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Shapira M, Dobysh A, Liaudanskaya A, Aucharova H, Dzichenka Y, Bokuts V, Jovanović-Šanta S, Yantsevich A. New insights into the substrate specificity of cholesterol oxidases for more aware application. Biochimie 2023; 220:1-10. [PMID: 38104713 DOI: 10.1016/j.biochi.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Cholesterol oxidases (ChOxes) are enzymes that catalyze the oxidation of cholesterol to cholest-4-en-3-one. These enzymes find wide applications across various diagnostic and industrial settings. In addition, as a pathogenic factor of several bacteria, they have significant clinical implications. The current classification system for ChOxes is based on the type of bond connecting FAD to the apoenzyme, which does not adequately illustrate the enzymatic and structural characteristics of these proteins. In this study, we have adopted an integrative approach, combining evolutionary analysis, classic enzymatic techniques and computational approaches, to elucidate the distinct features of four various ChOxes from Rhodococcus sp. (RCO), Cromobacterium sp. (CCO), Pseudomonas aeruginosa (PCO) and Burkhoderia cepacia (BCO). Comparative and evolutionary analysis of substrate-binding domain (SBD) and FAD-binding domain (FBD) helped to reveal the origin of ChOxes. We discovered that all forms of ChOxes had a common ancestor and that the structural differences evolved later during divergence. Further examination of amino acid variations revealed SBD as a more variable compared to FBD independently of FAD coupling mechanism. Revealed differences in amino acid positions turned out to be critical in determining common for ChOxes properties and those that account for the individual differences in substrate specificity. A novel look with the help of chemical descriptors on found distinct features were sufficient to attempt an alternative classification system aimed at application approach. While univocal characteristics necessary to establish such a system remain elusive, we were able to demonstrate the substrate and protein features that explain the differences in substrate profile.
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Affiliation(s)
- Michail Shapira
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus.
| | - Alexandra Dobysh
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Hanna Aucharova
- Technical University of Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Yaraslau Dzichenka
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Volha Bokuts
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Suzana Jovanović-Šanta
- University of Novi Sad Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Novi Sad, Serbia
| | - Aliaksey Yantsevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
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Martini MA, Rüdiger O, Breuer N, Nöring B, DeBeer S, Rodríguez-Maciá P, Birrell JA. The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism. J Am Chem Soc 2021; 143:18159-18171. [PMID: 34668697 PMCID: PMC8569811 DOI: 10.1021/jacs.1c07322] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[FeFe] hydrogenases are highly active enzymes for interconverting protons and electrons with hydrogen (H2). Their active site H-cluster is formed of a canonical [4Fe-4S] cluster ([4Fe-4S]H) covalently attached to a unique [2Fe] subcluster ([2Fe]H), where both sites are redox active. Heterolytic splitting and formation of H2 takes place at [2Fe]H, while [4Fe-4S]H stores electrons. The detailed catalytic mechanism of these enzymes is under intense investigation, with two dominant models existing in the literature. In one model, an alternative form of the active oxidized state Hox, named HoxH, which forms at low pH in the presence of the nonphysiological reductant sodium dithionite (NaDT), is believed to play a crucial role. HoxH was previously suggested to have a protonated [4Fe-4S]H. Here, we show that HoxH forms by simple addition of sodium sulfite (Na2SO3, the dominant oxidation product of NaDT) at low pH. The low pH requirement indicates that sulfur dioxide (SO2) is the species involved. Spectroscopy supports binding at or near [4Fe-4S]H, causing its redox potential to increase by ∼60 mV. This potential shift detunes the redox potentials of the subclusters of the H-cluster, lowering activity, as shown in protein film electrochemistry (PFE). Together, these results indicate that HoxH and its one-electron reduced counterpart Hred'H are artifacts of using a nonphysiological reductant, and not crucial catalytic intermediates. We propose renaming these states as the "dithionite (DT) inhibited" states Hox-DTi and Hred-DTi. The broader potential implications of using a nonphysiological reductant in spectroscopic and mechanistic studies of enzymes are highlighted.
