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Padayachee T, Lamb DC, Nelson DR, Syed K. Structure-Function Analysis of the Biotechnologically Important Cytochrome P450 107 (CYP107) Enzyme Family. Biomolecules 2023; 13:1733. [PMID: 38136604 PMCID: PMC10741444 DOI: 10.3390/biom13121733] [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: 11/03/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs; P450s) are a superfamily of heme-containing enzymes that are recognized for their vast substrate range and oxidative multifunctionality. CYP107 family members perform hydroxylation and epoxidation processes, producing a variety of biotechnologically useful secondary metabolites. Despite their biotechnological importance, a thorough examination of CYP107 protein structures regarding active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 44 CYP107 crystal structures were investigated in this study. We demonstrate that the CYP107 active site cavity is very flexible, with ligand binding reducing the volume of the active site in some situations and increasing volume size in other instances. Polar interactions between the substrate and active site residues result in crucial salt bridges and the formation of proton shuttling pathways. Hydrophobic interactions, however, anchor the substrate within the active site. The amino acid residues within the binding pocket influence substrate orientation and anchoring, determining the position of the hydroxylation site and hence direct CYP107's catalytic activity. Additionally, the amino acid dynamics within and around the binding pocket determine CYP107's multifunctionality. This study serves as a reference for understanding the structure-function analysis of CYP107 family members precisely and the structure-function analysis of P450 enzymes in general. Finally, this work will aid in the genetic engineering of CYP107 enzymes to produce novel molecules of biotechnological interest.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
| | - David C. Lamb
- Faculty of Medicine, Health and Life Sciences, Swansea University, Swansea SA2 8PP, UK;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
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2
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [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: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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3
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Enyoh CE, Wang Q, Ovuoraye PE, Maduka TO. Toxicity evaluation of microplastics to aquatic organisms through molecular simulations and fractional factorial designs. CHEMOSPHERE 2022; 308:136342. [PMID: 36087717 DOI: 10.1016/j.chemosphere.2022.136342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Molecular docking, molecular dynamics modelling, and fractional factorial design methodologies were used in the current work to examine the harmful effects of ten microplastic (MPs) such as polystyrene (PS), polyvinylchloride (PVC), polyurethane (PU), polymethyl methacrylate (PMMA), polyamide (PA), polyethylene terephthalate (PET), polyethylene (PE), polypropylene (PP), polychloropene (PCP) and polycarbonate (PC) on the aquatic organism (zebrafish). The toxicity was evaluated based on the docking of the MPs on cytochrome P450 (CYP P450) protein crystals. The binding affinities (ΔG) followed the order, PC (-6.9 kcal/mol) > PET (-6.1 kcal/mol) > PP (-5.8 kcal/mol) > PA (-5.6 kcal/mol) > PS (-5.1 kcal/mol) > PU (-4.1 kcal/mol) > PMMA (-3.9 kcal/mol) > PCP (-3.3 kcal/mol) > PVC (-2.4 kcal/mol) > PE (-2.1 kcal/mol). The primary driving factors for the binding of the MPs and the protein were hydrophobic force, and hydrogen bonding based on the molecular dynamics analysis and surrounding amino acid residues. Furthermore, a 210-5 fractional factorial design method was estimated to identify the main effect and second-order effects of MPs in a composite contamination system on binding affinity/energy to CYP450 receptor protein of zebrafish, combined with a fixed effects model. The findings showed that different MPs combinations had varying impacts on aquatic toxicity; as a consequence, the best combination of MPs with the lowest aquatic toxicity effect could be excluded. The factorial designs showed that the PU-PS and PP-PA combination and single PCP, has the most significant main effect on CYP450 receptor protein of zebrafish which translates to an optimum toxicity level of -4.61 kcal/mol. The investigation offers a theoretical foundation for identifying the hazardous impacts of MPs on aquatic life.
