1
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Wang K, Hong Q, Zhu C, Xu Y, Li W, Wang Y, Chen W, Gu X, Chen X, Fang Y, Shen Y, Liu S, Zhang Y. Metal-ligand dual-site single-atom nanozyme mimicking urate oxidase with high substrates specificity. Nat Commun 2024; 15:5705. [PMID: 38977710 PMCID: PMC11231224 DOI: 10.1038/s41467-024-50123-4] [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: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
In nature, coenzyme-independent oxidases have evolved in selective catalysis using isolated substrate-binding pockets. Single-atom nanozymes (SAzymes), an emerging type of non-protein artificial enzymes, are promising to simulate enzyme active centers, but owing to the lack of recognition sites, realizing substrate specificity is a formidable task. Here we report a metal-ligand dual-site SAzyme (Ni-DAB) that exhibited selectivity in uric acid (UA) oxidation. Ni-DAB mimics the dual-site catalytic mechanism of urate oxidase, in which the Ni metal center and the C atom in the ligand serve as the specific UA and O2 binding sites, respectively, characterized by synchrotron soft X-ray absorption spectroscopy, in situ near ambient pressure X-ray photoelectron spectroscopy, and isotope labeling. The theoretical calculations reveal the high catalytic specificity is derived from not only the delicate interaction between UA and the Ni center but also the complementary oxygen reduction at the beta C site in the ligand. As a potential application, a Ni-DAB-based biofuel cell using human urine is constructed. This work unlocks an approach of enzyme-like isolated dual sites in boosting the selectivity of non-protein artificial enzymes.
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Affiliation(s)
- Kaiyuan Wang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Qing Hong
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Caixia Zhu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yuan Xu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Wang Li
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Ying Wang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Wenhao Chen
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Xiang Gu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Xinghua Chen
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yanfeng Fang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yanfei Shen
- Medical School, Southeast University, Nanjing, 210009, China.
| | - Songqin Liu
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China
| | - Yuanjian Zhang
- Jiangsu Engineering Research Center for Carbon-Rich Materials and Devices, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Nanjing, 211189, China.
- Department of Oncology, Zhongda Hospital, Southeast University, Nanjing, 210009, China.
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2
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Bui S, Gil-Guerrero S, van der Linden P, Carpentier P, Ceccarelli M, Jambrina PG, Steiner RA. Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the α/β-hydrolase fold. Chem Sci 2023; 14:10547-10560. [PMID: 37799987 PMCID: PMC10548524 DOI: 10.1039/d3sc03044j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Protein fold adaptation to novel enzymatic reactions is a fundamental evolutionary process. Cofactor-independent oxygenases degrading N-heteroaromatic substrates belong to the α/β-hydrolase (ABH) fold superfamily that typically does not catalyze oxygenation reactions. Here, we have integrated crystallographic analyses under normoxic and hyperoxic conditions with molecular dynamics and quantum mechanical calculations to investigate its prototypic 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) member. O2 localization to the "oxyanion hole", where catalysis occurs, is an unfavorable event and the direct competition between dioxygen and water for this site is modulated by the "nucleophilic elbow" residue. A hydrophobic pocket that overlaps with the organic substrate binding site can act as a proximal dioxygen reservoir. Freeze-trap pressurization allowed the structure of the ternary complex with a substrate analogue and O2 bound at the oxyanion hole to be determined. Theoretical calculations reveal that O2 orientation is coupled to the charge of the bound organic ligand. When 1-H-3-hydroxy-4-oxoquinaldine is uncharged, O2 binds with its molecular axis along the ligand's C2-C4 direction in full agreement with the crystal structure. Substrate activation triggered by deprotonation of its 3-OH group by the His-Asp dyad, rotates O2 by approximately 60°. This geometry maximizes the charge transfer between the substrate and O2, thus weakening the double bond of the latter. Electron density transfer to the O2(π*) orbital promotes the formation of the peroxide intermediate via intersystem crossing that is rate-determining. Our work provides a detailed picture of how evolution has repurposed the ABH-fold architecture and its simple catalytic machinery to accomplish metal-independent oxygenation.
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Affiliation(s)
- Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King's College London London SE1 1UL UK
| | - Sara Gil-Guerrero
- Departamento de Química Física, University of Salamanca Salamanca 37008 Spain
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), Partnership for Soft Condensed Matter (PSCM) 71 Avenue des Martyrs Grenoble 38000 France
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38043 Grenoble France
- Université Grenoble Alpes, CNRS, CEA, Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM) UMR 5249 17 Avenue des Martyrs 38054 Grenoble France
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari Monserrato 09042 Italy
- IOM-CNR Unità di Cagliari, Cittadella Universitaria Monserrato 09042 Italy
| | - Pablo G Jambrina
- Departamento de Química Física, University of Salamanca Salamanca 37008 Spain
| | - Roberto A Steiner
- Randall Centre for Cell and Molecular Biophysics, King's College London London SE1 1UL UK
- Department of Biomedical Sciences, University of Padova Italy
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3
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Polyakov I, Kulakova A, Nemukhin A. Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3020016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Interaction of molecular oxygen 3O2 with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen 1O2 and superoxide O2●−. Despite the recently resolved crystal structures of miniSOG variants, oxygen-binding sites near the flavin chromophore are poorly characterized. We report the results of computational studies of the protein−oxygen systems using molecular dynamics (MD) simulations with force-field interaction potentials and quantum mechanics/molecular mechanics (QM/MM) potentials for the original miniSOG and the mutated protein. We found several oxygen-binding pockets and pointed out possible tunnels bridging the bulk solvent and the isoalloxazine ring of the chromophore. These findings provide an essential step toward understanding photophysical properties of miniSOG—an important singlet oxygen photosensitizer.
