1
|
Gupta A, Sang Y, Fontanesi C, Turin L, Naaman R. Effect of Anesthesia Gases on the Oxygen Reduction Reaction. J Phys Chem Lett 2023; 14:1756-1761. [PMID: 36779610 PMCID: PMC9940288 DOI: 10.1021/acs.jpclett.2c03753] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The oxygen reduction reaction (ORR) is of high importance, among others, because of its role in cellular respiration and in the operation of fuel cells. Recently, a possible relation between respiration and general anesthesia has been found. This work aims to explore whether anesthesia related gases affect the ORR. In ORR, oxygen which is in its triplet ground state is reduced to form products that are all in the singlet state. While this process is "in principle" forbidden because of spin conservation, it is known that if the electrons transferred in the ORR are spin-polarized, the reaction occurs efficiently. Here we show, in electrochemical experiments, that the efficiency of the oxygen reduction is reduced by the presence of general anesthetics in solution. We suggest that a spin-orbit coupling to the anesthetics depolarizes the spins. This causes both a reduction in reaction efficiency and a change in the reaction products. The findings may point to a possible relation between ORR efficiency and anesthetic action.
Collapse
Affiliation(s)
- Anu Gupta
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Yutao Sang
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Claudio Fontanesi
- Dip.
di Ingegneria, DIEF, MO26, University of
Modena, 41125 Modena, Italy
| | - Luca Turin
- Health
Sciences, The University of Buckingham Medical
School, Buckingham MK18 1EG, United Kingdom
| | - Ron Naaman
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
2
|
Abstract
Controlled reduction of oxygen is important for developing clean energy technologies, such as fuel cells, and is vital to the existence of aerobic organisms. The process starts with oxygen in a triplet ground state and ends with products that are all in singlet states. Hence, spin constraints in the oxygen reduction must be considered. Here, we show that the electron transfer efficiency from chiral electrodes to oxygen (oxygen reduction reaction) is enhanced over that from achiral electrodes. We demonstrate lower overpotentials and higher current densities for chiral catalysts versus achiral ones. This finding holds even for electrodes composed of heavy metals with large spin-orbit coupling. The effect results from the spin selectivity conferred on the electron current by the chiral assemblies, the chiral-induced spin selectivity effect.
Collapse
|
3
|
Prangé T, Carpentier P, Dhaussy AC, van der Linden P, Girard E, Colloc'h N. Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Crystallogr D Struct Biol 2022; 78:162-173. [DOI: 10.1107/s2059798321012134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
Collapse
|
4
|
Ortega P, Zanchet A, Sanz-Sanz C, Gómez-Carrasco S, González-Sánchez L, Jambrina PG. DpgC-Catalyzed Peroxidation of 3,5-Dihydroxyphenylacetyl-CoA (DPA-CoA): Insights into the Spin-Forbidden Transition and Charge Transfer Mechanisms*. Chemistry 2020; 27:1700-1712. [PMID: 32975323 DOI: 10.1002/chem.202002993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Indexed: 11/06/2022]
Abstract
Despite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O2 at room temperature because O2 is a diradical whereas most organic molecules are closed-shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non-relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet-singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical-pair between dioxygen and enolate is enough to promote spin-forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.
