biochar amendment of soil. Metabolomics was applied to analyze the metabolic profiles of amendment with biochar (BB) and biochar inoculated with functional bacteria (Pseudomonas putida) (BP) involved in phenanthrene (PHE) degradation. Additionally, metagenomic analysis was utilized to assess the impact of different treatments on PHE degradation by soil microorganisms. Results indicated that BB treatment decreased the PHE biodegradation of the soil indigenous bacterial consortium, but BP treatment alleviated this inhibitory effect. Metabolomics revealed the differential metabolite 9-phenanthrol was absent in the BB treatment, but was found in the control group (CK), and in the treatment inoculated with the Pseudomonas putida (Ps) and the BP treatment. Metagenomic analysis showed that biochar decreased the abundance of the cytochrome P450 monooxygenase (CYP116), which was detected in the Pseudomonas putida, thus alleviating the inhibitory effect of biochar on PHE degradation. Moreover, a noticeable delayed increase of functional gene abundance and enzymes abundance in the BB treatment was observed in the PHE degradation pathway. Our findings elucidate the mechanism of inhibition with biochar amendment and the alleviating effect of biochar inoculated with degrading bacteria.
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Affiliation(s)
- Jinfeng Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuexian Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ruili Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhengyi Hu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Biya Dong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Zong L, Zhang Y, Shao Z, Ljubic A, Jacobsen C, Gao R, Eser BE, Wang Y, Guo Z. Selective and Sustainable Production of Sub-terminal Hydroxy Fatty Acids by a Self-Sufficient CYP102 Enzyme from Bacillus Amyloliquefaciens. Chembiochem 2023; 24:e202300368. [PMID: 37406107 DOI: 10.1002/cbic.202300368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
Enzymatic hydroxylation of fatty acids by Cytochrome P450s (CYPs) offers an eco-friendly route to hydroxy fatty acids (HFAs), high-value oleochemicals with various applications in materials industry and with potential as bioactive compounds. However, instability and poor regioselectivity of CYPs are their main drawbacks. A newly discovered self-sufficient CYP102 enzyme, BAMF0695 from Bacillus amyloliquefaciens DSM 7, exhibits preference for hydroxylation of sub-terminal positions (ω-1, ω-2, and ω-3) of fatty acids. Our studies show that BAMF0695 has a broad temperature optimum (over 70 % of maximal enzymatic activity retained between 20 to 50 °C) and is highly thermostable (T50 >50 °C), affording excellent adaptive compatibility for bioprocesses. We further demonstrate that BAMF0695 can utilize renewable microalgae lipid as a substrate feedstock for HFA production. Moreover, through extensive site-directed and site-saturation mutagenesis, we isolated variants with high regioselectivity, a rare property for CYPs that usually generate complex regioisomer mixtures. BAMF0695 mutants were able to generate a single HFA regiosiomer (ω-1 or ω-2) with selectivities from 75 % up to 91 %, using C12 to C18 fatty acids. Overall, our results demonstrate the potential of a recent CYP and its variants for sustainable and green production of high-value HFAs.
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Affiliation(s)
- Li Zong
- Key Laboratory for Molecular Enzymology and Engineering The Ministry of Education, School of Life Science, Jilin University, Changchun, 130021, China
- Department of Biological and Chemical Engineering Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Yan Zhang
- Department of Biological and Chemical Engineering Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Zhengkang Shao
- Key Laboratory for Molecular Enzymology and Engineering The Ministry of Education, School of Life Science, Jilin University, Changchun, 130021, China
| | - Anita Ljubic
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800, Kgs. Lyngby, Denmark
- Current address: AGC Biologics, Vandtårnsvej 83, 2860, Søborg, Denmark
| | - Charlotte Jacobsen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800, Kgs. Lyngby, Denmark
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering The Ministry of Education, School of Life Science, Jilin University, Changchun, 130021, China
| | - Bekir Engin Eser
- Department of Biological and Chemical Engineering Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Yingwu Wang
- Key Laboratory for Molecular Enzymology and Engineering The Ministry of Education, School of Life Science, Jilin University, Changchun, 130021, China
| | - Zheng Guo
- Department of Biological and Chemical Engineering Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
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6
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Dolan JP, Cosgrove SC, Miller GJ. Biocatalytic Approaches to Building Blocks for Enzymatic and Chemical Glycan Synthesis. JACS AU 2023; 3:47-61. [PMID: 36711082 PMCID: PMC9875253 DOI: 10.1021/jacsau.2c00529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
While the field of biocatalysis has bloomed over the past 20-30 years, advances in the understanding and improvement of carbohydrate-active enzymes, in particular, the sugar nucleotides involved in glycan building block biosynthesis, have progressed relatively more slowly. This perspective highlights the need for further insight into substrate promiscuity and the use of biocatalysis fundamentals (rational design, directed evolution, immobilization) to expand substrate scopes toward such carbohydrate building block syntheses and/or to improve enzyme stability, kinetics, or turnover. Further, it explores the growing premise of using biocatalysis to provide simple, cost-effective access to stereochemically defined carbohydrate materials, which can undergo late-stage chemical functionalization or automated glycan synthesis/polymerization.