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Affiliation(s)
- Igor Polyakov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna Kulakova
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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4
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Maghsoud Y, Vázquez-Montelongo EA, Yang X, Liu C, Jing Z, Lee J, Harger M, Smith AK, Espinoza M, Guo HF, Kurie JM, Dalby KN, Ren P, Cisneros GA. Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. J Chem Inf Model 2023; 63:986-1001. [PMID: 36779232 PMCID: PMC10233724 DOI: 10.1021/acs.jcim.2c01448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The catalytic function of lysyl hydroxylase-2 (LH2), a member of the Fe(II)/αKG-dependent oxygenase superfamily, is to catalyze the hydroxylation of lysine to hydroxylysine in collagen, resulting in stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs). Reports show that high amounts of LH2 lead to the accumulation of HLCCs, causing fibrosis and specific types of cancer metastasis. Some members of the Fe(II)/αKG-dependent family have also been reported to have intramolecular O2 tunnels, which aid in transporting one of the required cosubstrates into the active site. While LH2 can be a promising target to combat these diseases, efficacious inhibitors are still lacking. We have used computational simulations to investigate a series of 44 small molecules as lead compounds for LH2 inhibition. Tunneling analyses indicate the existence of several intramolecular tunnels. The lengths of the calculated O2-transporting tunnels in holoenzymes are relatively longer than those in the apoenzyme, suggesting that the ligands may affect the enzyme's structure and possibly block (at least partially) the tunnels. The sequence alignment analysis between LH enzymes from different organisms shows that all of the amino acid residues with the highest occurrence rate in the oxygen tunnels are conserved. Our results suggest that the enolate form of diketone compounds establishes stronger interactions with the Fe(II) in the active site. Branching the enolate compounds with functional groups such as phenyl and pyridinyl enhances the interaction with various residues around the active site. Our results provide information about possible leads for further LH2 inhibition design and development.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Erik Antonio Vázquez-Montelongo
- Department of Physical Medicine and Rehabilitation, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Juhoon Lee
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ally K Smith
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Miguel Espinoza
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Hou-Fu Guo
- Department of Molecular and Cellular Biochemistry, College of Medicine, The University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77005, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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5
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Zhuang B, Vos MH, Aleksandrov A. Photochemical and Molecular Dynamics Studies of Halide Binding in Flavoenzyme Glucose Oxidase. Chembiochem 2022; 23:e202200227. [PMID: 35876386 DOI: 10.1002/cbic.202200227] [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: 04/20/2022] [Revised: 07/11/2022] [Indexed: 11/11/2022]
Abstract
Glucose oxidase (GOX), a characteristic flavoprotein oxidase with widespread industrial applications, binds fluoride (F - ) and chloride (Cl - ). We investigated binding properties of halide inhibitors of GOX through time-resolved spectral characterization of flavin-related photochemical processes and molecular dynamic simulations. Cl - and F - bind differently to the protein active site and have substantial but opposite effects on the population and decay of the flavin excited state. Cl - binds closer to the flavin, whose excited-state decays in <100 fs due to anion-π interactions. Such interactions appear absent in F - binding, which, however, significantly increases the active-site rigidity leading to more homogeneous, picosecond fluorescence decay kinetics. These findings are discussed in relation to the mechanism of halide inhibition of GOX by occupying the accommodation site of catalytic intermediates and increasing the active-site rigidity.
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Affiliation(s)
- Bo Zhuang
- Ecole Polytechnique, LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, FRANCE
| | - Marten H Vos
- CNRS UMR7645, Laboratory of Optics and Biosciences, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, FRANCE
| | - Alexey Aleksandrov
- Ecole Polytechnique, Laboratory of Optics and Biosciences, Department of Biology, rue du Saclay, 91128, Palaiseau, FRANCE
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6
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M.Abu-Dief A, Alotaibi NH, S.Al-Farraj E, Qasem HA, Alzahrani S, Mahfouz MK, Abdou A. Fabrication, Structural elucidation, DFT calculation and molecular docking studies of some novel adenine imine chelates for biomedical applications. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119961] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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7
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Abu-Dief AM, El-Khatib RM, Aljohani FS, Al-Abdulkarim HA, Alzahrani S, El-Sarrag G, Ismael M. Synthesis, Structural elucidation, DFT calculation, Biological studies and DNA Interaction of Some Aryl hydrazone Cr3+, Fe3+, and Cu2+ Chelates. Comput Biol Chem 2022; 97:107643. [DOI: 10.1016/j.compbiolchem.2022.107643] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/16/2022] [Accepted: 02/09/2022] [Indexed: 12/20/2022]
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8
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Lafaye C, Aumonier S, Torra J, Signor L, von Stetten D, Noirclerc-Savoye M, Shu X, Ruiz-González R, Gotthard G, Royant A, Nonell S. Riboflavin-binding proteins for singlet oxygen production. Photochem Photobiol Sci 2022; 21:1545-1555. [PMID: 35041199 DOI: 10.1007/s43630-021-00156-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022]
Abstract
miniSOG, developed as the first fully genetically encoded singlet oxygen photosensitiser, has found various applications in cell imaging and functional studies. Yet, miniSOG has suboptimal properties, including a low yield of singlet oxygen generation, which can nevertheless be improved tenfold upon blue light irradiation. In a previous study, we showed that this improvement was due to the photolysis of the miniSOG chromophore, flavin mononucleotide (FMN), into lumichrome, with concomitant removal of the phosphoribityl tail, thereby improving oxygen access to the alloxazine ring. We thus reasoned that a chromophore with a shorter tail would readily improve the photosensitizing properties of miniSOG. In this work, we show that the replacement of FMN by riboflavin (RF), which lacks the bulky phosphate group, significantly improves the singlet oxygen quantum yield (ΦΔ). We then proceeded to mutagenize the residues stabilizing the phosphate group of FMN to alter the chromophore specificity. We identified miniSOG-R57Q as a flavoprotein that selectively binds RF in cellulo, with a modestly improved ΦΔ. Our results show that it is possible to modify the flavin specificity of a given flavoprotein, thus providing a new option to tune its photophysical properties, including those leading to photosensitization. We also determined the structure of miniSOG-Q103L, a mutant with a much increased ΦΔ, which allowed us to postulate the existence of another access channel to FMN for molecular oxygen.