Collapse
Affiliation(s)
- Pablo Ortega
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
| | - Alexandre Zanchet
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain.,Instituto de Física Fundamental (CSIC), Madrid, 28006, Spain
| | - Cristina Sanz-Sanz
- Departamento de Química Física Aplicada, University Autónoma de Madrid, Madrid, 28049, Spain
| | | | | | - Pablo G Jambrina
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
| |
Collapse
|
5
|
Kannappan B, Cummins PL, Gready JE. Mechanism of Oxygenase-Pathway Reactions Catalyzed by Rubisco from Large-Scale Kohn-Sham Density Functional Calculations. J Phys Chem B 2019; 123:2833-2843. [PMID: 30845802 DOI: 10.1021/acs.jpcb.9b00518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco) is the primary carbon-fixing enzyme in photosynthesis, fixing CO2 to a 5-carbon sugar, RuBP, in a series of five reactions. However, it also catalyzes an oxygenase reaction by O2 addition to the same enolized RuBP substrate in an analogous reaction series in the same active site, producing a waste product and loss of photosynthetic efficiency. Starting from RuBP, the reactions are enolization to the enediolate form, addition of CO2 or O2 to form the carboxy or peroxo adduct, hydration to form a gemdiolate, scission of the C2-C3 bond of the original RuBP, and stereospecific or nonstereospecific protonation to form two molecules of the 3-carbon PGA product, or one molecule of PGA, one of 2-carbon PG (waste product), and one water molecule. Reducing the loss of efficiency from the oxygenase reaction is an attractive means to increase crop productivity. However, lack of understanding of key aspects of the catalytic mechanisms for both the carboxylase and oxygenase reactions, particularly those involving proton exchanges and roles of water molecules, has stymied efforts at re-engineering Rubisco to reduce losses from the oxygenation reaction. As the stable form of molecular oxygen is the triplet biradical state (3O2), its reaction with near-universal singlet-state molecules is formally spin forbidden. Although in oxygenase enzymes, 3O2 activation is usually achieved by one-electron transfers using transition-metal ions or organic cofactors, recently, cofactor-less oxygenases in which the substrate itself is the source of the electron for 3O2 activation have been identified, but in all such cases an aromatic ring stabilizes the substrate's negative charge. Here we present the first large-scale Kohn-Sham density functional theory study of the reaction mechanism of the Rubisco oxygenase pathway. First, we show that the enediolate substrate complexed to Mg2+ and its ligands extends the region for charge delocalization and stabilization of its negative charge to allow formation of a caged biradical enediolate-O2 complex. Thus, Rubisco is a unique type of oxygenase without precedent in the literature. Second, for the O2 addition to proceed to the singlet peroxo-adduct intermediate, the system must undergo an intersystem crossing. We found that the presence of protonated LYS334 is required to stabilize this intermediate and that both factors (strongly stabilized anion and protonated LYS334) facilitate a barrier-less activation of 3O2. This finding supports our recent proposal that deoxygenation, that is, reversal of gas binding, is possible. Third, as neither CO2 nor O2 binds to the enzyme, our findings support the proposal from our recent carboxylase study that the observed KC or KO (Michaelis-Menten constants) in the steady-state kinetics reflect the respective adducts, carboxy or peroxo. Fourth, after computing hydration pathways with water addition both syn and anti to C3, we found, in contrast to the results of our carboxylation study indicating anti addition, that in the oxygenation reaction only syn-hydration is capable of producing a stable gemdiolate that facilitates the rate-limiting C2-C3 bond scission to final products. Fifth, we propose that an excess proton we previously found was required in the carboxylation reaction for activating the C2-C3 bond scission is utilized in the oxygenation reaction for the required elimination of a water molecule. In summary, despite its oxygenase handicap, Rubisco's success in directing 75% of its substrate through the carboxylation pathway can be considered impressively effective. Although native C3 Rubiscos are in a fix with unwanted activity of 3O2 hampering its primary carboxylase function, mechanistic differences presented here with findings in our recent carboxylase study for both the gas-addition and subsequent reactions provide some clues as to how creative Rubisco re-engineering may offer a solution to reducing the oxygenase activity.
Collapse
Affiliation(s)
- Babu Kannappan
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| | - Peter L Cummins
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| | - Jill E Gready
- John Curtin School of Medical Research , The Australian National University , Canberra ACT 0200 , Australia
| |
Collapse
|
6
|
Ramon-Marquez T, Medina-Castillo AL, Fernandez-Gutierrez A, Fernandez-Sanchez JF. Evaluation of two sterically directed attachments of biomolecules on a coaxial nanofibre membrane to improve the development of optical biosensors. Talanta 2018; 187:83-90. [DOI: 10.1016/j.talanta.2018.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/25/2018] [Accepted: 05/01/2018] [Indexed: 02/08/2023]
|
7
|
Wei D, Huang X, Qiao Y, Rao J, Wang L, Liao F, Zhan CG. Catalytic Mechanisms for Cofactor-Free Oxidase-Catalyzed Reactions: Reaction Pathways of Uricase-Catalyzed Oxidation and Hydration of Uric Acid. ACS Catal 2017; 7:4623-4636. [PMID: 28890842 DOI: 10.1021/acscatal.7b00901] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
First-principles quantum mechanical/molecular mechanical (QM/MM)-free energy calculations have been performed to uncover how uricase catalyzes metabolic reactions of uric acid (UA), demonstrating that the entire reaction process of UA in uricase consists of two stages-oxidation followed by hydration. The oxidation consists of four steps: (1) chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, which is different from the previously proposed electron-transfer mechanism that involves a dianion intermediate (UA2-) during the catalytic reaction process; (2) proton transfer to the O2- anion (radical); (3) diradical recombination to form a peroxo intermediate; (4) dissociation of H2O2 to generate the dehydrourate. Hydration, for the most favorable pathway, is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. According to the calculated free energy profile, the hydration is the rate-determining step, and the corresponding free energy barrier of 16.2 kcal/mol is consistent with that derived from experimental kinetic data, suggesting that the computational insights into the catalytic mechanisms are reasonable. The mechanistic insights not only provide a mechanistic base for future rational design of uricase mutants with improved catalytic activity against uric acid as an improved enzyme therapy, but also are valuable for understanding a variety of other cofactor-free oxidase-catalyzed reactions involving an oxygen molecule.