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7
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Abstract
The P450 superfamily comprises some of the most powerful and versatile enzymes for the site-selective oxidation of small molecules. One of the main drawbacks for the applications of the P450s in biotechnology is that the majority of these enzymes is multicomponent in nature and requires the presence of suitable redox partners to support their functions. Nevertheless, the discovery of several self-sufficient P450s, namely those from Classes VII and VIII, has served as an inspiration for fusion approaches to generate chimeric P450 systems that are self-sufficient. In this Perspective, we highlight the domain organizations of the Class VII and Class VIII P450 systems, summarize recent case studies in the engineering of catalytically self-sufficient P450s based on these systems, and outline outstanding challenges in the field, along with several emerging technologies as potential solutions.
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Affiliation(s)
- Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX, 77005
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8
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Nowrouzi B, Lungang L, Rios-Solis L. Exploring optimal Taxol® CYP725A4 activity in Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:197. [PMID: 36123694 PMCID: PMC9484169 DOI: 10.1186/s12934-022-01922-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background CYP725A4 catalyses the conversion of the first Taxol® precursor, taxadiene, to taxadiene-5α-ol (T5α-ol) and a range of other mono- and di-hydroxylated side products (oxygenated taxanes). Initially known to undergo a radical rebound mechanism, the recent studies have revealed that an intermediate epoxide mediates the formation of the main characterised products of the enzyme, being T5α-ol, 5(12)-oxa-3(11)-cyclotaxane (OCT) and its isomer, 5(11)-oxa-3(11)-cyclotaxane (iso-OCT) as well as taxadienediols. Besides the high side product: main product ratio and the low main product titre, CYP725A4 is also known for its slow enzymatic activity, massively hindering further progress in heterologous production of Taxol® precursors. Therefore, this study aimed to systematically explore the key parameters for improving the regioselectivity and activity of eukaryotic CYP725A4 enzyme in a whole-cell eukaryotic biocatalyst, Saccharomyces cerevisiae. Results Investigating the impact of CYP725A4 and reductase gene dosages along with construction of self-sufficient proteins with strong prokaryotic reductases showed that a potential uncoupling event accelerates the formation of oxygenated taxane products of this enzyme, particularly the side products OCT and iso-OCT. Due to the harmful effect of uncoupling products and the reactive metabolites on the enzyme, the impact of flavins and irons, existing as prosthetic groups in CYP725A4 and reductase, were examined in both their precursor and ready forms, and to investigate the changes in product distribution. We observed that the flavin adenine dinucleotide improved the diterpenoids titres and biomass accumulation. Hemin was found to decrease the titre of iso-OCT and T5α-ol, without impacting the side product OCT, suggesting the latter being the major product of CYP725A4. The interaction between this iron and the iron precursor, δ-Aminolevulinic acid, seemed to improve the production of these diterpenoids, further denoting that iso-OCT and T5α-ol were the later products. While no direct correlation between cellular-level oxidative stress and oxygenated taxanes was observed, investigating the impact of salt and antioxidant on CYP725A4 further showed the significant drop in OCT titre, highlighting the possibility of enzymatic-level uncoupling event and reactivity as the major mechanism behind the enzyme activity. To characterise the product spectrum and production capacity of CYP725A4 in the absence of cell growth, resting cell assays with optimal neutral pH revealed an array of novel diterpenoids along with higher quantities of characterised diterpenoids and independence of the oxygenated product spectra from the acidity effect. Besides reporting on the full product ranges of CYP725A4 in yeast for the first time, the highest total taxanes of around 361.4 ± 52.4 mg/L including 38.1 ± 8.4 mg/L of T5α-ol was produced herein at a small, 10-mL scale by resting cell assay, where the formation of some novel diterpenoids relied on the prior existence of other diterpenes/diterpenoids as shown by statistical analyses. Conclusions This study shows how rational strain engineering combined with an efficient design of experiment approach systematically uncovered the promoting effect of uncoupling for optimising the formation of the early oxygenated taxane precursors of Taxol®. The provided strategies can effectively accelerate the design of more efficient Taxol®-producing yeast strains. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01922-1.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, UK.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, EH9 3BD, UK