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Affiliation(s)
- Céline Lafaye
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - David von Stetten
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Marjolaine Noirclerc-Savoye
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, 94158-9001, USA.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94158-9001, USA
| | - Rubén Ruiz-González
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Guillaume Gotthard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Antoine Royant
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France. .,European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France.
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain.
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9
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Abu-Dief AM, El-khatib RM, Sayed SME, Alzahrani S, Alkhatib F, El-Sarrag G, Ismael M. Tailoring, structural elucidation, DFT calculation, DNA interaction and pharmaceutical applications of some aryl hydrazone Mn(II), Cu(II) and Fe(III) complexes. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131017] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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Structural and biochemical insights into a hyperthermostable urate oxidase from Thermobispora bispora for hyperuricemia and gout therapy. Int J Biol Macromol 2021; 188:914-923. [PMID: 34403675 DOI: 10.1016/j.ijbiomac.2021.08.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 01/21/2023]
Abstract
Microbial urate oxidase has emerged as a potential source of therapeutic properties for hyperuricemia in arthritic gout and renal disease. The thermostability and long-term thermal tolerance of the enzyme need to be established to prolong its therapeutic effects. Here, we present the biochemical and structural aspects of a hyperthermostable urate oxidase (TbUox) from the thermophilic microorganism Thermobispora bispora. Enzymatic characterization of TbUox revealed that it was active over a wide range of temperatures, from 30 to 70 °C, with optimal activity at 65 °C and pH 8.0, which suggests its applicability under physiological conditions. Moreover, TbUox exhibits high thermostability from 10 to 65 °C, with Tm of 70.3 °C and near-neutral pH stability from pH 7.0 to 8.0 and high thermal tolerance. The crystal structures of TbUox revealed a distinct feature of the C-terminal loop extensions that may help with protein stability via inter-subunit interactions. In addition, the high thermal tolerance of TbUox may be contributed by the extensive inter-subunit contacts via salt bridges, hydrogen bonds, and hydrophobic interactions. The findings in this study provide a molecular basis for the thermophilic TbUox urate oxidase for application in hyperuricemia and gout therapy.
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11
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Molecular Elucidation of a Urate Oxidase from Deinococcus radiodurans for Hyperuricemia and Gout Therapy. Int J Mol Sci 2021; 22:ijms22115611. [PMID: 34070642 PMCID: PMC8199477 DOI: 10.3390/ijms22115611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/02/2022] Open
Abstract
Urate oxidase initiates the uric acid degradation pathways and is extensively used for protein drug development for gout therapy and serum uric acid diagnosis. We first present the biochemical and structural elucidation of a urate oxidase from the extremophile microorganism Deinococcus radiodurans (DrUox). From enzyme characterization, DrUox showed optimal catalytic ability at 30 °C and pH 9.0 with high stability under physiological conditions. Only the Mg2+ ion moderately elevated its activity, which indicates the characteristic of the cofactor-free urate oxidase family. Of note, DrUox is thermostable in mesophilic conditions. It retains almost 100% activity when incubated at 25 °C and 37 °C for 24 h. In this study, we characterized a thermostable urate oxidase, DrUox with high catalytic efficiency and thermal stability, which strengthens its potential for medical applications.
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12
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Du K, Zemerov SD, Carroll PJ, Dmochowski IJ. Paramagnetic Shifts and Guest Exchange Kinetics in Co nFe 4-n Metal-Organic Capsules. Inorg Chem 2020; 59:12758-12767. [PMID: 32851844 DOI: 10.1021/acs.inorgchem.0c01816] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the magnetic resonance properties and exchange kinetics of guest molecules in a series of hetero-bimetallic capsules, [ConFe4-nL6]4- (n = 1-3), where L2- = 4,4'-bis[(2-pyridinylmethylene)amino]-[1,1'-biphenyl]-2,2'-disulfonate. H bond networks between capsule sulfonates and guanidinium cations promote the crystallization of [ConFe4-nL6]4-. The following four isostructural crystals are reported: two guest-free forms, (C(NH2)3)4[Co1.8Fe2.2L6]·69H2O (1) and (C(NH2)3)4[Co2.7Fe1.3L6]·73H2O (2), and two Xe- and CFCl3-encapsulated forms, (C(NH2)3)4[(Xe)0.8Co1.8Fe2.2L6]·69H2O (3) and (C(NH2)3)4[(CFCl3)Co2.0Fe2.0L6]·73H2O (4), respectively. Structural analyses reveal that Xe induces negligible structural changes in 3, while the angles between neighboring phenyl groups expand by ca. 3° to accommodate the much larger guest, CFCl3, in 4. These guest-encapsulated [ConFe4-nL6]4- molecules reveal 129Xe and 19F chemical shift changes of ca. -22 and -10 ppm at 298 K, respectively, per substitution of low-spin FeII by high-spin CoII. Likewise, the temperature dependence of the 129Xe and 19F NMR resonances increases by 0.1 and 0.06 ppm/K, respectively, with each additional paramagnetic CoII center. The optimal temperature for hyperpolarized (hp) 129Xe chemical exchange saturation transfer (hyper-CEST) with [ConFe4-nL6]4- capsules was found to be inversely proportional to the number of CoII centers, n, which is consistent with the Xe chemical exchange accelerating as the portals expand. The systematic study was facilitated by the tunability of the [M4L6]4- capsules, further highlighting these metal-organic systems for developing responsive sensors with highly shifted 129Xe resonances.
