1
|
Jóźwik IK, Bombino E, Abdulmughni A, Hartz P, Rozeboom HJ, Wijma HJ, Kappl R, Janssen DB, Bernhardt R, Thunnissen AMWH. Regio- and stereoselective steroid hydroxylation by CYP109A2 from Bacillus megaterium explored by X-ray crystallography and computational modeling. FEBS J 2023; 290:5016-5035. [PMID: 37453052 DOI: 10.1111/febs.16906] [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: 12/12/2022] [Revised: 05/31/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
The P450 monooxygenase CYP109A2 from Bacillus megaterium DSM319 was previously found to convert vitamin D3 (VD3) to 25-hydroxyvitamin D3. Here, we show that this enzyme is also able to convert testosterone in a highly regio- and stereoselective manner to 16β-hydroxytestosterone. To reveal the structural determinants governing the regio- and stereoselective steroid hydroxylation reactions catalyzed by CYP109A2, two crystal structures of CYP109A2 were solved in similar closed conformations, one revealing a bound testosterone in the active site pocket, albeit at a nonproductive site away from the heme-iron. To examine whether the closed crystal structures nevertheless correspond to a reactive conformation of CYP109A2, docking and molecular dynamics (MD) simulations were performed with testosterone and vitamin D3 (VD3) present in the active site. These MD simulations were analyzed for catalytically productive conformations, the relative occurrences of which were in agreement with the experimentally determined stereoselectivities if the predicted stability of each carbon-hydrogen bond was taken into account. Overall, the first-time determination and analysis of the catalytically relevant 3D conformation of CYP109A2 will allow for future small molecule ligand screening in silico, as well as enabling site-directed mutagenesis toward improved enzymatic properties of this enzyme.
Collapse
Affiliation(s)
- Ilona K Jóźwik
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Elvira Bombino
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Ammar Abdulmughni
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Philip Hartz
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Henriette J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Reinhard Kappl
- Department of Biophysics, CIPMM, School of Medicine, Saarland University, Saarbrücken, Germany
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Andy-Mark W H Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| |
Collapse
|
2
|
Bahramian Nasab S, Homaei A, Fernandez-Lafuente R, Del Arco J, Fernández-Lucas J. A Novel, Highly Potent NADPH-Dependent Cytochrome P450 Reductase from Waste Liza klunzingeri Liver. Mar Drugs 2023; 21:md21020099. [PMID: 36827140 PMCID: PMC9964268 DOI: 10.3390/md21020099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
The use of marine enzymes as catalysts for biotechnological applications is a topical subject. Marine enzymes usually display better operational properties than their animal, plant or bacterial counterparts, enlarging the range of possible biotechnological applications. Due to the fact that cytochrome P450 enzymes can degrade many different toxic environmental compounds, these enzymes have emerged as valuable tools in bioremediation processes. The present work describes the isolation, purification and biochemical characterization of a liver NADPH-dependent cytochrome P450 reductase (CPR) from the marine fish Liza klunzingeri (LkCPR). Experimental results revealed that LkCPR is a monomer of approximately 75 kDa that is active in a wide range of pH values (6-9) and temperatures (40-60 °C), showing the highest catalytic activity at pH 8 and 50 °C. The activation energy of the enzyme reaction was 16.3 kcal mol-1 K-1. The KM values for cytochrome C and NADPH were 8.83 μM and 7.26 μM, and the kcat values were 206.79 s-1 and 202.93 s-1, respectively. LkCPR displayed a specific activity versus cytochrome C of 402.07 µmol min-1 mg1, the highest activity value described for a CPR up to date (3.2-4.7 times higher than the most active reported CPRs) and showed the highest thermostability described for a CPR. Taking into account all these remarkable catalytic features, LkCPR offers great potential to be used as a suitable biocatalyst.
Collapse
Affiliation(s)
- Soudeh Bahramian Nasab
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas P.O. Box 3995, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas P.O. Box 3995, Iran
- Correspondence:
| | | | - Jon Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid Urbanización El Bosque, E-28670 Villaviciosa de Odón, 28670 Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid Urbanización El Bosque, E-28670 Villaviciosa de Odón, 28670 Madrid, Spain
- Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, Barranquilla 080002, Colombia
| |
Collapse
|
3
|
Thomson RES, D'Cunha SA, Hayes MA, Gillam EMJ. Use of engineered cytochromes P450 for accelerating drug discovery and development. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:195-252. [PMID: 35953156 DOI: 10.1016/bs.apha.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.