| | - Liang Lungang
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, UK.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, EH9 3BD, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, UK. .,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, EH9 3BD, UK. .,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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9
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EPR characterization of the heme domain of a self-sufficient cytochrome P450 (CYP116B5). J Inorg Biochem 2022; 231:111785. [DOI: 10.1016/j.jinorgbio.2022.111785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 11/19/2022]
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10
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Behrendorff JBYH. Reductive Cytochrome P450 Reactions and Their Potential Role in Bioremediation. Front Microbiol 2021; 12:649273. [PMID: 33936006 PMCID: PMC8081977 DOI: 10.3389/fmicb.2021.649273] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Cytochrome P450 enzymes, or P450s, are haem monooxygenases renowned for their ability to insert one atom from molecular oxygen into an exceptionally broad range of substrates while reducing the other atom to water. However, some substrates including many organohalide and nitro compounds present little or no opportunity for oxidation. Under hypoxic conditions P450s can perform reductive reactions, contributing electrons to drive reductive elimination reactions. P450s can catalyse dehalogenation and denitration of a range of environmentally persistent pollutants including halogenated hydrocarbons and nitroamine explosives. P450-mediated reductive dehalogenations were first discovered in the context of human pharmacology but have since been observed in a variety of organisms. Additionally, P450-mediated reductive denitration of synthetic explosives has been discovered in bacteria that inhabit contaminated soils. This review will examine the distribution of P450-mediated reductive dehalogenations and denitrations in nature and discuss synthetic biology approaches to developing P450-based reagents for bioremediation.
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Affiliation(s)
- James B. Y. H. Behrendorff
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, Canberra, ACT, Australia
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11
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Correddu D, Di Nardo G, Gilardi G. Self-Sufficient Class VII Cytochromes P450: From Full-Length Structure to Synthetic Biology Applications. Trends Biotechnol 2021; 39:1184-1207. [PMID: 33610332 DOI: 10.1016/j.tibtech.2021.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/25/2022]
Abstract
Members of class VII cytochromes P450 are catalytically self-sufficient enzymes containing a phthalate dioxygenase reductase-like domain fused to the P450 catalytic domain. Among these, CYP116B46 is the first enzyme for which the 3D structure of the whole polypeptide chain has been solved, shedding light on the interaction between its domains, which is crucial for catalysis. Most of these enzymes have been isolated from extremophiles or detoxifying bacteria that can carry out regio- and enantioselective oxidation of compounds of biotechnological interest. Protein engineering has generated mutants that can perform challenging organic reactions such as the anti-Markovnikov alkene oxidation. This potential, combined with the detailed 3D structure, forms the basis for further directed evolution studies aimed at widening their biotechnological exploitation.
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Affiliation(s)
- Danilo Correddu
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy.
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12
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Advances in enzymatic oxyfunctionalization of aliphatic compounds. Biotechnol Adv 2021; 51:107703. [PMID: 33545329 DOI: 10.1016/j.biotechadv.2021.107703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 12/27/2022]
Abstract
Selective oxyfunctionalizations of aliphatic compounds are difficult chemical reactions, where enzymes can play an important role due to their stereo- and regio-selectivity and operation under mild reaction conditions. P450 monooxygenases are well-known biocatalysts that mediate oxyfunctionalization reactions in different living organisms (from bacteria to humans). Unspecific peroxygenases (UPOs), discovered in fungi, have arisen as "dream biocatalysts" of great biotechnological interest because they catalyze the oxyfunctionalization of aliphatic and aromatic compounds, avoiding the necessity of expensive cofactors and regeneration systems, and only depending on H2O2 for their catalysis. Here, we summarize recent advances in aliphatic oxyfunctionalization reactions by UPOs, as well as the molecular determinants of the enzyme structures responsible for their activities, emphasizing the differences found between well-known P450s and the novel fungal peroxygenases.