Collapse
Affiliation(s)
- Donghui Wei
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Xiaoqin Huang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Center
for Theoretical Biological Physics, and Center for Research Computing, Rice University, Houston, Texas 77030, United States,
| | - Yan Qiao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan 450001, P. R. China
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
| | - Jingjing Rao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Lu Wang
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Fei Liao
- Key
Laboratory of Medical Laboratory Diagnostics of the Education Ministry,
College of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, China
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States,
- Molecular
Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536, United States
| |
Collapse
|
8
|
Oksanen E, Chen JCH, Fisher SZ. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules. Molecules 2017; 22:molecules22040596. [PMID: 28387738 PMCID: PMC6154725 DOI: 10.3390/molecules22040596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/21/2022] Open
Abstract
The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.
Collapse
Affiliation(s)
- Esko Oksanen
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biochemistry and Structural Biology, Lund University, Sölvegatan 39, 22362 Lund, Sweden.
| | - Julian C-H Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Suzanne Zoë Fisher
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
| |
Collapse
|
9
|
Silva PJ. Refining the reaction mechanism of O 2 towards its co-substrate in cofactor-free dioxygenases. PeerJ 2016; 4:e2805. [PMID: 28028471 PMCID: PMC5178339 DOI: 10.7717/peerj.2805] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/19/2016] [Indexed: 11/21/2022] Open
Abstract
Cofactor-less oxygenases perform challenging catalytic reactions between singlet co-substrates and triplet oxygen, in spite of apparently violating the spin-conservation rule. In 1-H-3-hydroxy-4-oxoquinaldine-2,4-dioxygenase, the active site has been suggested by quantum chemical computations to fine tune triplet oxygen reactivity, allowing it to interact rapidly with its singlet substrate without the need for spin inversion, and in urate oxidase the reaction is thought to proceed through electron transfer from the deprotonated substrate to an aminoacid sidechain, which then feeds the electron to the oxygen molecule. In this work, we perform additional quantum chemical computations on these two systems to elucidate several intriguing features unaddressed by previous workers. These computations establish that in both enzymes the reaction proceeds through direct electron transfer from co-substrate to O2 followed by radical recombination, instead of minimum-energy crossing points between singlet and triplet potential energy surfaces without formal electron transfer. The active site does not affect the reactivity of oxygen directly but is crucial for the generation of the deprotonated form of the co-substrates, which have redox potentials far below those of their protonated forms and therefore may transfer electrons to oxygen without sizeable thermodynamic barriers. This mechanism seems to be shared by most cofactor-less oxidases studied so far.
Collapse
Affiliation(s)
- Pedro J Silva
- FP-ENAS/Fac. de Ciências da Saúde, Universidade Fernando Pessoa , Porto , Portugal
| |
Collapse
|
10
|
Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA. Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase. Angew Chem Int Ed Engl 2014; 53:13710-4. [PMID: 25314114 PMCID: PMC4502973 DOI: 10.1002/anie.201405485] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Indexed: 11/16/2022]
Abstract
Cofactor-free oxidases and oxygenases promote and control the reactivity of O2 with limited chemical tools at their disposal. Their mechanism of action is not completely understood and structural information is not available for any of the reaction intermediates. Near-atomic resolution crystallography supported by in crystallo Raman spectroscopy and QM/MM calculations showed unambiguously that the archetypical cofactor-free uricase catalyzes uric acid degradation via a C5(S)-(hydro)peroxide intermediate. Low X-ray doses break specifically the intermediate C5-OO(H) bond at 100 K, thus releasing O2 in situ, which is trapped above the substrate radical. The dose-dependent rate of bond rupture followed by combined crystallographic and Raman analysis indicates that ionizing radiation kick-starts both peroxide decomposition and its regeneration. Peroxidation can be explained by a mechanism in which the substrate radical recombines with superoxide transiently produced in the active site.