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Affiliation(s)
- Kang Du
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Serge D Zemerov
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Patrick J Carroll
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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13
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Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Nat Chem Biol 2020; 16:556-563. [DOI: 10.1038/s41589-020-0476-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/08/2020] [Indexed: 11/08/2022]
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14
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Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prangé T, Brunori M, Colloc’h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCRJ 2019; 6:832-842. [PMID: 31576217 PMCID: PMC6760443 DOI: 10.1107/s2052252519008157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Life and Environmental Sciences, New York–Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli–IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Avella
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy
| | - Cécile Exertier
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thierry Prangé
- CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France
| | - Maurizio Brunori
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nathalie Colloc’h
- ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France
| | - Beatrice Vallone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
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15
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Torra J, Lafaye C, Signor L, Aumonier S, Flors C, Shu X, Nonell S, Gotthard G, Royant A. Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein. Sci Rep 2019; 9:2428. [PMID: 30787421 PMCID: PMC6382843 DOI: 10.1038/s41598-019-38955-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/11/2019] [Indexed: 11/15/2022] Open
Abstract
miniSOG is the first flavin-binding protein that has been developed with the specific aim of serving as a genetically-encodable light-induced source of singlet oxygen (1O2). We have determined its 1.17 Å resolution structure, which has allowed us to investigate its mechanism of photosensitization using an integrated approach combining spectroscopic and structural methods. Our results provide a structural framework to explain the ability of miniSOG to produce 1O2 as a competition between oxygen- and protein quenching of its triplet state. In addition, a third excited-state decay pathway has been identified that is pivotal for the performance of miniSOG as 1O2 photosensitizer, namely the photo-induced transformation of flavin mononucleotide (FMN) into lumichrome, which increases the accessibility of oxygen to the flavin FMN chromophore and makes protein quenching less favourable. The combination of the two effects explains the increase in the 1O2 quantum yield by one order of magnitude upon exposure to blue light. Besides, we have identified several surface electron-rich residues that are progressively photo-oxidized, further contributing to facilitate the production of 1O2. Our results help reconcile the apparent poor level of 1O2 generation by miniSOG and its excellent performance in correlative light and electron microscopy experiments.
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Affiliation(s)
- Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona, 08017, Spain
| | - Céline Lafaye
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, F-38043, Grenoble, France
| | - Cristina Flors
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience), Ciudad Universitaria de Cantoblanco, C/Faraday 9, 28049, Madrid, Spain.,Nanobiotechnology Unit Associated to the National Center for Biotechnology (CNB-CSIC-IMDEA), Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, 94158-9001, United States.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California, 94158-9001, United States
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona, 08017, Spain.
| | | | - Antoine Royant
- Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale), F-38000, Grenoble, France. .,European Synchrotron Radiation Facility, F-38043, Grenoble, France.
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16
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Saleem-Batcha R, Teufel R. Structural methods for probing the interaction of flavoenzymes with dioxygen and its surrogates. Methods Enzymol 2019; 620:349-363. [DOI: 10.1016/bs.mie.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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17
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Enzymatic control of dioxygen binding and functionalization of the flavin cofactor. Proc Natl Acad Sci U S A 2018; 115:4909-4914. [PMID: 29686059 DOI: 10.1073/pnas.1801189115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O2) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O2, as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O2-pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O2 within a flavoenzyme's active site enables the regiospecific formation of a covalent flavin-oxygen adduct and oxygenating species (i.e., the flavin-N5-oxide) by mimicking a critical transition state. This study unambiguously demonstrates how enzymes may control the O2 functionalization of an organic cofactor as prerequisite for oxidative catalysis. Our work thus illustrates how O2 reactivity can be harnessed in an enzymatic environment and provides crucial knowledge for future rational design of O2-reactive enzymes.
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18
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Torabifard H, Cisneros GA. Computational investigation of O 2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O 2 transport. Chem Sci 2017; 8:6230-6238. [PMID: 28989656 PMCID: PMC5628400 DOI: 10.1039/c7sc00997f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
E. Coli AlkB catalyzes the direct dealkylation of various alkylated bases in damaged DNA. The diffusion of molecular oxygen to the active site in AlkB is an essential step for the oxidative dealkylation activity. Despite detailed studies on the stepwise oxidation mechanism of AlkB, there is no conclusive picture of how O2 molecules reach the active site of the protein. Yu et al. (Nature, 439, 879) proposed the existence of an intra-molecular tunnel based on their initial crystal structures of AlkB. We have employed computational simulations to investigate possible migration pathways inside AlkB for O2 molecules. Extensive molecular dynamics (MD) simulations, including explicit ligand sampling and potential of mean force (PMF) calculations, have been performed to provide a microscopic description of the O2 delivery pathway in AlkB. Analysis of intra-molecular tunnels using the CAVER software indicates two possible pathways for O2 to diffuse into the AlkB active site. Explicit ligand sampling simulations suggests that only one of these tunnels provides a viable route. The free energy path for an oxygen molecule to travel along each of these tunnels has been determined with AMBER and AMOEBA. Both PMFs indicate passive transport of O2 from the surface of the protein. However, the inclusion of explicit polarization shows a very large barrier for diffusion of the co-substrate out of the active site, compared with the non-polarizable potential. In addition, our results suggest that the mutation of a conserved residue along the tunnel, Y178, has dramatic effects on the dynamics of AlkB and on the transport of O2 along the tunnel.
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Affiliation(s)
- Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76203 , USA .
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19
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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: 67] [Impact Index Per Article: 9.6] [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.
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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
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20
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O'Dell WB, Agarwal PK, Meilleur F. Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610502] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division Oak Ridge National Laboratory P.O. Box 2008 Oak Ridge TN 37831 USA
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21
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O'Dell WB, Agarwal PK, Meilleur F. Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angew Chem Int Ed Engl 2016; 56:767-770. [PMID: 28004877 DOI: 10.1002/anie.201610502] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Indexed: 01/26/2023]
Abstract
Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. We have determined high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed "pre-bound" molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygen activation. These results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme-substrate complex.