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13
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14
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Wang Z, Shaik S, Wang B. Conformational Motion of Ferredoxin Enables Efficient Electron Transfer to Heme in the Full-Length P450 TT. J Am Chem Soc 2021; 143:1005-1016. [PMID: 33426875 DOI: 10.1021/jacs.0c11279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 monooxygenases (P450s) are versatile biocatalysts used in natural products biosynthesis, xenobiotic metabolisms, and biotechnologies. In P450s, the electrons required for O2 activation are supplied by NAD(P)H through stepwise electron transfers (ETs) mediated by redox partners. While much is known about the machinery of the catalytic cycle of P450s, the mechanisms of long-range ET are largely unknown. Very recently, the first crystal structure of full-length P450TT was solved. This enables us to decipher the interdomain ET mechanism between the [2Fe-2S]-containing ferredoxin and the heme, by use of molecular dynamics simulations. In contrast to the "distal" conformation characterized in the crystal structure where the [2Fe-2S] cluster is ∼28 Å away from heme-Fe, our simulations demonstrated a "proximal" conformation of [2Fe-2S] that is ∼17 Å [and 13.7 Å edge-to-edge] away from heme-Fe, which may enable the interdomain ET. Key residues involved in ET pathways and interdomain complexation were identified, some of which have already been verified by recent mutation studies. The conformational transit of ferredoxin between "distal" and "proximal" was found to be controlled mostly by the long-range electrostatic interactions between the ferredoxin domain and the other two domains. Furthermore, our simulations show that the full-length P450TT utilizes a flexible ET pathway that resembles either P450Scc or P450cam. Thus, this study provides a uniform picture of the ET process between reductase domains and heme domain.
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Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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15
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 499] [Impact Index Per Article: 166.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
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Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
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16
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Chen CC, Min J, Zhang L, Yang Y, Yu X, Guo RT. Advanced Understanding of the Electron Transfer Pathway of Cytochrome P450s. Chembiochem 2020; 22:1317-1328. [PMID: 33232569 DOI: 10.1002/cbic.202000705] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Indexed: 11/08/2022]
Abstract
Cytochrome P450s are heme-thiolate enzymes that participate in carbon source assimilation, natural compound biosynthesis and xenobiotic metabolism in all kingdoms of life. P450s can catalyze various reactions by using a wide range of organic compounds, thus exhibiting great potential in biotechnological applications. The catalytic reactions of P450s are driven by electron equivalents that are sourced from pyridine nucleotides and delivered by cognate or matching redox partners (RPs). The electron transfer (ET) route from RPs to P450s involves one or more redox center-containing domains. As the rate of ET is one of the main determinants of P450 efficacy, an in-depth understanding of the P450 ET pathway should increase our knowledge of these important enzymes and benefit their further applications. Here, the various P450 RP systems along with current understanding of their ET routes will be reviewed. Notably, state-of-the-art structural studies of the two main types of self-sufficient P450 will also be summarized.
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Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Hubei Key Laboratory of Industrial Biotechnology School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, P. R. China
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17
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Nguyen KT, Nguyen NL, Milhim M, Nguyen VT, Lai THN, Nguyen HH, Le TTX, Phan TTM, Bernhardt R. Characterization of a thermophilic cytochrome P450 of the CYP203A subfamily from Binh Chau hot spring in Vietnam. FEBS Open Bio 2020; 11:124-132. [PMID: 33176055 PMCID: PMC7780096 DOI: 10.1002/2211-5463.13033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Cytochromes P450 (CYPs or P450s) comprise a superfamily of heme-containing monooxygenases that are involved in a variety of biological processes. CYPs have broad utilities in industry, but most exhibit low thermostability, limiting their use on an industrial scale. Highly thermostable enzymes can be obtained from thermophiles in geothermal areas, including hot springs, offshore oil-producing wells and volcanoes. Here, we report the identification of a gene encoding for a thermophilic CYP from the Binh Chau hot spring metagenomic database, which was designated as P450-T2. The deduced amino acid sequence showed the highest identity of 73.15% with CYP203A1 of Rhodopseudomonas palustris, supporting that P450-T2 is a member of the CYP203A subfamily. Recombinant protein expression yielded 541 nm. The optimal temperature and pH of P450-T2 were 50 °C and 8.0, respectively. The half-life of P450-T2 was 50.2 min at 50 °C, and its melting temperature was 56.80 ± 0.08 °C. It was found to accept electrons from all tested redox partners systems, with BmCPR-Fdx2 being the most effective partner. Screening for putative substrates revealed binding of phenolic compounds, such as l-mimosine and emodin, suggesting a potential application of this new thermophilic P450 in the production of the corresponding hydroxylated products.