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Affiliation(s)
- Christian Ebere Enyoh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
| | - Qingyue Wang
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Prosper E Ovuoraye
- Department of Chemical Engineering, Federal University of Petroleum Resources, PMB 1221, Effurun, Nigeria
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4
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Takahashi S. Studies on Streptomyces sp. SN-593: reveromycin biosynthesis, β-carboline biomediator activating LuxR family regulator, and construction of terpenoid biosynthetic platform. J Antibiot (Tokyo) 2022; 75:432-444. [PMID: 35778609 DOI: 10.1038/s41429-022-00539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces represents an important reservoir for biologically active natural products. Understanding the biosynthetic mechanism and the mode of gene expression is important for enhanced metabolite production and evaluation of biological activities. This review provides an overview of biosynthetic studies investigating reveromycin and β-carboline biomediators that enhanced the production of reveromycin in Streptomyces sp. SN-593 through activation of the LuxR family regulator. Furthermore, based on the optimal expression of a pathway specific regulator controlling the mevalonate pathway gene cluster, Streptomyces sp. SN-593 was developed as a platform for terpenoid compounds mass production.
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Affiliation(s)
- Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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5
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Zhang L, Wang Q. Harnessing P450 Enzyme for Biotechnology and Synthetic Biology. Chembiochem 2021; 23:e202100439. [PMID: 34542923 DOI: 10.1002/cbic.202100439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/18/2021] [Indexed: 12/29/2022]
Abstract
Cytochrome P450 enzymes (P450s, CYPs) catalyze the oxidative transformation of a wide range of organic substrates. Their functions are crucial to xenobiotic metabolism and steroid transformation in humans and other organisms. The enzymes are promising for synthetic biology applications but limited by several drawbacks including low turnover rates, poor stability, the dependance of expensive cofactors and redox partners, and the narrow substrate scope. To conquer these obstacles, emerging strategies including substrate engineering, usage of decoy and decoy-based small molecules auxiliaries, designing of artificial enzyme cascades and the incorporation of materials have been explored based on the unique properties of P450s. These strategies can be applied to a wide range of P450s and can be combined with protein engineering to improve the enzymatic activities. This minireview will focus on some recent developments of these strategies which have been used to leverage P450 catalysis. Remaining challenges and future opportunities will also be discussed.
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Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.,Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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6
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Chen B, Luo S, Zhang S, Ju Y, Gu Q, Xu J, Yang XL, Zhou H. Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase. Nat Commun 2021; 12:1616. [PMID: 33712620 PMCID: PMC7955072 DOI: 10.1038/s41467-021-21902-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023] Open
Abstract
The polyketide natural product reveromycin A (RM-A) exhibits antifungal, anticancer, anti-bone metastasis, anti-periodontitis and anti-osteoporosis activities by selectively inhibiting eukaryotic cytoplasmic isoleucyl-tRNA synthetase (IleRS). Herein, a co-crystal structure suggests that the RM-A molecule occupies the substrate tRNAIle binding site of Saccharomyces cerevisiae IleRS (ScIleRS), by partially mimicking the binding of tRNAIle. RM-A binding is facilitated by the copurified intermediate product isoleucyl-adenylate (Ile-AMP). The binding assays confirm that RM-A competes with tRNAIle while binding synergistically with L-isoleucine or intermediate analogue Ile-AMS to the aminoacylation pocket of ScIleRS. This study highlights that the vast tRNA binding site of the Rossmann-fold catalytic domain of class I aminoacyl-tRNA synthetases could be targeted by a small molecule. This finding will inform future rational drug design.