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Affiliation(s)
- William B O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
| | - Pratul K Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville and Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University and Biology and Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
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22
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Lafumat B, Mueller-Dieckmann C, Leonard G, Colloc'h N, Prangé T, Giraud T, Dobias F, Royant A, van der Linden P, Carpentier P. Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel `soak-and-freeze' methodology. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716010992] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Molecular oxygen (O2) is a key player in many fundamental biological processes. However, the combination of the labile nature and poor affinity of O2 often makes this substrate difficult to introduce into crystals at sufficient concentrations to enable protein/O2 interactions to be deciphered in sufficient detail. To overcome this problem, a gas pressure cell has been developed specifically for the `soak-and-freeze' preparation of crystals of O2-dependent biological molecules. The `soak-and-freeze' method uses high pressure to introduce oxygen molecules or krypton atoms (O2 mimics) into crystals which, still under high pressure, are then cryocooled for X-ray data collection. Here, a proof of principle of the gas pressure cell and the methodology developed is demonstrated with crystals of enzymes (lysozyme, thermolysin and urate oxidase) that are known to absorb and bind molecular oxygen and/or krypton. The successful results of these experiments lead to the suggestion that the soak-and-freeze method could be extended to studies involving a wide range of gases of biological, medical and/or environmental interest, including carbon monoxide, ethylene, methane and many others.
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23
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Di Russo NV, Condurso HL, Li K, Bruner SD, Roitberg AE. Oxygen diffusion pathways in a cofactor-independent dioxygenase. Chem Sci 2015; 6:6341-6348. [PMID: 26508997 PMCID: PMC4618494 DOI: 10.1039/c5sc01638j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A combination of experimental and computational studies reveals the main O2 diffusion pathways, providing insight into how cofactor-independent oxygenases control stereospecificity and prevent oxidative inactivation.
Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O2 diffusion is emerging, where specific channels guide O2 to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O2 reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O2 at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O2 in the absence of cofactors or metals, the way O2 reaches the active site is similar to that reported for other O2-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O2 access that are conserved among very different types of proteins.
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Affiliation(s)
- Natali V Di Russo
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Heather L Condurso
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Kunhua Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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24
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Crystal structure of Bacillus fastidious uricase reveals an unexpected folding of the C-terminus residues crucial for thermostability under physiological conditions. Appl Microbiol Biotechnol 2015; 99:7973-86. [DOI: 10.1007/s00253-015-6520-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 02/22/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
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25
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Zafred D, Steiner B, Teufelberger AR, Hromic A, Karplus PA, Schofield CJ, Wallner S, Macheroux P. Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction. FEBS J 2015; 282:3060-74. [PMID: 25619330 DOI: 10.1111/febs.13212] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
Abstract
UNLABELLED The ability of flavoenzymes to reduce dioxygen varies greatly, and is controlled by the protein environment, which may cause either a rapid reaction (oxidases) or a sluggish reaction (dehydrogenases). Previously, a 'gatekeeper' amino acid residue was identified that controls the reactivity to dioxygen in proteins from the vanillyl alcohol oxidase superfamily of flavoenzymes. We have identified an alternative gatekeeper residue that similarly controls dioxygen reactivity in the grass pollen allergen Phl p 4, a member of this superfamily that has glucose dehydrogenase activity and the highest redox potential measured in a flavoenzyme. A substitution at the alternative gatekeeper site (I153V) transformed the enzyme into an efficient oxidase by increasing dioxygen reactivity by a factor of 60,000. An inverse exchange (V169I) in the structurally related berberine bridge enzyme (BBE) decreased its dioxygen reactivity by a factor of 500. Structural and biochemical characterization of these and additional variants showed that our model enzymes possess a cavity that binds an anion and resembles the 'oxyanion hole' in the proximity of the flavin ring. We showed also that steric control of access to this site is the most important parameter affecting dioxygen reactivity in BBE-like enzymes. Analysis of flavin-dependent oxidases from other superfamilies revealed similar structural features, suggesting that dioxygen reactivity may be governed by a common mechanistic principle. DATABASE Structural data are available in PDB database under the accession numbers 4PVE, 4PVH, 4PVJ, 4PVK, 4PWB, 4PWC and 4PZF.
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Affiliation(s)
- Domen Zafred
- Institute of Biochemistry, Graz University of Technology, Austria.,Institute of Molecular Biosciences, University of Graz, Austria
| | - Barbara Steiner
- Institute of Biochemistry, Graz University of Technology, Austria
| | | | - Altijana Hromic
- Institute of Molecular Biosciences, University of Graz, Austria
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | | | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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26
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Sedláček V, Ptáčková N, Rejmontová P, Kučera I. The flavoprotein FerB ofParacoccus denitrificansbinds to membranes, reduces ubiquinone and superoxide, and acts as anin vivoantioxidant. FEBS J 2014; 282:283-96. [DOI: 10.1111/febs.13126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Vojtĕch Sedláček
- Department of Biochemistry; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Nikola Ptáčková
- Department of Biochemistry; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Petra Rejmontová
- Department of Biochemistry; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Igor Kučera
- Department of Biochemistry; Faculty of Science; Masaryk University; Brno Czech Republic
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27
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Meersman F, McMillan PF. High hydrostatic pressure: a probing tool and a necessary parameter in biophysical chemistry. Chem Commun (Camb) 2014; 50:766-75. [PMID: 24286104 DOI: 10.1039/c3cc45844j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High pressures extending up to several thousands of atmospheres provide extreme conditions for biological organisms to survive. Recent studies are investigating the survival mechanisms and biological function of microorganisms under natural and laboratory conditions extending into the GigaPascal range, with applications to understanding the Earth's deep biosphere and food technology. High pressure has also emerged as a useful tool and physical parameter for probing changes in the structure and functional properties of biologically important macromolecules and polymers encountered in soft matter science. Here we highlight some areas of current interest in high pressure biophysics and physical chemistry that are emerging at the frontier of this cross-disciplinary field.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, UK.
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28
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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.