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Affiliation(s)
- Kim-Thoa Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc-Lan Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mohammed Milhim
- Department of Biochemistry, Saarland University, Saarbrucken, Germany
| | - Van-Tung Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Hong-Nhung Lai
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huy-Hoang Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Thanh-Xuan Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Tuyet-Minh Phan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrucken, Germany
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18
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Chakrabarty S, Wang Y, Perkins JC, Narayan ARH. Scalable biocatalytic C-H oxyfunctionalization reactions. Chem Soc Rev 2020; 49:8137-8155. [PMID: 32701110 PMCID: PMC8177087 DOI: 10.1039/d0cs00440e] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Catalytic C-H oxyfunctionalization reactions have garnered significant attention in recent years with their ability to streamline synthetic routes toward complex molecules. Consequently, there have been significant strides in the design and development of catalysts that enable diversification through C-H functionalization reactions. Enzymatic C-H oxygenation reactions are often complementary to small molecule based synthetic approaches, providing a powerful tool when deployable on preparative-scale. This review highlights key advances in scalable biocatalytic C-H oxyfunctionalization reactions developed within the past decade.
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Affiliation(s)
- Suman Chakrabarty
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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19
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A Novel Thermostable Cytochrome P450 from Sequence-Based Metagenomics of Binh Chau Hot Spring as a Promising Catalyst for Testosterone Conversion. Catalysts 2020. [DOI: 10.3390/catal10091083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biotechnological applications of cytochromes P450 show difficulties, such as low activity, thermal and/or solvent instability, narrow substrate specificity and redox partner dependence. In an attempt to overcome these limitations, an exploitation of novel thermophilic P450 enzymes from nature via uncultured approaches is desirable due to their great advantages that can resolve nearly all mentioned impediments. From the metagenomics library of the Binh Chau hot spring, an open reading frame (ORF) encoding a thermostable cytochrome P450—designated as P450-T3—which shared 66.6% amino acid sequence identity with CYP109C2 of Sorangium cellulosum So ce56 was selected for further identification and characterization. The ORF was synthesized artificially and heterologously expressed in Escherichia coli C43(DE3) using the pET17b system. The purified enzyme had a molecular weight of approximately 43 kDa. The melting temperature of the purified enzyme was 76.2 °C and its apparent half-life at 60 °C was 38.7 min. Redox partner screening revealed that P450-T3 was reduced well by the mammalian AdR-Adx4-108 and the yeast Arh1-Etp1 redox partners. Lauric acid, palmitic acid, embelin, retinoic acid (all-trans) and retinoic acid (13-cis) demonstrated binding to P450-T3. Interestingly, P450-T3 also bound and converted testosterone. Overall, P450-T3 might become a good candidate for biocatalytic applications on a larger scale.
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20
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Finnigan JD, Young C, Cook DJ, Charnock SJ, Black GW. Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:289-320. [PMID: 32951814 DOI: 10.1016/bs.apcsb.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).
