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Kirk ML, Lepluart J, Yang J. Resonance Raman spectroscopy of pyranopterin molybdenum enzymes. J Inorg Biochem 2022; 235:111907. [PMID: 35932756 PMCID: PMC10575615 DOI: 10.1016/j.jinorgbio.2022.111907] [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: 01/30/2022] [Revised: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Resonance Raman spectroscopy (rR) is a powerful spectroscopic probe that is widely used for studying the geometric and electronic structure of metalloproteins. In this focused review, we detail how resonance Raman spectroscopy has contributed to a greater understanding of electronic structure, geometric structure, and the reaction mechanisms of pyranopterin molybdenum enzymes. The review focuses on the enzymes sulfite oxidase (SO), dimethyl sulfoxide reductase (DMSOR), xanthine oxidase (XO), and carbon monoxide dehydrogenase. Specifically, we highlight how Mo-Ooxo, Mo-Ssulfido, Mo-Sdithiolene, and dithiolene CC vibrational modes, isotope and heavy atom perturbations, resonance enhancement, and associated Raman studies of small molecule analogs have provided detailed insight into the nature of these metalloenzyme active sites.
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Affiliation(s)
- Martin L Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, United States.
| | - Jesse Lepluart
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, United States
| | - Jing Yang
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, United States
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2
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Control of carbon monoxide dehydrogenase orientation by site-specific immobilization enables direct electrical contact between enzyme cofactor and solid surface. Commun Biol 2022; 5:390. [PMID: 35474238 PMCID: PMC9042819 DOI: 10.1038/s42003-022-03335-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Controlling the orientation of redox enzymes on electrode surfaces is essential in the development of direct electron transfer (DET)-based bioelectrocatalytic systems. The electron transfer (ET) distance varies according to the enzyme orientation when immobilized on an electrode surface, which influences the interfacial ET rate. We report control of the orientation of carbon monoxide dehydrogenase (CODH) as a model enzyme through the fusion of gold-binding peptide (gbp) at either the N- or the C-terminus, and at both termini to strengthen the binding interactions between the fusion enzyme and the gold surface. Key factors influenced by the gbp fusion site are described. Collectively, our data show that control of the CODH orientation on an electrode surface is achieved through the presence of dual tethering sites, which maintains the enzyme cofactor within a DET-available distance (<14 Å), thereby promoting DET at the enzyme-electrode interface.
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Rovaletti A, Moro G, Cosentino U, Ryde U, Greco C. Can water act as a nucleophile in CO oxidation catalysed by Mo/Cu CO-dehydrogenase? Answers from theory. Chemphyschem 2022; 23:e202200053. [PMID: 35170169 PMCID: PMC9310835 DOI: 10.1002/cphc.202200053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/14/2022] [Indexed: 11/14/2022]
Abstract
The aerobic CO dehydrogenase from Oligotropha carboxidovorans is an environmentally crucial bacterial enzyme for maintenance of subtoxic concentration of CO in the lower atmosphere, as it allows for the oxidation of CO to CO2 which takes place at its Mo−Cu heterobimetallic active site. Despite extensive experimental and theoretical efforts, significant uncertainties still concern the reaction mechanism for the CO oxidation. In this work, we used the hybrid quantum mechanical/molecular mechanical approach to evaluate whether a water molecule present in the active site might act as a nucleophile upon formation of the new C−O bond, a hypothesis recently suggested in the literature. Our study shows that activation of H2O can be favoured by the presence of the Mo=Oeq group. However, overall our results suggest that mechanisms other than the nucleophilic attack by Mo=Oeq to the activated carbon of the CO substrate are not likely to constitute reactive channels for the oxidation of CO by the enzyme.
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Affiliation(s)
- Anna Rovaletti
- University of Milano-Bicocca: Universita degli Studi di Milano-Bicocca, Department of Earth and Environmental Sciences, ITALY
| | - Giorgio Moro
- University of Milano-Bicocca: Universita degli Studi di Milano-Bicocca, Department of Biotechnology and Biosciences, ITALY
| | - Ugo Cosentino
- University of Milano-Bicocca: Universita degli Studi di Milano-Bicocca, Department of Earth and Environmental Sciences, ITALY
| | - Ulf Ryde
- Lund University: Lunds Universitet, Department of Theoretical Chemistry, ITALY
| | - Claudio Greco
- Università degli Studi di Milano-Bicocca: Universita degli Studi di Milano-Bicocca, earth and environmental sciences, Piazza della Scienza 1, 20126, Milan, ITALY
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4
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Reginald SS, Etzerodt M, Fapyane D, Chang IS. Functional Expression of a Mo-Cu-Dependent Carbon Monoxide Dehydrogenase (CODH) and Its Use as a Dissolved CO Bio-microsensor. ACS Sens 2021; 6:2772-2782. [PMID: 34253013 DOI: 10.1021/acssensors.1c01243] [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] [Indexed: 11/28/2022]
Abstract
Herein, we report the heterologous expression in Escherichia coli of a Mo-Cu-containing carbon monoxide dehydrogenase (Mo-Cu CODH) from Hydrogenophaga pseudoflava, which resulted in an active protein catalyzing CO oxidation to CO2. By supplying the E. coli growth medium with Na2MoO4 (Mo) and CuSO4 (Cu), the Mo-Cu CODH metal cofactors precursors, the expressed L-subunit was found to have CO-oxidation activity even without the M- and S- subunits. This successful expression of CO-oxidizing-capable single L-subunit provides direct evidence of its role as the catalytic center of Mo-Cu CODH that has not been discovered and studied before. Subsequently, we used the expressed protein to construct a CO bio-microsensor based on a newly developed fast and sensitive Clark-type CO2 transducer using an aprotic solvent/ionic liquid electrolyte. The CO bio-microsensor exhibited a linear response to CO concentration in the 0-9 μM range, with a limit of detection (LOD) of 15 nM CO. The sensor uses a mixture of Mo-Cu CODH's L-subunit/Mo, Cu cofactors/methylene blue, confined in the enzyme chamber that is placed in front of a CO2 transducer. The optimized sensor's sensitivity and performance were retained to levels of at least 80% for 1 week of continuous polarization and operation in an aqueous medium. We have also demonstrated the use of an alkaline front-trap solution to make a completely O2/CO2 interference-free microsensor. The CO bio-microsensor developed in this study is potentially useful as an analytical tool for the detection of trace CO in dissolved form for monitoring dissolved CO concentration dynamics in natural or synthetic systems.