Collapse
Affiliation(s)
- Soi Bui
- Randall Division of Cell and Molecular Biophysics, King's College LondonNew Hunt's House, Guy's Campus, London SE1 1UL (UK)
| | - David von Stetten
- European Synchrotron Radiation FacilityCS 40220, 38043 Grenoble Cedex 9 (France)
| | - Pablo G Jambrina
- Department of Chemistry, King's College LondonBritannia House 7 Trinity Street, London, SE1 1DB (UK)
| | - Thierry Prangé
- LCRB, UMR 8015-Université Paris Descartes-CNRSFaculté de Pharmacie 75270 Paris Cedex 06 (France)
| | - Nathalie Colloc'h
- ISTCT, UMR 6301-UCBN-CNRS-CEA-Normandie UniversitéCentre Cyceron, 14074 Caen Cedex (France)
| | - Daniele de Sanctis
- European Synchrotron Radiation FacilityCS 40220, 38043 Grenoble Cedex 9 (France)
| | - Antoine Royant
- European Synchrotron Radiation FacilityCS 40220, 38043 Grenoble Cedex 9 (France)
- Institut de Biologie StructuraleUMR 5075 Université Grenoble Alpes-CNRS-CEA, CS10090, 38044 Grenoble Cedex 9 (France)
| | - Edina Rosta
- Department of Chemistry, King's College LondonBritannia House 7 Trinity Street, London, SE1 1DB (UK)
| | - Roberto A Steiner
- Randall Division of Cell and Molecular Biophysics, King's College LondonNew Hunt's House, Guy's Campus, London SE1 1UL (UK)
| |
Collapse
|
11
|
Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA. Direct Evidence for a Peroxide Intermediate and a Reactive Enzyme-Substrate-Dioxygen Configuration in a Cofactor-free Oxidase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
12
|
Gabison L, Colloc’h N, Prangé T. Azide inhibition of urate oxidase. Acta Crystallogr F Struct Biol Commun 2014; 70:896-902. [PMID: 25005084 PMCID: PMC4089527 DOI: 10.1107/s2053230x14011753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 05/21/2014] [Indexed: 02/04/2023] Open
Abstract
The inhibition of urate oxidase (UOX) by azide was investigated by X-ray diffraction techniques and compared with cyanide inhibition. Two well characterized sites for reagents are present in the enzyme: the dioxygen site and the substrate-binding site. To examine the selectivity of these sites towards azide inhibition, several crystallization conditions were developed. UOX was co-crystallized with azide (N3) in the presence or absence of either uric acid (UA, the natural substrate) or 8-azaxanthine (8AZA, a competitive inhibitor). In a second set of experiments, previously grown orthorhombic crystals of the UOX-UA or UOX-8AZA complexes were soaked in sodium azide solutions. In a third set of experiments, orthorhombic crystals of UOX with the exchangeable ligand 8-nitroxanthine (8NXN) were soaked in a solution containing uric acid and azide simultaneously (competitive soaking). In all assays, the soaking periods were either short (a few hours) or long (one or two months). These different experimental conditions showed that one or other of the sites, or the two sites together, could be inhibited. This also demonstrated that azide not only competes with dioxygen as cyanide does but also competes with the substrate for its enzymatic site. A model in agreement with experimental data would be an azide in equilibrium between two sites, kinetically in favour of the dioxygen site and thermodynamically in favour of the substrate-binding site.