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Affiliation(s)
| | - Carl Young
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | - Darren J Cook
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | | | - Gary W Black
- Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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21
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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22
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Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase. Nat Commun 2020; 11:2676. [PMID: 32472090 PMCID: PMC7260179 DOI: 10.1038/s41467-020-16500-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/07/2020] [Indexed: 01/12/2023] Open
Abstract
Cytochrome P450 monooxygenases are versatile heme-thiolate enzymes that catalyze a wide range of reactions. Self-sufficient cytochrome P450 enzymes contain the redox partners in a single polypeptide chain. Here, we present the crystal structure of full-length CYP116B46, a self-sufficient P450. The continuous polypeptide chain comprises three functional domains, which align well with the direction of electrons traveling from FMN to the heme through the [2Fe-2S] cluster. FMN and the [2Fe-2S] cluster are positioned closely, which facilitates efficient electron shuttling. The edge-to-edge straight-line distance between the [2Fe-2S] cluster and heme is approx. 25.3 Å. The role of several residues located between the [2Fe-2S] cluster and heme in the catalytic reaction is probed in mutagenesis experiments. These findings not only provide insights into the intramolecular electron transfer of self-sufficient P450s, but are also of interest for biotechnological applications of self-sufficient P450s. Self-sufficient cytochrome P450 monooxygenases, which contain all redox partners in a single polypeptide chain, are of interest for biotechnological applications. Here, the authors present the crystal structure of full-length Thermobispora bispora CYP116B46 and discuss the potential electron transfer pathway.
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23
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Luirink RA, Verkade‐Vreeker MCA, Commandeur JNM, Geerke DP. A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion. Chembiochem 2020; 21:1461-1472. [PMID: 31919943 PMCID: PMC7318578 DOI: 10.1002/cbic.201900751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Indexed: 12/21/2022]
Abstract
The regio- (and stereo-)selectivity and specific activity of cytochrome P450s are determined by the accessibility of potential sites of metabolism (SOMs) of the bound substrate relative to the heme, and the activation barrier of the regioselective oxidation reaction(s). The accessibility of potential SOMs depends on the relative binding free energy (ΔΔGbind ) of the catalytically active substrate-binding poses, and the probability of the substrate to adopt a transition-state geometry. An established experimental method to measure activation energies of enzymatic reactions is the analysis of reaction rate constants at different temperatures and the construction of Arrhenius plots. This is a challenge for multistep P450-catalyzed processes that involve redox partners. We introduce a modified Arrhenius approach to overcome the limitations in studying P450 selectivity, which can be applied in multiproduct enzyme catalysis. Our approach gives combined information on relative activation energies, ΔΔGbind values, and collision entropies, yielding direct insight into the basis of selectivity in substrate conversion.
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Affiliation(s)
- Rosa A. Luirink
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | | | - Jan N. M. Commandeur
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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24
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Exploring the Biocatalytic Potential of Fe/α‐Ketoglutarate‐Dependent Halogenases. Chemistry 2020; 26:7336-7345. [DOI: 10.1002/chem.201905752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/18/2022]
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25
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Sheldon RA, Brady D, Bode ML. The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis. Chem Sci 2020; 11:2587-2605. [PMID: 32206264 PMCID: PMC7069372 DOI: 10.1039/c9sc05746c] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
Enzymes are excellent catalysts that are increasingly being used in industry and academia. This perspective is primarily aimed at synthetic organic chemists with limited experience using enzymes and provides a general and practical guide to enzymes and their synthetic potential, with particular focus on recent applications.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
- Department of Biotechnology , Delft University of Technology , Delft , The Netherlands
| | - Dean Brady
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
| | - Moira L Bode
- Molecular Sciences Institute , School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa .
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26
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Crystal structure of bacterial CYP116B5 heme domain: New insights on class VII P450s structural flexibility and peroxygenase activity. Int J Biol Macromol 2019; 140:577-587. [PMID: 31430491 DOI: 10.1016/j.ijbiomac.2019.08.141] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 11/22/2022]
Abstract
Class VII cytochromes P450 are self-sufficient enzymes carrying a phthalate family oxygenase-like reductase domain and a P450 domain fused in a single polypeptide chain. The biocatalytic applications of CYP116B members are limited by the need of the NADPH cofactor and the lack of crystal structures as a starting point for protein engineering. Nevertheless, we demonstrated that the heme domain of CYP116B5 can use hydrogen peroxide as electron donor bypassing the need of NADPH. Here, we report the crystal structure of CYP116B5 heme domain in complex with histidine at 2.6 Å of resolution. The structure reveals the typical P450 fold and a closed conformation with an active site cavity of 284 Å3 in volume, accommodating a histidine molecule forming a hydrogen bond with the water molecule present as 6th heme iron ligand. MD simulations in the absence of any ligand revealed the opening of a tunnel connecting the active site to the protein surface through the movement of F-, G- and H-helices. A structural alignment with bacterial cytochromes P450 allowed the identification of amino acids in the proximal heme site potentially involved in peroxygenase activity. The availability of the crystal structure provides the bases for the structure-guided design of new biocatalysts.