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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
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29
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Colloc'h N, Prangé T. Functional relevance of the internal hydrophobic cavity of urate oxidase. FEBS Lett 2014; 588:1715-9. [PMID: 24657440 DOI: 10.1016/j.febslet.2014.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Urate oxidase from Aspergillus flavus is a 135 kDa homo-tetramer which has a hydrophobic cavity buried within each monomer and located close to its active site. Crystallographic studies under moderate gas pressure and high hydrostatic pressure have shown that both gas presence and high pressure would rigidify the cavity leading to an inhibition of the catalytic activity. Analysis of the cavity volume variations and functional modifications suggest that the flexibility of the cavity would be an essential parameter for the active site efficiency. This cavity would act as a connecting vessel to give flexibility to the neighboring active site, and its expansion under pure oxygen pressure reveals that it might serve as a transient reservoir on its pathway to the active site.
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Affiliation(s)
- Nathalie Colloc'h
- CERVoxy Team, ISTCT UMR 6301, CNRS, Centre Cyceron, Caen, France; ISTCT UMR 6301, CEA, DSV/I2BM, Caen, France; ISTCT UMR 6301, Université de Caen Basse-Normandie, Normandie Université, Caen, France.
| | - Thierry Prangé
- LCRB UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75006 Paris, France
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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.
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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.
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31
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Murakawa T, Hayashi H, Sunami T, Kurihara K, Tamada T, Kuroki R, Suzuki M, Tanizawa K, Okajima T. High-resolution crystal structure of copper amine oxidase fromArthrobacter globiformis: assignment of bound diatomic molecules as O2. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2483-94. [DOI: 10.1107/s0907444913023196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/18/2013] [Indexed: 11/10/2022]
Abstract
The crystal structure of a copper amine oxidase fromArthrobacter globiformiswas determined at 1.08 Å resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight ∼200) as a cryoprotectant. The final crystallographicRfactor andRfreewere 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overallBfactor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of ∼70 000. About 40% of the presumed H atoms were observed as clear electron densities in theFo−Fcdifference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site.
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32
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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.
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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
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Cazade PA, Meuwly M. Oxygen migration pathways in NO-bound truncated hemoglobin. Chemphyschem 2012; 13:4276-86. [PMID: 23161831 DOI: 10.1002/cphc.201200608] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/28/2012] [Indexed: 11/10/2022]
Abstract
Atomistic simulations of dioxygen (O(2)) dynamics and migration in nitric oxide-bound truncated Hemoglobin N (trHbN) of Mycobacterium tuberculosis are reported. From more than 100 ns of simulations the connectivity network involving the metastable states for localization of the O(2) ligand is built and analyzed. It is found that channel I is the primary entrance point for O(2) whereas channel II is predominantly an exit path although access to the protein active site is also possible. For O(2) a new site compared to nitric oxide, from which reaction with the heme group can occur, was found. As this site is close to the heme iron, it could play an important role in the dioxygenation mechanism as O(2) can remain there for hundreds of picoseconds after which it can eventually leave the protein, while NO is localized in Xe2. The present study supports recent experimental work which proposed that O(2) docks in alternative pockets than Xe close to the reactive site. Similar to other proteins, a phenylalanine residue (Phe62) plays the role of a gate along the access route in channel I. The most highly connected site is the Xe3 pocket which is a "hub" and free energy barriers between the different metastable states are ≈1.5 kcal mol(-1) which allows facile O(2) migration within the protein.
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Affiliation(s)
- Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056, Basel, Switzerland
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34
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Frankel LK, Sallans L, Limbach PA, Bricker TM. Identification of oxidized amino acid residues in the vicinity of the Mn(4)CaO(5) cluster of Photosystem II: implications for the identification of oxygen channels within the Photosystem. Biochemistry 2012; 51:6371-7. [PMID: 22827410 DOI: 10.1021/bi300650n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As a light-driven water-plastoquinone oxidoreductase, Photosystem II produces molecular oxygen as an enzymatic product. Additionally, under a variety of stress conditions, reactive oxygen species are produced at or near the active site for oxygen evolution. In this study, Fourier-transform ion cyclotron resonance mass spectrometry was used to identify oxidized amino acid residues located in several core Photosystem II proteins (D1, D2, CP43, and CP47) isolated from spinach Photosystem II membranes. While the majority of these oxidized residues (81%) are located on the oxygenated solvent-exposed surface of the complex, several residues on the CP43 protein ((354)E, (355)T, (356)M, and (357)R) which are in close proximity (<15 Å) to the Mn(4)CaO(5) active site are also modified. These residues appear to be associated with putative oxygen/reactive oxygen species exit channel(s) in the photosystem. These results are discussed within the context of a number of computational studies which have identified putative oxygen channels within the photosystem.
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Affiliation(s)
- Laurie K Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, USA
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35
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Tian H, Guo Y, Gao X, Yao W. PEGylation enhancement of pH stability of uricase via inhibitive tetramer dissociation. J Pharm Pharmacol 2012; 65:53-63. [DOI: 10.1111/j.2042-7158.2012.01575.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract
Objectives
Previously, PEGylated uricase was demonstrated to maintain catalytic activity at pH 5.8, the isoelectric point of uricase, where native uricase ceases to function. To find out whether PEGylation could enhance pH stability of uricase, the enzyme activity to pH curve was completely characterized.
Methods
Complete characterization of the enzyme activity to pH curve, indicating an inverted bell-shaped relationship not previously documented, is presented. PEGylation enhancement of uricase stability at a pH lower than that commonly found in the liver, can be explored by dynamic dissociation of uricase using ultrafiltration and size-exclusion chromatography.
Key findings
The results suggest the role of PEGylation in enhanced pH stability is via inhibition of subunit disintegration. The mechanism of this effect is characterized by the wrapping of PEG chains around uricase, providing a flexible shell preventing subunit disintegration. The presence of notable PEGylation-induced changes in uricase supports this mechanism and include improved enzyme-substrate affinity and elevated thermal stability.
Conclusions
Characterization of PEGylated uricase provides a basis for the rational design of therapeutic PEGylated proteins.