Collapse
Affiliation(s)
- Raine E S Thomson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephlina A D'Cunha
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D AstraZeneca, Mölndal, Sweden
| | - Elizabeth M J Gillam
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Adam S, Franz L, Milhim M, Bernhardt R, Kalinina OV, Koehnke J. Characterization of the Stereoselective P450 Enzyme BotCYP Enables the In Vitro Biosynthesis of the Bottromycin Core Scaffold. J Am Chem Soc 2020; 142:20560-20565. [PMID: 33249843 DOI: 10.1021/jacs.0c10361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bottromycins are ribosomally synthesized and post-translationally modified peptide natural product antibiotics that are effective against high-priority human pathogens such as methicillin-resistant Staphylococcus aureus. The total synthesis of bottromycins involves at least 17 steps, with a poor overall yield. Here, we report the characterization of the cytochrome P450 enzyme BotCYP from a bottromycin biosynthetic gene cluster. We determined the structure of a close BotCYP homolog and used our data to conduct the first large-scale survey of P450 enzymes associated with RiPP biosynthetic gene clusters. We demonstrate that BotCYP converts a C-terminal thiazoline to a thiazole via an oxidative decarboxylation reaction and provides stereochemical resolution for the pathway. Our data enable the two-pot in vitro production of the bottromycin core scaffold and may allow the rapid generation of bottromycin analogues for compound development.
Collapse
Affiliation(s)
- Sebastian Adam
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
| | - Laura Franz
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
| | - Mohammed Milhim
- Department of Biochemistry, Saarland University, Campus Geb. B2.2, 66123 Saarbrücken, Germany
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Campus Geb. B2.2, 66123 Saarbrücken, Germany
| | - Olga V Kalinina
- Research Group Drug Bioinformatics, HIPS, HZI, 66123 Saarbrücken, Germany.,Faculty of Medicine, Saarland University, 66424 Homburg, Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany.,School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis. Sci Rep 2019; 9:20088. [PMID: 31882753 PMCID: PMC6934812 DOI: 10.1038/s41598-019-56516-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022] Open
Abstract
Cytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called “uncoupling”, whereby NAD(P)H derived electrons are lost due to the reduced intermediates’ (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2–22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.
Collapse
|
8
|
Ebrecht AC, van der Bergh N, Harrison STL, Smit MS, Sewell BT, Opperman DJ. Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis. Sci Rep 2019; 9:20088. [PMID: 31882753 DOI: 10.1101/711317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/04/2019] [Indexed: 05/28/2023] Open
Abstract
Cytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called "uncoupling", whereby NAD(P)H derived electrons are lost due to the reduced intermediates' (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2-22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.
Collapse
Affiliation(s)
- Ana C Ebrecht
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Naadia van der Bergh
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Martha S Smit
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7700, South Africa.
| | - Diederik J Opperman
- Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa.
- South African DST-NRF Centre of Excellence in Catalysis (c*Change), University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
| |
Collapse
|
9
|
Expanding the promoter toolbox of Bacillus megaterium. J Biotechnol 2019; 294:38-48. [DOI: 10.1016/j.jbiotec.2019.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 02/02/2023]
|
10
|
Molecular mechanism of metabolic NAD(P)H-dependent electron-transfer systems: The role of redox cofactors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:233-258. [PMID: 30419202 DOI: 10.1016/j.bbabio.2018.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 12/14/2022]
Abstract
NAD(P)H-dependent electron-transfer (ET) systems require three functional components: a flavin-containing NAD(P)H-dehydrogenase, one-electron carrier and metal-containing redox center. In principle, these ET systems consist of one-, two- and three-components, and the electron flux from pyridine nucleotide cofactors, NADPH or NADH to final electron acceptor follows a linear pathway: NAD(P)H → flavin → one-electron carrier → metal containing redox center. In each step ET is primarily controlled by one- and two-electron midpoint reduction potentials of protein-bound redox cofactors in which the redox-linked conformational changes during the catalytic cycle are required for the domain-domain interactions. These interactions play an effective ET reactions in the multi-component ET systems. The microsomal and mitochondrial cytochrome P450 (cyt P450) ET systems, nitric oxide synthase (NOS) isozymes, cytochrome b5 (cyt b5) ET systems and methionine synthase (MS) ET system include a combination of multi-domain, and their organizations display similarities as well as differences in their components. However, these ET systems are sharing of a similar mechanism. More recent structural information obtained by X-ray and cryo-electron microscopy (cryo-EM) analysis provides more detail for the mechanisms associated with multi-domain ET systems. Therefore, this review summarizes the roles of redox cofactors in the metabolic ET systems on the basis of one-electron redox potentials. In final Section, evolutionary aspects of NAD(P)H-dependent multi-domain ET systems will be discussed.