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27
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Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
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28
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Klenk JM, Kontny LH, Escobedo-Hinojosa W, Nebel BA, Hauer B. Oxyfunctionalization of nonsteroidal anti-inflammatory drugs by filamentous-fungi. J Appl Microbiol 2019; 127:724-738. [PMID: 31173436 DOI: 10.1111/jam.14342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/04/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022]
Abstract
AIMS We aimed to expand the microbial biocatalyst platform to generate essential oxyfunctionalized standards for pharmaceutical, toxicological and environmental research. In particular, we examined the production of oxyfunctionalized nonsteroidal anti-inflammatory drugs (NSAIDs) by filamentous-fungi. METHODS AND RESULTS Four NSAIDs; diclofenac, ibuprofen, naproxen and mefenamic acid were used as substrates for oxyfunctionalization in a biocatalytic process involving three filamentous-fungi strains; Beauveria bassiana, Clitocybe nebularis and Mucor hiemalis. Oxyfunctionalized metabolites that are major degradation intermediates formed by Cytochrome P450 monooxygenases in human metabolism were produced in isolated yields of up to 99% using 1 g l-1 of substrate. In addition, a novel compound, 3',4'-dihydroxydiclofenac, was produced by B. bassiana. Proteomic analysis identified CYP548A5 that might be responsible for diclofenac oxyfunctionalization in B. bassiana. CONCLUSIONS Efficient fungi catalysed oxyfunctionalization was achieved when using NSAIDs as substrates. High purities and isolated yields of the produced metabolites were achieved. SIGNIFICANCE AND IMPACT OF THE STUDY The lack of current efficient synthetic strategies for oxyfunctionalization of NSAIDs is a bottleneck to perform pharmacokinetic, pharmacodynamic and toxicological analysis for the pharmaceutical industry. Additionally, oxyfunctionalized derivatives are needed for tracking the fate and impact of such metabolites in the environment. Herein, we described a fungi catalysed process that surpasses previously reported strategies in terms of efficiency, to synthesize oxyfunctionalized NSAIDs.
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Affiliation(s)
- J M Klenk
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - L H Kontny
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - W Escobedo-Hinojosa
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - B A Nebel
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - B Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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29
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Manning J, Tavanti M, Porter JL, Kress N, De Visser SP, Turner NJ, Flitsch SL. Regio‐ and Enantio‐selective Chemo‐enzymatic C−H‐Lactonization of Decanoic Acid to (S)‐δ‐Decalactone. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jack Manning
- Manchester Institute of Biotechnology (MIB)School of ChemistryThe University of Manchester 131 Princess Street M1 7DN Manchester UK
| | - Michele Tavanti
- Manchester Institute of Biotechnology (MIB)School of ChemistryThe University of Manchester 131 Princess Street M1 7DN Manchester UK
| | - Joanne L. Porter
- Manchester Institute of Biotechnology (MIB)School of ChemistryThe University of Manchester 131 Princess Street M1 7DN Manchester UK
| | - Nico Kress
- Manchester Institute of Biotechnology (MIB)School of ChemistryThe University of Manchester 131 Princess Street M1 7DN Manchester UK
| | - Sam P. De Visser
- School of Chemical Engineering and Analytical ScienceThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology (MIB)School of ChemistryThe University of Manchester 131 Princess Street M1 7DN Manchester UK
| | - Sabine L. Flitsch
- Manchester Institute of Biotechnology (MIB)School of ChemistryThe University of Manchester 131 Princess Street M1 7DN Manchester UK
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Manning J, Tavanti M, Porter JL, Kress N, De Visser SP, Turner NJ, Flitsch SL. Regio- and Enantio-selective Chemo-enzymatic C-H-Lactonization of Decanoic Acid to (S)-δ-Decalactone. Angew Chem Int Ed Engl 2019; 58:5668-5671. [PMID: 30861252 DOI: 10.1002/anie.201901242] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 12/18/2022]
Abstract
The conversion of saturated fatty acids to high value chiral hydroxy-acids and lactones poses a number of synthetic challenges: the activation of unreactive C-H bonds and the need for regio- and stereoselectivity. Here the first example of a wild-type cytochrome P450 monooxygenase (CYP116B46 from Tepidiphilus thermophilus) capable of enantio- and regioselective C5 hydroxylation of decanoic acid 1 to (S)-5-hydroxydecanoic acid 2 is reported. Subsequent lactonization yields (S)-δ-decalactone 3, a high value fragrance compound, with greater than 90 % ee. Docking studies provide a rationale for the high regio- and enantioselectivity of the reaction.