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Affiliation(s)
- Bingyi Chen
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China ,grid.12981.330000 0001 2360 039XResearch Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China
| | - Siting Luo
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China ,grid.12981.330000 0001 2360 039XResearch Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China
| | - Songxuan Zhang
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China ,grid.12981.330000 0001 2360 039XResearch Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China
| | - Yingchen Ju
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China ,grid.12981.330000 0001 2360 039XResearch Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China
| | - Qiong Gu
- grid.12981.330000 0001 2360 039XResearch Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China
| | - Jun Xu
- grid.12981.330000 0001 2360 039XResearch Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China
| | - Xiang-Lei Yang
- grid.214007.00000000122199231Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037 USA
| | - Huihao Zhou
- grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China ,grid.12981.330000 0001 2360 039XResearch Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006 China
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7
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Sun G, Hu C, Mei Q, Luo M, Chen X, Li Z, Liu Y, Deng Z, Zhang Z, Sun Y. Uncovering the cytochrome P450-catalyzed methylenedioxy bridge formation in streptovaricins biosynthesis. Nat Commun 2020; 11:4501. [PMID: 32908132 PMCID: PMC7481197 DOI: 10.1038/s41467-020-18336-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
Streptovaricin C is a naphthalenic ansamycin antibiotic structurally similar to rifamycins with potential anti-MRSA bioactivities. However, the formation mechanism of the most fascinating and bioactivity-related methylenedioxy bridge (MDB) moiety in streptovaricins is unclear. Based on genetic and biochemical evidences, we herein clarify that the P450 enzyme StvP2 catalyzes the MDB formation in streptovaricins, with an atypical substrate inhibition kinetics. Furthermore, X-ray crystal structures in complex with substrate and structure-based mutagenesis reveal the intrinsic details of the enzymatic reaction. The mechanism of MDB formation is proposed to be an intramolecular nucleophilic substitution resulting from the hydroxylation by the heme core and the keto-enol tautomerization via a crucial catalytic triad (Asp89-His92-Arg72) in StvP2. In addition, in vitro reconstitution uncovers that C6-O-methylation and C4-O-acetylation of streptovaricins are necessary prerequisites for the MDB formation. This work provides insight for the MDB formation and adds evidence in support of the functional versatility of P450 enzymes. Streptovaricin C is an antibiotic containing a methylenedioxy bridge (MDB) moiety essential for its activity. Here, the authors show that a P450 monooxygenase StvP2 catalyses MDB formation, report its crystal structure in complex with the substrate, and elucidate mechanistic details of MDB formation.
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Affiliation(s)
- Guo Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Chaoqun Hu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Qing Mei
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Minghe Luo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Xu Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Zhengyuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Yuanzhen Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China
| | - Zhengyu Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China.
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China.
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8
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Kanoh N, Kawamata-Asano A, Suzuki K, Takahashi Y, Miyazawa T, Nakamura T, Moriya T, Hirano H, Osada H, Iwabuchi Y, Takahashi S. An integrated screening system for the selection of exemplary substrates for natural and engineered cytochrome P450s. Sci Rep 2019; 9:18023. [PMID: 31792277 PMCID: PMC6888865 DOI: 10.1038/s41598-019-54473-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/14/2019] [Indexed: 11/26/2022] Open
Abstract
Information about substrate and product selectivity is critical for understanding the function of cytochrome P450 monooxygenases. In addition, comprehensive understanding of changes in substrate selectivity of P450 upon amino acid mutation would enable the design and creation of engineered P450s with desired selectivities. Therefore, systematic methods for obtaining such information are required. Herein, we developed an integrated P450 substrate screening system for the selection of “exemplary” substrates for a P450 of interest. The established screening system accurately selected the known exemplary substrates and also identified previously unknown exemplary substrates for microbial-derived P450s from a library containing sp3-rich synthetic small molecules. Synthetically potent transformations were also found by analyzing the reactions and oxidation products. The screening system was applied to analyze the substrate selectivity of the P450 BM3 mutants F87A and F87A/A330W, which acquired an ability to hydroxylate non-natural substrate steroids regio- and stereoselectively by two amino acid mutations. The distinct transition of exemplary substrates due to each single amino acid mutation was revealed, demonstrating the utility of the established system.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan. .,Institute of Medicinal Chemistry, Hoshi University, 2-4-1 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Ayano Kawamata-Asano
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Kana Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Yusuke Takahashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takemichi Nakamura
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takashi Moriya
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Hirano
- Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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9
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He F, Mori T, Morita I, Nakamura H, Alblova M, Hoshino S, Awakawa T, Abe I. Molecular basis for the P450-catalyzed C–N bond formation in indolactam biosynthesis. Nat Chem Biol 2019; 15:1206-1213. [DOI: 10.1038/s41589-019-0380-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022]
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10
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Tsutsumi H, Katsuyama Y, Izumikawa M, Takagi M, Fujie M, Satoh N, Shin-ya K, Ohnishi Y. Unprecedented Cyclization Catalyzed by a Cytochrome P450 in Benzastatin Biosynthesis. J Am Chem Soc 2018; 140:6631-6639. [DOI: 10.1021/jacs.8b02769] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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11
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Kinanthraquinone, a new anthraquinone carboxamide isolated from Streptomyces reveromyceticus SN-593-44. J Antibiot (Tokyo) 2018; 71:480-482. [DOI: 10.1038/s41429-017-0020-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022]
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12
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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13
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Chemical and biological studies of reveromycin A. J Antibiot (Tokyo) 2016; 69:723-730. [PMID: 27270304 DOI: 10.1038/ja.2016.57] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
The research on antibiotics requires the integration of broad areas, such as microbiology, organic chemistry, biochemistry and pharmacology. It is similar to the field of chemical biology that is recently popular as an approach for drug discovery. When we isolate a new compound from a microorganism, we can pursue the interesting research on chemistry and biology. In this review, I would like to introduce our achievements in relation to reveromycin A.