Collapse
|
11
|
Binding modes of CYP106A2 redox partners determine differences in progesterone hydroxylation product patterns. Commun Biol 2018; 1:99. [PMID: 30271979 PMCID: PMC6123783 DOI: 10.1038/s42003-018-0104-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/27/2018] [Indexed: 11/17/2022] Open
Abstract
Natural redox partners of bacterial cytochrome P450s (P450s) are mostly unknown. Therefore, substrate conversions are performed with heterologous redox partners; in the case of CYP106A2 from Bacillus megaterium ATCC 13368, bovine adrenodoxin (Adx) and adrenodoxin reductase (AdR). Our aim was to optimize the redox system for CYP106A2 for improved product formation by testing 11 different combinations of redox partners. We found that electron transfer protein 1(516–618) showed the highest yield of the main product, 15β-hydroxyprogesterone, and, furthermore, produced a reduced amount of unwanted polyhydroxylated side products. Molecular protein–protein docking indicated that this is caused by subtle structural changes leading to alternative binding modes of both redox enzymes. Stopped-flow measurements analyzing the CYP106A2 reduction and showing substantial differences in the apparent rate constants supported this conclusion. The study provides for the first time to our knowledge rational explanations for differences in product patterns of a cytochrome P450 caused by difference in the binding mode of the redox partners. Tanja Sagadin et al. show that different redox systems can be used to tune the rate selectivity and yield of progesterone conversion by the cytochrome P450 CYP106A2. They screen 11 redox partner combinations and identify specific combinations that may be used to improve biotechnological production of mono- and polyhydroxylated products.
Collapse
|
12
|
Abdulmughni A, Jóźwik IK, Brill E, Hannemann F, Thunnissen AMWH, Bernhardt R. Biochemical and structural characterization of CYP109A2, a vitamin D 3 25-hydroxylase from Bacillus megaterium. FEBS J 2017; 284:3881-3894. [PMID: 28940959 DOI: 10.1111/febs.14276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/07/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022]
Abstract
Cytochrome P450 enzymes are increasingly investigated due to their potential application as biocatalysts with high regio- and/or stereo-selectivity and under mild conditions. Vitamin D3 (VD3 ) metabolites are of pharmaceutical importance and are applied for the treatment of VD3 deficiency and other disorders. However, the chemical synthesis of VD3 derivatives shows low specificity and low yields. In this study, cytochrome P450 CYP109A2 from Bacillus megaterium DSM319 was expressed, purified, and shown to oxidize VD3 with high regio-selectivity. The in vitro conversion, using cytochrome P450 reductase (BmCPR) and ferredoxin (Fdx2) from the same strain, showed typical Michaelis-Menten reaction kinetics. A whole-cell system in B. megaterium overexpressing CYP109A2 reached 76 ± 5% conversion after 24 h and allowed to identify the main product by NMR analysis as 25-hydroxylated VD3 . Product yield amounted to 54.9 mg·L-1 ·day-1 , rendering the established whole-cell system as a highly promising biocatalytic route for the production of this valuable metabolite. The crystal structure of substrate-free CYP109A2 was determined at 2.7 Å resolution, displaying an open conformation. Structural analysis predicts that CYP109A2 uses a highly similar set of residues for VD3 binding as the related VD3 hydroxylases CYP109E1 from B. megaterium and CYP107BR1 (Vdh) from Pseudonocardia autotrophica. However, the folds and sequences of the BC loops in these three P450s are highly divergent, leading to differences in the shape and apolar/polar surface distribution of their active site pockets, which may account for the observed differences in substrate specificity and the regio-selectivity of VD3 hydroxylation. DATABASE The atomic coordinates and structure factors have been deposited in the Protein Data Bank with accession code 5OFQ (substrate-free CYP109A2). ENZYMES Cytochrome P450 monooxygenase CYP109A2, EC 1.14.14.1, UniProt ID: D5DF88, Ferredoxin, UniProt ID: D5DFQ0, cytochrome P450 reductase, EC 1.8.1.2, UniProt ID: D5DGX1.