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Affiliation(s)
- Hong Tian
- College of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuan Guo
- College of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Xiangdong Gao
- College of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Wenbing Yao
- College of Life Science and Technology, China Pharmaceutical University, Nanjing, China
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Siitonen V, Blauenburg B, Kallio P, Mäntsälä P, Metsä-Ketelä M. Discovery of a Two-Component Monooxygenase SnoaW/SnoaL2 Involved in Nogalamycin Biosynthesis. ACTA ACUST UNITED AC 2012; 19:638-46. [DOI: 10.1016/j.chembiol.2012.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/16/2012] [Accepted: 04/04/2012] [Indexed: 11/30/2022]
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Zhang C, Fan K, Zhang W, Zhu R, Zhang L, Wei D. Structure-based characterization of canine-human chimeric uricases and its evolutionary implications. Biochimie 2012; 94:1412-20. [PMID: 22481018 DOI: 10.1016/j.biochi.2012.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 03/21/2012] [Indexed: 02/04/2023]
Abstract
Uricase was lost in hominoids during primate evolution, but the inactivation mechanism remains controversial. To investigate the inactivation process of hominoid uricase, chimeric constructions between canine and human uricase were employed to screen the target regions that may contain labile or inactivated mutations in deduced human uricase. Four chimeric uricases were constructed and showed different enzymatic characteristics. Homology modeling, rational site-directed mutagenesis and DNA alignment were used to analyze the changes. Arg119 is conserved in functional mammalian uricases and its side-chains are crucial in maintaining the stability of the β-barrel core. A single CGT (Arg) to CAT (His) mutation at codon 119 that is shared by the human and great ape clade greatly reduces this stability and could cause the loss of uricase activity. We speculate that this missense mutation occurred first and inactivated the uricase protein in humans and great apes and that later the known nonsense mutation at codon 33 occurred and silenced the uricase gene. A single GTC (Val) to GCC (Ala) mutation at codon 296 in canine uricase is regarded as deleterious structural mutation, but such kinds of deleterious mutations have been widely accumulated in extant mammalian uricases. We speculate that a reduction in uricase activity has been an evolutionary tendency in mammals. Moreover, from structure-activity analysis of helix 2 in ancestral primate uricase, we suggest that before the inactivation of hominoid uricase, deleterious structural evolutionary changes had occurred in ancestral primates. The loss of hominoid uricase should be caused by progressive multistep mutations rather than a single mutation event.
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Affiliation(s)
- Chun Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, PR China
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38
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Collins MD, Kim CU, Gruner SM. High-pressure protein crystallography and NMR to explore protein conformations. Annu Rev Biophys 2011; 40:81-98. [PMID: 21275639 DOI: 10.1146/annurev-biophys-042910-155304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-pressure methods for solving protein structures by X-ray crystallography and NMR are maturing. These techniques are beginning to impact our understanding of thermodynamic and structural features that define not only the protein's native conformation, but also the higher free energy conformations. The ability of high-pressure methods to visualize these mostly unexplored conformations provides new insight into protein function and dynamics. In this review, we begin with a historical discussion of high-pressure structural studies, with an eye toward early results that paved the way to mapping the multiple conformations of proteins. This is followed by an examination of several recent studies that emphasize different strengths and uses of high-pressure structural studies, ranging from basic thermodynamics to the suggestion of high-pressure structural methods as a tool for protein engineering.
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Affiliation(s)
- Marcus D Collins
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195-7290, USA
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39
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Pipolo S, Percudani R, Cammi R. Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra. Org Biomol Chem 2011; 9:5149-55. [PMID: 21647520 DOI: 10.1039/c1ob05433c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The enzymatic oxidation of urate leads to the sequential formation of optically active intermediates with unknown stereochemistry: (-)-5-hydroxyisourate (HIU) and (-)-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). In accordance with the observation that a defect in HIU hydrolase causes hepatocarcinoma in mouse, a detoxification role has been proposed for the enzymes accelerating the conversion of HIU and OHCU into optically active (+)-allantoin. The enzymatic products of urate oxidation are normally not present in humans, but are formed in patients treated with urate oxidase. We used time-dependent density functional theory (TDDFT) to compute the electronic circular dichroism (ECD) spectra of the chiral compounds of urate degradation (HIU, OHCU, allantoin) and we compared the results with experimentally measured ECD spectra. The calculated ECD spectra for (S)-HIU and (S)-OHCU reproduced well the experimental spectra obtained through the enzymatic degradation of urate. Less conclusive results were obtained with allantoin, although the computed optical rotations in the transparent region supported the original assignment of the (+)-S configuration. These absolute configuration assignments can facilitate the study of the enzymes involved in urate metabolism and help us to understand the mechanism leading to the toxicity of urate oxidation products.
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Affiliation(s)
- Silvio Pipolo
- Dipartimento di Chimica G.I.A.F, Universitá di Parma, 43100, Parma, Italy
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40
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Kommoju PR, Chen ZW, Bruckner RC, Mathews FS, Jorns MS. Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate. Biochemistry 2011; 50:5521-34. [PMID: 21568312 DOI: 10.1021/bi200388g] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A single basic residue above the si-face of the flavin ring is the site of oxygen activation in glucose oxidase (GOX) (His516) and monomeric sarcosine oxidase (MSOX) (Lys265). Crystal structures of both flavoenzymes exhibit a small pocket at the oxygen activation site that might provide a preorganized binding site for superoxide anion, an obligatory intermediate in the two-electron reduction of oxygen. Chloride binds at these polar oxygen activation sites, as judged by solution and structural studies. First, chloride forms spectrally detectable complexes with GOX and MSOX. The protonated form of His516 is required for tight binding of chloride to oxidized GOX and for rapid reaction of reduced GOX with oxygen. Formation of a binary MSOX·chloride complex requires Lys265 and is not observed with Lys265Met. Binding of chloride to MSOX does not affect the binding of a sarcosine analogue (MTA, methylthioactetate) above the re-face of the flavin ring. Definitive evidence is provided by crystal structures determined for a binary MSOX·chloride complex and a ternary MSOX·chloride·MTA complex. Chloride binds in the small pocket at a position otherwise occupied by a water molecule and forms hydrogen bonds to four ligands that are arranged in approximate tetrahedral geometry: Lys265:NZ, Arg49:NH1, and two water molecules, one of which is hydrogen bonded to FAD:N5. The results show that chloride (i) acts as an oxygen surrogate, (ii) is an effective probe of polar oxygen activation sites, and (iii) provides a valuable complementary tool to the xenon gas method that is used to map nonpolar oxygen-binding cavities.