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Affiliation(s)
- Stacy Simai Reginald
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Deby Fapyane
- Aarhus University Centre of Water Technology (WATEC), Department of Bioscience, Aarhus University, Ny Munkegade 116, Aarhus 8000, Denmark
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
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5
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Kalimuthu P, Petitgenet M, Niks D, Dingwall S, Harmer JR, Hille R, Bernhardt PV. The oxidation-reduction and electrocatalytic properties of CO dehydrogenase from Oligotropha carboxidovorans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148118. [PMID: 31734195 DOI: 10.1016/j.bbabio.2019.148118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/19/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023]
Abstract
CO dehydrogenase (CODH) from the Gram-negative bacterium Oligotropha carboxidovorans is a complex metalloenzyme from the xanthine oxidase family of molybdenum-containing enzymes, bearing a unique binuclear Mo-S-Cu active site in addition to two [2Fe-2S] clusters (FeSI and FeSII) and one equivalent of FAD. CODH catalyzes the oxidation of CO to CO2 with the concomitant introduction of reducing equivalents into the quinone pool, thus enabling the organism to utilize CO as sole source of both carbon and energy. Using a variety of EPR monitored redox titrations and spectroelectrochemistry, we report the redox potentials of CO dehydrogenase at pH 7.2 namely MoVI/V, MoV/IV, FeSI2+/+, FeSII2+/+, FAD/FADH and FADH/FADH-. These potentials are systematically higher than the corresponding potentials seen for other members of the xanthine oxidase family of Mo enzymes, and are in line with CODH utilising the higher potential quinone pool as an electron acceptor instead of pyridine nucleotides. CODH is also active when immobilised on a modified Au working electrode as demonstrated by cyclic voltammetry in the presence of CO.
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Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Mélanie Petitgenet
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Stephanie Dingwall
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane 4072, Australia
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
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Rovaletti A, Bruschi M, Moro G, Cosentino U, Greco C. The Challenging in silico Description of Carbon Monoxide Oxidation as Catalyzed by Molybdenum-Copper CO Dehydrogenase. Front Chem 2019; 6:630. [PMID: 30687693 PMCID: PMC6334162 DOI: 10.3389/fchem.2018.00630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/03/2018] [Indexed: 01/05/2023] Open
Abstract
Carbon monoxide (CO) is a highly toxic gas to many living organisms. However, some microorganisms are able to use this molecule as the sole source of carbon and energy. Soil bacteria such as the aerobic Oligotropha carboxidovorans are responsible for the annual removal of about 2x108 tons of CO from the atmosphere. Detoxification through oxidation of CO to CO2 is enabled by the MoCu-dependent CO-dehydrogenase enzyme (MoCu-CODH) which-differently from other enzyme classes with similar function-retains its catalytic activity in the presence of atmospheric O2. In the last few years, targeted advancements have been described in the field of bioengineering and biomimetics, which is functional for future technological exploitation of the catalytic properties of MoCu-CODH and for the reproduction of its reactivity in synthetic complexes. Notably, a growing interest for the quantum chemical investigation of this enzyme has recently also emerged. This mini-review compiles the current knowledge of the MoCu-CODH catalytic cycle, with a specific focus on the outcomes of theoretical studies on this enzyme class. Rather controversial aspects from different theoretical studies will be highlighted, thus illustrating the challenges posed by this system as far as the application of density functional theory and hybrid quantum-classical methods are concerned.
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Affiliation(s)
- Anna Rovaletti
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Maurizio Bruschi
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Giorgio Moro
- Dipartimento di Biotecnologie e Bioscienze, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Ugo Cosentino
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Claudio Greco
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
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Ibdah A, Alduwikat S. Thermochemistry and Bond Nature of Oxo and Thio Ligands in Rhenium(V) Catalysts and Rhenium(VII) Intermediates: Density Functional Calculations. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Abdellatif Ibdah
- Department of Chemistry Jordan University of Science and Technology Irbid Jordan
| | - Salwa Alduwikat
- Department of Chemistry Jordan University of Science and Technology Irbid Jordan
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