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Affiliation(s)
- Maria Alessandra Martini
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Nina Breuer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Birgit Nöring
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patricia Rodríguez-Maciá
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, U.K
| | - James A Birrell
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
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G Jayanthi K, S K S. Cholesterol oxidase immobilized inulin based nanocomposite as the sensing material for cholesterol in biological and food samples. Enzyme Microb Technol 2020; 140:109631. [PMID: 32912691 DOI: 10.1016/j.enzmictec.2020.109631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 01/16/2023]
Abstract
In the present study, inulin based nanocomposite viz., TiO2-MWCNT@Inulin was prepared by embedding Inulin (a biopolymer extracted from Allium sativum L.) with TiO2 and MWCNTs. The morphology of the prepared nanocomposite was characterized by High Resolution transmission electron microscopy (HRTEM). Cholesterol oxidase (ChOx) enzyme was then immobilized into the nanocomposite and the immobilization was examined by UV-vis and FT-IR spectral studies. The ChOx immobilized nanocomposite was integrated into carbon paste (CP) matrix to prepare the working electrode for the sensing of cholesterol. Electrochemical characterization of the modified CP/TiO2-MWCNT@Inulin/ChOx electrode was done by cyclic voltammetric (CV) and electrochemical impedance spectroscopic (EIS) studies. Differential pulse voltammetric (DPV) studies were carried out to determine the concentration of cholesterol at the interface of the newly fabricated electrode. The fabricated electrode demonstrated a linear range from 83 μM to 14.28 mM, low limit of detection (35 μM), good sensitivity (21.26 μA mM-1 cm-2), low Km (0.49 mM), high stability (120 days) and good selectivity. The presence of Inulin biopolymer played a vital role in attaching ChOx enzyme firmly to the nanocomposite thereby enhancing the stability and electron transfer efficiency of the electrode. The analysis of product that was formed within the electrochemical cell during the electrochemical oxidation of cholesterol was performed by using sodium nitroprusside. This resulted in a deep purple coloured solution which suggested the electrochemical conversion of cholesterol to cholestenone. The practical applicability of the fabricated electrode was also assessed by the determination of cholesterol in spiked blood serum and milk samples.
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Affiliation(s)
| | - Suja S K
- Department of Chemistry, Lady Doak College, Madurai, India.
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Kerber T, Vrielink A. The role of hydrogen atoms in redox catalysis by the flavoenzyme cholesterol oxidase. Methods Enzymol 2020; 634:361-377. [PMID: 32093840 DOI: 10.1016/bs.mie.2019.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Flavoenzymes comprise a large class of proteins that carry out a diverse range of important redox chemistry. Although X-ray crystal structures of many flavoenzymes have been determined, there are still unresolved questions regarding the actual oxidation state of the flavin cofactors in these structures due to photoreduction by the ionizing radiation of the X-ray beam during the diffraction experiment. Additionally, the ability to visualize hydrogen atoms in X-ray structures is difficult due to the weak scattering capability of these atoms. Since hydrogen atoms affect the electrostatic nature of enzyme active sites and play important roles in the chemistry of key amino acid residues, visualizing the precise positions of these atoms provides a more detailed understanding of their role in enzyme catalysis. Single crystal neutron diffraction is an alternative method to structure determination, circumventing problems associated with photoreduction of the sample thus providing a clearer view of the structural features of a flavoenzyme in different redox states. Additionally, the larger neutron scattering factors for hydrogen and deuterium atoms enables one to visualize these atoms much more easily than from X-ray scattering measurements. In this chapter we give an overview of neutron and X-ray crystallography studies on the flavoenzyme, cholesterol oxidase and how the observations of unusual hydrogen atom positions provide insight into the redox chemistry of the flavin cofactor.
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Affiliation(s)
- Tatiana Kerber
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.