Collapse
Affiliation(s)
- Laure Gabison
- Faculty of Pharmacy, UMR 8015 CNRS Laboratoire de Cristallographie et RMN Biologiques, 4 Avenue de l’Observatoire, 75006 Paris, France
| | - Nathalie Colloc’h
- ISTCT, UMR 6301–CNRS–Université de Caen–Normandie Université–CEA, Centre Cyceron, Boulevard Becquerel, 14074 Caen CEDEX, France
| | - Thierry Prangé
- Faculty of Pharmacy, UMR 8015 CNRS Laboratoire de Cristallographie et RMN Biologiques, 4 Avenue de l’Observatoire, 75006 Paris, France
| |
Collapse
|
13
|
Oksanen E, Blakeley MP, El-Hajji M, Ryde U, Budayova-Spano M. The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. PLoS One 2014; 9:e86651. [PMID: 24466188 PMCID: PMC3900588 DOI: 10.1371/journal.pone.0086651] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/16/2013] [Indexed: 12/02/2022] Open
Abstract
Urate oxidase transforms uric acid to 5-hydroxyisourate without the help of cofactors, but the catalytic mechanism has remained enigmatic, as the protonation state of the substrate could not be reliably deduced. We have determined the neutron structure of urate oxidase, providing unique information on the proton positions. A neutron crystal structure inhibited by a chloride anion at 2.3 Å resolution shows that the substrate is in fact 8-hydroxyxanthine, the enol tautomer of urate. We have also determined the neutron structure of the complex with the inhibitor 8-azaxanthine at 1.9 Å resolution, showing the protonation states of the K10–T57–H256 catalytic triad. Together with X-ray data and quantum chemical calculations, these structures allow us to identify the site of the initial substrate protonation and elucidate why the enzyme is inhibited by a chloride anion.
Collapse
Affiliation(s)
- Esko Oksanen
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
| | | | | | - Ulf Ryde
- Department of Theoretical Chemistry Lund University, Lund, Sweden
| | - Monika Budayova-Spano
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
- * E-mail:
| |
Collapse
|
14
|
Thierbach S, Bui N, Zapp J, Chhabra SR, Kappl R, Fetzner S. Substrate-assisted O2 activation in a cofactor-independent dioxygenase. ACTA ACUST UNITED AC 2014; 21:217-25. [PMID: 24388758 DOI: 10.1016/j.chembiol.2013.11.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/22/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022]
Abstract
In contrast to the majority of O2-activating enzymes, which depend on an organic cofactor or a metal ion for catalysis, a particular group of structurally unrelated oxygenases is functional without any cofactor. In this study, we characterized the mechanism of O2 activation in the reaction pathway of a cofactor-independent dioxygenase with an α/β-hydrolase fold, which catalyzes the oxygenolytic cleavage of 2-alkyl-3-hydroxy-4(1H)-quinolones. Chemical analysis and electron paramagnetic resonance spectroscopic data revealed that O2 activation in the enzyme's active site is substrate-assisted, relying on single electron transfer from the bound substrate anion to O2 to form a radical pair, which recombines to a C2-peroxide intermediate. Thus, an oxygenase can function without a cofactor, if the organic substrate itself, after activation to a (carb)anion by an active-site base, is intrinsically reactive toward molecular oxygen.
Collapse
Affiliation(s)
- Sven Thierbach
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Nguyen Bui
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Josef Zapp
- Pharmaceutical Biology, Saarland University, Campus, Building C2, 66123 Saarbrücken, Germany
| | - Siri Ram Chhabra
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Reinhard Kappl
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany.
| |
Collapse
|
15
|
Bonnot F, Iavarone AT, Klinman JP. Multistep, eight-electron oxidation catalyzed by the cofactorless oxidase, PqqC: identification of chemical intermediates and their dependence on molecular oxygen. Biochemistry 2013; 52:4667-75. [PMID: 23718207 DOI: 10.1021/bi4003315] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The final step of the biosynthesis of prokaryotic cofactor PQQ is catalyzed by PqqC, a cofactorless oxidase that brings about a ring closure and overall eight-electron oxidation of its substrate. Time-dependent acid quenching and subsequent high-performance liquid chromatography separation and mass spectrometric analyses of reaction mixtures were performed to correlate the structures of intermediates with previously observed UV-visible signatures. The reaction is composed of four stepwise oxidations: three steps use O2 as the two-electron acceptor, and the fourth uses hydrogen peroxide (H2O2). The chemical nature of the intermediates, the stoichiometry of the reaction, and their dependence on the oxygen concentration indicate that the third oxidation uses the product, H2O2, from the preceding step to produce water. The last oxidation step can also be studied separately and is a reaction between O2 and PQQH2 trapped in the active site. This oxidation is approximately 10 times slower than the reoxidation of PQQH2 in solution. From the order of the four oxidation steps and their sensitivity to O2 concentration, we propose a progressive closure of the active site as the enzyme proceeds through its catalytic cycle.
Collapse
Affiliation(s)
- Florence Bonnot
- Department of Chemistry, ‡Department of Molecular and Cell Biology, and §California Institute for Quantitative Biosciences (QB3), University of California , Berkeley, California 94720, United States
| | | | | |
Collapse
|