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Doğru EK, Sakallı T, Liu G, Sayers Z, Surmeli NB. Small angle X-ray scattering analysis of thermophilic cytochrome P450 CYP119 and the effects of the N-terminal histidine tag. Int J Biol Macromol 2024; 265:131026. [PMID: 38522710 DOI: 10.1016/j.ijbiomac.2024.131026] [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: 01/11/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Combining size exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and molecular dynamics (MD) analysis is a promising approach to investigate protein behavior in solution, particularly for understanding conformational changes due to substrate binding in cytochrome P450s (CYPs). This study investigates conformational changes in CYP119, a thermophilic CYP from Sulfolobus acidocaldarius that exhibits structural flexibility similar to mammalian CYPs. Although the crystal structure of ligand-free (open state) and ligand-bound (closed state) forms of CYP119 is known, the overall structure of the enzyme in solution has not been explored until now. It was found that theoretical scattering profiles from the crystal structures of CYP119 did not align with the SAXS data, but conformers from MD simulations, particularly starting from the open state (46 % of all frames), agreed well. Interestingly, a small percentage of closed-state conformers also fit the data (9 %), suggesting ligand-free CYP119 samples ligand-bound conformations. Ab initio SAXS models for N-His tagged CYP119 revealed a tail-like unfolded structure impacting protein flexibility, which was confirmed by in silico modeling. SEC-SAXS analysis of N-His CYP119 indicated pentameric structures in addition to monomers in solution, affecting the stability and activity of the enzyme. This study adds insights into the conformational dynamics of CYP119 in solution.
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Affiliation(s)
- Ekin Kestevur Doğru
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Tuğçe Sakallı
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Goksin Liu
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Zehra Sayers
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Nur Basak Surmeli
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye.
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2
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Peidro-Guzmán H, Pérez-Llano Y, González-Abradelo D, Fernández-López MG, Dávila-Ramos S, Aranda E, Hernández DRO, García AO, Lira-Ruan V, Pliego OR, Santana MA, Schnabel D, Jiménez-Gómez I, Mouriño-Pérez RR, Aréchiga-Carvajal ET, Del Rayo Sánchez-Carbente M, Folch-Mallol JL, Sánchez-Reyes A, Vaidyanathan VK, Cabana H, Gunde-Cimerman N, Batista-García RA. Transcriptomic analysis of polyaromatic hydrocarbon degradation by the halophilic fungus Aspergillus sydowii at hypersaline conditions. Environ Microbiol 2020; 23:3435-3459. [PMID: 32666586 DOI: 10.1111/1462-2920.15166] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/11/2020] [Accepted: 07/12/2020] [Indexed: 01/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are among the most persistent xenobiotic compounds, with high toxicity effects. Mycoremediation with halophilic Aspergillus sydowii was used for their removal from a hypersaline medium (1 M NaCl). A. sydowii metabolized PAHs as sole carbon sources, resulting in the removal of up to 90% for both PAHs [benzo [a] pyrene (BaP) and phenanthrene (Phe)] after 10 days. Elimination of Phe and BaP was almost exclusively due to biotransformation and not adsorption by dead mycelium and did not correlate with the activity of lignin modifying enzymes (LME). Transcriptomes of A. sydowii grown on PAHs, or on glucose as control, both at hypersaline conditions, revealed 170 upregulated and 76 downregulated genes. Upregulated genes were related to starvation, cell wall remodelling, degradation and metabolism of xenobiotics, DNA/RNA metabolism, energy generation, signalling and general stress responses. Changes of LME expression levels were not detected, while the chloroperoxidase gene, possibly related to detoxification processes in fungi, was strongly upregulated. We propose that two parallel metabolic pathways (mitochondrial and cytosolic) are involved in degradation and detoxification of PAHs in A. sydowii resulting in intracellular oxidation of PAHs. To the best of our knowledge, this is the most comprehensive transcriptomic analysis on fungal degradation of PAHs.
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Affiliation(s)
- Heidy Peidro-Guzmán
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Yordanis Pérez-Llano
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Deborah González-Abradelo
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Maikel Gilberto Fernández-López
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Elisabet Aranda
- Instituto Universitario de Investigación del Agua, Universidad de Granada, Granada, Spain
| | | | - Angélica Ortega García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Verónica Lira-Ruan
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Oscar Ramírez Pliego
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - María Angélica Santana
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Denhi Schnabel
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Irina Jiménez-Gómez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Rosa R Mouriño-Pérez
- Centro de Investigación Cientifica y Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Elva T Aréchiga-Carvajal
- Facultad de Ciencias Biológicas, Unidad de Manipulación Genética, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | | | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Ayixon Sánchez-Reyes
- Cátedras Conacyt - Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Hubert Cabana
- Faculté de Genié, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Nina Gunde-Cimerman
- Departament of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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3
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Petrović D, Bokel A, Allan M, Urlacher VB, Strodel B. Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation. J Chem Inf Model 2018. [PMID: 29522682 DOI: 10.1021/acs.jcim.8b00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Engineering high chemo-, regio-, and stereoselectivity is a prerequisite for enzyme usage in organic synthesis. Cytochromes P450 can oxidize a broad range of substrates, including macrocycles, which are becoming popular scaffolds for therapeutic agents. However, a large conformational space explored by macrocycles not only reduces the selectivity of oxidation but also impairs computational enzyme design strategies based on docking and molecular dynamics (MD) simulations. We present a novel design workflow that uses enhanced-sampling Hamiltonian replica exchange (HREX) MD and focuses on quantifying the substrate binding for suggesting the mutations to be made. This computational approach is applied to P450 BM3 with the aim to shift regioselectively toward one of the numerous possible positions during β-cembrenediol oxidation. The predictions are experimentally tested and the resulting product distributions validate our design strategy, as single mutations led up to 5-fold regioselectivity increases. We thus conclude that the HREX-MD-based workflow is a promising tool for the identification of positions for mutagenesis aiming at P450 enzymes with improved regioselectivity.