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Affiliation(s)
- Jack Manning
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Michele Tavanti
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Joanne L Porter
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Nico Kress
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Sam P De Visser
- School of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Nicholas J Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Sabine L Flitsch
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
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Dangi B, Park H, Oh TJ. Effects of Alternative Redox Partners and Oxidizing Agents on CYP154C8 Catalytic Activity and Product Distribution. Chembiochem 2018; 19:2273-2282. [PMID: 30136363 DOI: 10.1002/cbic.201800284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/23/2018] [Indexed: 12/11/2022]
Abstract
CYP154C8 catalyzes the hydroxylation of diverse steroids, as has previously been demonstrated, by using an NADH-dependent system including putidaredoxin and putidaredoxin reductase as redox partner proteins carrying electrons from NADH. In other reactions, CYP154C8 reconstituted with spinach ferredoxin and NADPH-dependent ferredoxin reductase displayed catalytic activity different from that of the NADH-dependent system. The NADPH-dependent system showed multistep oxidation of progesterone and other substrates including androstenedione, testosterone, and nandrolone. (Diacetoxyiodo)benzene was employed to generate compound I (FeO3+ ), actively supporting the redox reactions catalyzed by CYP154C8. In addition to 16α-hydroxylation, progesterone and 11-oxoprogesterone also underwent hydroxylation at the 6β-position in reactions supported by (diacetoxyiodo)benzene. CYP154C8 was active in the presence of high concentrations (>10 mm) of H2 O2 , with optimum conversion surprisingly being achieved at ≈75 mm H2 O2 . More importantly, H2 O2 tolerance by CYP154C8 was evident in the very low heme oxidation rate constant (K) even at high concentrations of H2 O2 . Our results demonstrate that alternative redox partners and oxidizing agents influence the catalytic efficiency and product distribution of a cytochrome P450 enzyme. More importantly, these choices affected the type and selectivity of reaction catalyzed by the P450 enzyme.
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Affiliation(s)
- Bikash Dangi
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Genome-based BioIT Convergence Institute, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
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Tavanti M, Porter JL, Levy CW, Gómez Castellanos JR, Flitsch SL, Turner NJ. The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s. Biochem Biophys Res Commun 2018; 501:846-850. [PMID: 29738765 DOI: 10.1016/j.bbrc.2018.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023]
Abstract
The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes.
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Affiliation(s)
- Michele Tavanti
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - Joanne L Porter
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - Colin W Levy
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - J Rubén Gómez Castellanos
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Sabine L Flitsch
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom.
| | - Nicholas J Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom.
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Li RJ, Xu JH, Chen Q, Zhao J, Li AT, Yu HL. Enhancing the Catalytic Performance of a CYP116B Monooxygenase by Transdomain Combination Mutagenesis. ChemCatChem 2018. [DOI: 10.1002/cctc.201800054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ren-Jie Li
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jian-He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Qi Chen
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jing Zhao
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin 300308 P.R. China
| | - Ai-Tao Li
- Hubei Collaborative Innovation Center for, Green Transformation of Bio-resources; Hubei Key Laboratory of Industrial Biotechnology; College of Life Sciences; Hubei University; Wuhan 430062 P.R. China
| | - Hui-Lei Yu
- Laboratory of Biocatalysis and Synthetic Biotechnology; State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
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Porter JL, Manning J, Sabatini S, Tavanti M, Turner NJ, Flitsch SL. Characterisation of CYP102A25 fromBacillus marmarensisand CYP102A26 fromPontibacillus halophilus: P450 Homologues of BM3 with Preference towards Hydroxylation of Medium-Chain Fatty Acids. Chembiochem 2018; 19:513-520. [DOI: 10.1002/cbic.201700598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Joanne L. Porter
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Jack Manning
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Selina Sabatini
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Michele Tavanti
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Sabine L. Flitsch
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
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