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Hyun KA, Liang X, Xu Y, Kim SY, Boo KH, Park JS, Chi WJ, Hyun CG. Analysis of the Setomimycin Biosynthetic Gene Cluster from Streptomyces nojiriensis JCM3382 and Evaluation of Its α-Glucosidase Inhibitory Activity Using Molecular Docking and Molecular Dynamics Simulations. Int J Mol Sci 2024; 25:10758. [PMID: 39409089 PMCID: PMC11476836 DOI: 10.3390/ijms251910758] [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: 08/31/2024] [Revised: 09/30/2024] [Accepted: 10/04/2024] [Indexed: 10/19/2024] Open
Abstract
The formation of atroposelective biaryl compounds in plants and fungi is well understood; however, polyketide aglycone synthesis and dimerization in bacteria remain unclear. Thus, the biosynthetic gene cluster (BGC) responsible for antibacterial setomimycin production from Streptomyces nojiriensis JCM3382 was examined in comparison with the BGCs of spectomycin, julichromes, lincolnenins, and huanglongmycin. The setomimycin BGC includes post-polyketide synthase (PKS) assembly/cycling enzymes StmD (C-9 ketoreductase), StmE (aromatase), and StmF (thioesterase) as key components. The heterodimeric TcmI-like cyclases StmH and StmK are proposed to aid in forming the setomimycin monomer. In addition, StmI (P-450) is predicted to catalyze the biaryl coupling of two monomeric setomimycin units, with StmM (ferredoxin) specific to the setomimycin BGC. The roles of StmL and StmN, part of the nuclear transport factor 2 (NTF-2)-like protein family and unique to setomimycin BGCs, could particularly interest biochemists and combinatorial biologists. α-Glucosidase, a key enzyme in type 2 diabetes, hydrolyzes carbohydrates into glucose, thereby elevating blood glucose levels. This study aimed to assess the α-glucosidase inhibitory activity of EtOAc extracts of JCM 3382 and setomimycin. The JCM 3382 EtOAc extract and setomimycin exhibited greater potency than the standard inhibitor, acarbose, with IC50 values of 285.14 ± 2.04 μg/mL and 231.26 ± 0.41 μM, respectively. Molecular docking demonstrated two hydrogen bonds with maltase-glucoamylase chain A residues Thr205 and Lys480 (binding energy = -6.8 kcal·mol-1), two π-π interactions with Trp406 and Phe450, and one π-cation interaction with Asp542. Residue-energy analysis highlighted Trp406 and Phe450 as key in setomimycin's binding to maltase-glucoamylase. These findings suggest that setomimycin is a promising candidate for further enzymological research and potential antidiabetic therapy.
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Affiliation(s)
- Kyung-A Hyun
- Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju 63243, Republic of Korea; (K.-A.H.); (K.-H.B.)
| | - Xuhui Liang
- Jeju Inside Agency and Cosmetic Science Center, Department of Beauty and Cosmetology, Jeju National University, Jeju 63243, Republic of Korea; (X.L.); (Y.X.)
| | - Yang Xu
- Jeju Inside Agency and Cosmetic Science Center, Department of Beauty and Cosmetology, Jeju National University, Jeju 63243, Republic of Korea; (X.L.); (Y.X.)
| | - Seung-Young Kim
- Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asan 31460, Republic of Korea;
| | - Kyung-Hwan Boo
- Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju 63243, Republic of Korea; (K.-A.H.); (K.-H.B.)
| | - Jin-Soo Park
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea;
| | - Won-Jae Chi
- Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Chang-Gu Hyun
- Jeju Inside Agency and Cosmetic Science Center, Department of Beauty and Cosmetology, Jeju National University, Jeju 63243, Republic of Korea; (X.L.); (Y.X.)
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Gilep A, Varaksa T, Bukhdruker S, Kavaleuski A, Ryzhykau Y, Smolskaya S, Sushko T, Tsumoto K, Grabovec I, Kapranov I, Okhrimenko I, Marin E, Shevtsov M, Mishin A, Kovalev K, Kuklin A, Gordeliy V, Kaluzhskiy L, Gnedenko O, Yablokov E, Ivanov A, Borshchevskiy V, Strushkevich N. Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450. Front Mol Biosci 2023; 9:1100032. [PMID: 36699703 PMCID: PMC9868604 DOI: 10.3389/fmolb.2022.1100032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Ferredoxins are small iron-sulfur proteins and key players in essential metabolic pathways. Among all types, 3Fe-4S ferredoxins are less studied mostly due to anaerobic requirements. Their complexes with cytochrome P450 redox partners have not been structurally characterized. In the present work, we solved the structures of both 3Fe-4S ferredoxins from M. tuberculosis-Fdx alone and the fusion FdxE-CYP143. Our SPR analysis demonstrated a high-affinity binding of FdxE to CYP143. According to SAXS data, the same complex is present in solution. The structure reveals extended multipoint interactions and the shape/charge complementarity of redox partners. Furthermore, FdxE binding induced conformational changes in CYP143 as evident from the solved CYP143 structure alone. The comparison of FdxE-CYP143 and modeled Fdx-CYP51 complexes further revealed the specificity of ferredoxins. Our results illuminate the diversity of electron transfer complexes for the production of different secondary metabolites.