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Affiliation(s)
- Dušan Petrović
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Ansgar Bokel
- Institute of Biochemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
| | - Matthew Allan
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany.,Schreyer Honors College , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Vlada B Urlacher
- Institute of Biochemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätsstraße 1 , 40225 Düsseldorf , Germany
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4
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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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5
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Ponzone C, Berlanda D, Donzelli F, Acquati V, Ciulla R, Negrini A, Rovati M, Evangelista D, Fata E, Ciceri D, Perterlongo F, Cabri W. Biotransformation of colchicinoids into their corresponding 3-O-glucosyl derivatives by selected strains of Bacillus megaterium. Mol Biotechnol 2014; 56:653-9. [PMID: 24553816 DOI: 10.1007/s12033-014-9741-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Natural colchicinoids and their semisynthetic derivatives are important active ingredients for pharmaceutical applications. Thiocolchicoside (3-demethoxy-3-glucosyloxythiocolchicine) is used in several countries as standard therapy for the treatment of diseases of the muscle-skeletal system, due to its potent antiinflammatory and myorelaxant properties. Manufacturing of thiocolchicoside requires a key step, the regioselective demethylation and glucosylation of chemically derivative thiocolchicine. High selectivity and efficiency of this transformation cannot be achieved in a satisfactory way with a chemical approach. In particular, the chemical demethylation, a part from requiring toxic and aggressive reagents, generates a complex mixture of products with no industrial usefulness. We report herein an efficient, direct and green biotransformation of thiocolchicine into thiocolchicoside, performed by a specific strain of Bacillus megaterium. The same process, with minor modifications, can be used to convert the by-product 3-O-demethyl-thiocolchicine into thiocolchicoside. In addition, we describe the B. megaterium strain selection process and the best conditions for this effective double biotransformation. The final product has a pharmaceutical quality, and the process has been industrialised.
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Affiliation(s)
- Cesare Ponzone
- Indena S.p.A., Via Don Minzoni, 6, Settala, 20090, Milan, Italy,
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6
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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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7
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Enhanced bioconversion of colchicine to regiospecific 3-demethylated colchicine (3-DMC) by whole cell immobilization of recombinant E. coli harboring P450 BM-3 gene. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:205-20. [DOI: 10.1016/j.bbapap.2012.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 01/11/2023]
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9
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Barry SM, Challis GL. Tailoring reactions catalyzed by heme-dependent enzymes: spectroscopic characterization of the L-tryptophan-nitrating cytochrome P450 TxtE. Methods Enzymol 2012; 516:171-94. [PMID: 23034229 DOI: 10.1016/b978-0-12-394291-3.00001-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
There is a truly vast quantity of research articles and textbooks, aimed at a variety of audiences, on cytochromes P450. However, a large amount of specialized terminology has become associated with these enzymes, which can be daunting to those new to the field. The aim of this chapter is to give a brief overview of the functions and importance of cytochromes P450 with particular emphasis on their roles as tailoring enzymes in natural product biosynthetic pathways. Differences between the biosynthetic enzymes and their catabolic counterparts are highlighted. Assays used to investigate substrate binding to cytochromes P450 are described using TxtE, a recently discovered unique nitrating enzyme involved in thaxtomin A biosynthesis, as an example.
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Affiliation(s)
- Sarah M Barry
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
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10
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Dubey KK, Jawed A, Haque S. Structural and metabolic correlation for Bacillus megaterium ACBT03 in response to colchicine biotransformation. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711060099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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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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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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Statistical optimization of process variables for the production of an anticancer drug (colchicine derivatives) through fermentation: at scale-up level. N Biotechnol 2011; 28:79-85. [DOI: 10.1016/j.nbt.2010.07.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 06/10/2010] [Accepted: 07/09/2010] [Indexed: 11/15/2022]
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14
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Whitehouse CJC, Yang W, Yorke JA, Rowlatt BC, Strong AJF, Blanford CF, Bell SG, Bartlam M, Wong LL, Rao Z. Structural Basis for the Properties of Two Single-Site Proline Mutants of CYP102A1 (P450BM3). Chembiochem 2010; 11:2549-56. [DOI: 10.1002/cbic.201000421] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Construction of recombinant Escherichia coli for enhanced bioconversion of colchicine into 3-demethylated colchicine at 70l bioreactor level. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Dubey KK, Ray A, Behera B. Production of demethylated colchicine through microbial transformation and scale-up process development. Process Biochem 2008. [DOI: 10.1016/j.procbio.2007.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Tishkov VI, Popov VO. Protein engineering of formate dehydrogenase. ACTA ACUST UNITED AC 2006; 23:89-110. [PMID: 16546445 DOI: 10.1016/j.bioeng.2006.02.003] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 02/03/2006] [Accepted: 02/06/2006] [Indexed: 11/24/2022]
Abstract
NAD+-dependent formate dehydrogenase (FDH, EC 1.2.1.2) is one of the best enzymes for the purpose of NADH regeneration in dehydrogenase-based synthesis of optically active compounds. Low operational stability and high production cost of native FDHs limit their application in commercial production of chiral compounds. The review summarizes the results on engineering of bacterial and yeast FDHs aimed at improving their chemical and thermal stability, catalytic activity, switch in coenzyme specificity from NAD+ to NADP+ and overexpression in Escherichia coli cells.
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Affiliation(s)
- Vladimir I Tishkov
- Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119992, Russia.
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