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Yoshida H, Kojima K, Shiota M, Yoshimatsu K, Yamazaki T, Ferri S, Tsugawa W, Kamitori S, Sode K. X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein. Acta Crystallogr D Struct Biol 2019; 75:841-851. [PMID: 31478907 PMCID: PMC6719666 DOI: 10.1107/s2059798319010878] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe-4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Katsuhiro Kojima
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masaki Shiota
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Keiichi Yoshimatsu
- Department of Chemistry, Missouri State University, Springfield, MO 65897, USA
| | - Tomohiko Yamazaki
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Stefano Ferri
- Department of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Wakako Tsugawa
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
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Aleksandrov A. A Molecular Mechanics Model for Flavins. J Comput Chem 2019; 40:2834-2842. [DOI: 10.1002/jcc.26061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/03/2019] [Accepted: 08/04/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Alexey Aleksandrov
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique IP Paris, 91128 Palaiseau France
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Yu LJ, Golden E, Chen N, Zhao Y, Vrielink A, Karton A. Computational insights for the hydride transfer and distinctive roles of key residues in cholesterol oxidase. Sci Rep 2017; 7:17265. [PMID: 29222497 PMCID: PMC5722936 DOI: 10.1038/s41598-017-17503-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/27/2017] [Indexed: 11/10/2022] Open
Abstract
Cholesterol oxidase (ChOx), a member of the glucose-methanol-choline (GMC) family, catalyzes the oxidation of the substrate via a hydride transfer mechanism and concomitant reduction of the FAD cofactor. Unlike other GMC enzymes, the conserved His447 is not the catalytic base that deprotonates the substrate in ChOx. Our QM/MM MD simulations indicate that the Glu361 residue acts as a catalytic base facilitating the hydride transfer from the substrate to the cofactor. We find that two rationally chosen point mutations (His447Gln and His447Asn) cause notable decreases in the catalytic activity. The binding free energy calculations show that the Glu361 and His447 residues are important in substrate binding. We also performed high-level double-hybrid density functional theory simulations using small model systems, which support the QM/MM MD results. Our work provides a basis for unraveling the substrate oxidation mechanism in GMC enzymes in which the conserved histidine does not act as a base.
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Affiliation(s)
- Li-Juan Yu
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Emily Golden
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Nanhao Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.,Department of Chemistry, University of California, Davis, California, 95616, United States
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng, 475004, China.
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Amir Karton
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.
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Harb LH, Arooj M, Vrielink A, Mancera RL. Computational site-directed mutagenesis studies of the role of the hydrophobic triad on substrate binding in cholesterol oxidase. Proteins 2017; 85:1645-1655. [PMID: 28508424 DOI: 10.1002/prot.25319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/21/2017] [Accepted: 05/08/2017] [Indexed: 11/10/2022]
Abstract
Cholesterol oxidase (ChOx) is a flavoenzyme that oxidizes and isomerizes cholesterol (CHL) to form cholest-4-en-3-one. Molecular docking and molecular dynamics simulations were conducted to predict the binding interactions of CHL in the active site. Several key interactions (E361-CHL, N485-FAD, and H447-CHL) were identified and which are likely to determine the correct positioning of CHL relative to flavin-adenine dinucleotide (FAD). Binding of CHL also induced changes in key residues of the active site leading to the closure of the oxygen channel. A group of residues, Y107, F444, and Y446, known as the hydrophobic triad, are believed to affect the binding of CHL in the active site. Computational site-directed mutagenesis of these residues revealed that their mutation affects the conformations of key residues in the active site, leading to non-optimal binding of CHL and to changes in the structure of the oxygen channel, all of which are likely to reduce the catalytic efficiency of ChOx. Proteins 2017; 85:1645-1655. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Laith Hisham Harb
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, WA, 6845, Australia
| | - Mahreen Arooj
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, WA, 6845, Australia
| | - Alice Vrielink
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, 6009, Australia
| | - Ricardo L Mancera
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, WA, 6845, Australia
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An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase. Sci Rep 2017; 7:40517. [PMID: 28098177 PMCID: PMC5241826 DOI: 10.1038/srep40517] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023] Open
Abstract
The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.
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