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Affiliation(s)
- Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus,Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Tatsiana Varaksa
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anton Kavaleuski
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Yury Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Sviatlana Smolskaya
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Tatsiana Sushko
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mikhail Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- European Molecular Biology Laboratory, Hamburg Unit C/O DESY, Hamburg, Germany
| | - Alexander Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Valentin Gordeliy
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Leonid Kaluzhskiy
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Oksana Gnedenko
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Evgeniy Yablokov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Alexis Ivanov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia,*Correspondence: Valentin Borshchevskiy, ; Natallia Strushkevich,
| | - Natallia Strushkevich
- Skolkovo Institute of Science and Technology, Moscow, Russia,*Correspondence: Valentin Borshchevskiy, ; Natallia Strushkevich,
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Lau ICK, Feyereisen R, Nelson DR, Bell SG. Analysis and preliminary characterisation of the cytochrome P450 monooxygenases from Frankia sp. EuI1c (Frankia inefficax sp.). Arch Biochem Biophys 2019; 669:11-21. [PMID: 31082352 DOI: 10.1016/j.abb.2019.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Frankia bacteria are nitrogen fixing species from the Actinobacterium phylum which live on the root nodules of plants. They have been hypothesised to have significant potential for natural product biosynthesis. The cytochrome P450 monooxygenase complement of Frankia sp. EuI1c (Frankia inefficax sp.), which comprises 68 members, was analysed. Several members belonged to previously uncharacterised bacterial P450 families. There was an unusually high number of CYP189 family members (21) suggesting that this family has undergone gene duplication events which are classified as "blooms". The likely electron transfer partners for the P450 enzymes were also identified and analysed. These consisted of predominantly [3Fe-4S] cluster containing ferredoxins (eight), a single [2Fe-2S] ferredoxin and a couple of ferredoxin reductases. Three of these CYP family members were produced and purified, using Escherichia coli as a host, and their substrate range was characterised. CYP1027H1 and CYP150A20 bound a broad range of norisoprenoids and terpenoids. CYP1074A2 was highly specific for certain steroids including testosterone, progesterone, stanolone and 4-androstene-3,17-dione. It is likely that steroids are the physiological substrates of CYP1074A2. These results also give an indication that terpenoids are the likely substrates of CYP1027H1 and CYP150A2. The large number of P450s belonging to distinct families as well as the associated electron transfer partners found in different Frankia strains highlights the importance of this family of enzymes has in the secondary metabolism of these bacteria.
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Affiliation(s)
- Ian C K Lau
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - René Feyereisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David R Nelson
- University of Tennessee Health Science Center, Dept. of Microbiology, Immunology and Biochemistry, 858 Madison Ave. Suite G01, Memphis, TN, 38163, USA
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia.
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Child SA, Bradley JM, Pukala TL, Svistunenko DA, Le Brun NE, Bell SG. Electron transfer ferredoxins with unusual cluster binding motifs support secondary metabolism in many bacteria. Chem Sci 2018; 9:7948-7957. [PMID: 30542550 PMCID: PMC6237146 DOI: 10.1039/c8sc01286e] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/21/2018] [Indexed: 01/06/2023] Open
Abstract
The proteins responsible for controlling electron transfer in bacterial secondary metabolism are not always known or characterised. Here we demonstrate that many bacteria contain a set of unfamiliar ferredoxin encoding genes which are associated with those of cytochrome P450 (CYP) monooxygenases and as such are involved in anabolic and catabolic metabolism. The model organism Mycobacterium marinum M contains eleven of these genes which encode [3Fe-4S] or [4Fe-4S] single cluster containing ferredoxins but which have unusual iron-sulfur cluster binding motif sequences, CXX?XXC(X) n CP, where '?' indicates a variable amino acid residue. Rather than a cysteine residue, which is highly conserved in [4Fe-4S] clusters, or alanine or glycine residues, which are common in [3Fe-4S] ferredoxins, these genes encode at this position histidine, asparagine, tyrosine, serine, threonine or phenylalanine. We have purified, characterised and reconstituted the activity of several of these CYP/electron transfer partner systems and show that all those examined contain a [3Fe-4S] cluster. Furthermore, the ferredoxin used and the identity of the variable motif residue in these proteins affects the functionality of the monooxygenase system and has a significant influence on the redox properties of the ferredoxins. Similar ferredoxin encoding genes were identified across Mycobacterium species, including in the pathogenic M. tuberculosis and M. ulcerans, as well as in a wide range of other bacteria such as Rhodococcus and Streptomyces. In the majority of instances these are associated with CYP genes. These ferredoxin systems are important in controlling electron transfer across bacterial secondary metabolite production processes which include antibiotic and pigment formation among others.
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Affiliation(s)
- Stella A Child
- Department of Chemistry , University of Adelaide , SA 5005 , Australia .
| | - Justin M Bradley
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK
| | - Tara L Pukala
- Department of Chemistry , University of Adelaide , SA 5005 , Australia .
| | - Dimitri A Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester CO4 3SQ , UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry , School of Chemistry , University of East Anglia , Norwich Research Park , Norwich , NR4 7TJ , UK
| | - Stephen G Bell
- Department of Chemistry , University of Adelaide , SA 5005 , Australia .
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