Collapse
Affiliation(s)
- Ammar Abdulmughni
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Ilona K Jóźwik
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Elisa Brill
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Frank Hannemann
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Andy-Mark W H Thunnissen
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| |
Collapse
|
13
|
Harris KL, Thomson RES, Strohmaier SJ, Gumulya Y, Gillam EMJ. Determinants of thermostability in the cytochrome P450 fold. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:97-115. [PMID: 28822812 DOI: 10.1016/j.bbapap.2017.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/19/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
Cytochromes P450 are found throughout the biosphere in a wide range of environments, serving a multitude of physiological functions. The ubiquity of the P450 fold suggests that it has been co-opted by evolution many times, and likely presents a useful compromise between structural stability and conformational flexibility. The diversity of substrates metabolized and reactions catalyzed by P450s makes them attractive starting materials for use as biocatalysts of commercially useful reactions. However, process conditions impose different requirements on enzymes to those in which they have evolved naturally. Most natural environments are relatively mild, and therefore most P450s have not been selected in Nature for the ability to withstand temperatures above ~40°C, yet industrial processes frequently require extended incubations at much higher temperatures. Thus, there has been considerable interest and effort invested in finding or engineering thermostable P450 systems. Numerous P450s have now been identified in thermophilic organisms and analysis of their structures provides information as to mechanisms by which the P450 fold can be stabilized. In addition, protein engineering, particularly by directed or artificial evolution, has revealed mutations that serve to stabilize particular mesophilic enzymes of interest. Here we review the current understanding of thermostability as it applies to the P450 fold, gleaned from the analysis of P450s characterized from thermophilic organisms and the parallel engineering of mesophilic forms for greater thermostability. We then present a perspective on how this information might be used to design stable P450 enzymes for industrial application. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
Collapse
Affiliation(s)
- Kurt L Harris
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Silja J Strohmaier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia.
| |
Collapse
|
14
|
Genome shuffling of Colletotrichum lini for improving 3β,7α,15α-trihydroxy-5-androsten-17-one production from dehydroepiandrosterone. ACTA ACUST UNITED AC 2017; 44:937-947. [DOI: 10.1007/s10295-017-1918-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 02/05/2017] [Indexed: 10/20/2022]
Abstract
Abstract
3β,7α,15α-Trihydroxy-5-androsten-17-one (7α,15α-diOH-DHEA) is a key intermediate of the novel oral contraceptive Yasmin. It can be catalyzed from dehydroepiandrosterone (DHEA) through Colletotrichum lini. Improvement of 7α,15α-diOH-DHEA production was performed through recursive protoplast fusion of C. lini ST in a genome shuffling format. 7α,15α-diOH-DHEA yield of the best performing recombinant C. lini ST-F307 reached 6.08 g/L from 10 g/L DHEA, and this was 94.9% higher than that of the initial C. lini ST strain. Through optimized conditions, the 7α,15α-diOH-DHEA yield was increased to 9.32 g/L from 12 g/L DHEA, with 1.5% ethanol as cosolvent. This is the highest reported substrate concentration and 7α,15α-diOH-DHEA production with one-step substrate addition. Moreover, C. lini ST-F307 showed high P450 enzyme activity and gene transcript levels of several cytochrome P450s, and this might contribute to the enhancement of 7α,15α-diOH-DHEA production. Genome shuffling was an efficient approach to breed high-yield strains.
Collapse
|
15
|
Khatri Y, Schifrin A, Bernhardt R. Investigating the effect of available redox protein ratios for the conversion of a steroid by a myxobacterial CYP260A1. FEBS Lett 2017; 591:1126-1140. [PMID: 28281299 DOI: 10.1002/1873-3468.12619] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 11/11/2022]
Abstract
Since cytochromes P450 are external monooxygenases, available surrogate redox partners have been used to reconstitute the P450 activity. However, the effect of various ratios of P450s and the redox proteins have not been extensively studied so far, although different combinations of the redox partners have shown variations in substrate conversion. To address this issue, CYP260A1 was reconstituted with various ratios of adrenodoxin and adrenodoxin reductase to convert 11-deoxycorticosterone, and the products were characterized by NMR. We show the effect of the available redox protein ratios not only on the P450 catalytic activity but also on the product pattern.
Collapse
Affiliation(s)
- Yogan Khatri
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | | | - Rita Bernhardt
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| |
Collapse
|
16
|
Milhim M, Putkaradze N, Abdulmughni A, Kern F, Hartz P, Bernhardt R. Identification of a new plasmid-encoded cytochrome P450 CYP107DY1 from Bacillus megaterium with a catalytic activity towards mevastatin. J Biotechnol 2016; 240:68-75. [DOI: 10.1016/j.jbiotec.2016.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 11/26/2022]
|