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Chu LL, Pandey RP, Jung N, Jung HJ, Kim EH, Sohng JK. Hydroxylation of diverse flavonoids by CYP450 BM3 variants: biosynthesis of eriodictyol from naringenin in whole cells and its biological activities. Microb Cell Fact 2016; 15:135. [PMID: 27495155 PMCID: PMC4974697 DOI: 10.1186/s12934-016-0533-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/27/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cytochrome P450 monooxygenase constitutes a significant group of oxidative enzymes that can introduce an oxygen atom in a high regio- and stereo-selectivity mode. We used the Bacillus megaterium cytochrome P450 BM3 (CYP450 BM3) and its variants namely mutant 13 (M13) and mutant 15 (M15) for the hydroxylation of diverse class of flavonoids. RESULTS Among 20 flavonoids, maximum seven flavonoids were hydroxylated by the variants while none of these molecules were accepted by CYP450 BM3 in in vitro reaction. Moreover, M13 exhibited higher conversion of substrates than M15 and CYP450 BM3 enzymes. We found that M13 carried out regiospecific 3'-hydroxylation reaction of naringenin with the highest conversion among all the tested flavonoids. The apparent K m and k cat values of M13 for naringenin were 446 µM and 1.955 s(-1), respectively. In whole-cell biotransformation experiment with 100 µM of naringenin in M9 minimal medium with 2 % glucose in shake flask culture, M13 showed 2.14- and 13.96-folds higher conversion yield in comparison with M15 (16.11 %) and wild type (2.47 %). The yield of eriodictyol was 46.95 µM [~40.7 mg (13.5 mg/L)] in a 3-L volume lab scale fermentor at 48 h in the same medium exhibiting approximately 49.81 % conversion of the substrate. In addition, eriodictyol exhibited higher antibacterial and anticancer potential than naringenin, flavanone and hesperetin. CONCLUSIONS We elucidated that eriodictyol being produced from naringenin using recombinant CYP450 BM3 and its variants from B. megaterium, which shows an approach for the production of important hydroxylated compounds of various polyphenols that may span pharmaceutical industries.
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Affiliation(s)
- Luan Luong Chu
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Narae Jung
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Hye Jin Jung
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea.,Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk, 363-883, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea. .,Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, South Korea.
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Guengerich FP, Waterman MR, Egli M. Recent Structural Insights into Cytochrome P450 Function. Trends Pharmacol Sci 2016; 37:625-640. [PMID: 27267697 PMCID: PMC4961565 DOI: 10.1016/j.tips.2016.05.006] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/07/2016] [Accepted: 05/11/2016] [Indexed: 02/08/2023]
Abstract
Cytochrome P450 (P450) enzymes are important in the metabolism of drugs, steroids, fat-soluble vitamins, carcinogens, pesticides, and many other types of chemicals. Their catalytic activities are important issues in areas such as drug-drug interactions and endocrine function. During the past 30 years, structures of P450s have been very helpful in understanding function, particularly the mammalian P450 structures available in the past 15 years. We review recent activity in this area, focusing on the past 2 years (2014-2015). Structural work with microbial P450s includes studies related to the biosynthesis of natural products and the use of parasitic and fungal P450 structures as targets for drug discovery. Studies on mammalian P450s include the utilization of information about 'drug-metabolizing' P450s to improve drug development and also to understand the molecular bases of endocrine dysfunction.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
| | - Michael R Waterman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
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