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Affiliation(s)
- Phaneeswara-Rao Kommoju
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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41
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Gabison L, Chopard C, Colloc'h N, Peyrot F, Castro B, Hajji ME, Altarsha M, Monard G, Chiadmi M, Prangé T. X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase. Proteins 2011; 79:1964-76. [DOI: 10.1002/prot.23022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 02/09/2011] [Accepted: 02/11/2011] [Indexed: 11/11/2022]
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42
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RoseFigura JM, Puehringer S, Schwarzenbacher R, Toyama H, Klinman JP. Characterization of a protein-generated O₂ binding pocket in PqqC, a cofactorless oxidase catalyzing the final step in PQQ production. Biochemistry 2011; 50:1556-66. [PMID: 21155540 DOI: 10.1021/bi1015474] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PQQ is an exogenous, tricyclic, quino-cofactor for a number of bacterial dehydrogenases. The final step of PQQ formation is catalyzed by PqqC, a cofactorless oxidase. This study focuses on the activation of molecular oxygen in an enzyme active site without metal or cofactor and has identified a specific oxygen binding and activating pocket in PqqC. The active site variants H154N, Y175F,S, and R179S were studied with the goal of defining the site of O(2) binding and activation. Using apo-glucose dehydrogenase to assay for PQQ production, none of the mutants in this "O(2) core" are capable of PQQ/PQQH(2) formation. Spectrophotometric assays give insight into the incomplete reactions being catalyzed by these mutants. Active site variants Y175F, H154N, and R179S form a quinoid intermediate (Figure 1) anaerobically. Y175S is capable of proceeding further from quinoid to quinol, whereas Y175F, H154N, and R179S require O(2) to produce the quinol species. None of the mutations precludes substrate/product binding or oxygen binding. Assays for the oxidation of PQQH(2) to PQQ show that these O(2) core mutants are incapable of catalyzing a rate increase over the reaction in buffer, whereas H154N can catalyze the oxidation of PQQH(2) to PQQ in the presence of H(2)O(2) as an electron acceptor. Taken together, these data indicate that none of the targeted mutants can react fully to form quinone even in the presence of bound O(2). The data indicate a successful separation of oxidative chemistry from O(2) binding. The residues H154, Y175, and R179 are proposed to form a core O(2) binding structure that is essential for efficient O(2) activation.
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Affiliation(s)
- Jordan M RoseFigura
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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43
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Lautier T, Ezanno P, Baffert C, Fourmond V, Cournac L, Fontecilla-Camps JC, Soucaille P, Bertrand P, Meynial-Salles I, Léger C. The quest for a functional substrate access tunnel in FeFe hydrogenase. Faraday Discuss 2011; 148:385-407; discussion 421-41. [DOI: 10.1039/c004099c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Estarellas C, Frontera A, Quiñonero D, Deyà PM. Relevant Anion-π Interactions in Biological Systems: The Case of Urate Oxidase. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005635] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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45
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Estarellas C, Frontera A, Quiñonero D, Deyà PM. Relevant Anion-π Interactions in Biological Systems: The Case of Urate Oxidase. Angew Chem Int Ed Engl 2010; 50:415-8. [DOI: 10.1002/anie.201005635] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Girard E, Marchal S, Perez J, Finet S, Kahn R, Fourme R, Marassio G, Dhaussy AC, Prangé T, Giffard M, Dulin F, Bonneté F, Lange R, Abraini JH, Mezouar M, Colloc'h N. Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure. Biophys J 2010; 98:2365-73. [PMID: 20483346 DOI: 10.1016/j.bpj.2010.01.058] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/26/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022] Open
Abstract
Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms.
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Affiliation(s)
- Eric Girard
- Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA CNRS UJF, Grenoble, France
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47
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Bento I, Silva CS, Chen Z, Martins LO, Lindley PF, Soares CM. Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer. BMC STRUCTURAL BIOLOGY 2010; 10:28. [PMID: 20822511 PMCID: PMC2944330 DOI: 10.1186/1472-6807-10-28] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 09/07/2010] [Indexed: 01/24/2023]
Abstract
BACKGROUND Laccases are enzymes that couple the oxidation of substrates with the reduction of dioxygen to water. They are the simplest members of the multi-copper oxidases and contain at least two types of copper centres; a mononuclear T1 and a trinuclear that includes two T3 and one T2 copper ions. Substrate oxidation takes place at the mononuclear centre whereas reduction of oxygen to water occurs at the trinuclear centre. RESULTS In this study, the CotA laccase from Bacillus subtilis was used as a model to understand the mechanisms taking place at the molecular level, with a focus in the trinuclear centre. The structures of the holo-protein and of the oxidised form of the apo-protein, which has previously been reconstituted in vitro with Cu(I), have been determined. The former has a dioxygen moiety between the T3 coppers, while the latter has a monoatomic oxygen, here interpreted as a hydroxyl ion. The UV/visible spectra of these two forms have been analysed in the crystals and compared with the data obtained in solution. Theoretical calculations on these and other structures of CotA were used to identify groups that may be responsible for channelling the protons that are needed for reduction of dioxygen to water. CONCLUSIONS These results present evidence that Glu 498 is the only proton-active group in the vicinity of the trinuclear centre. This strongly suggests that this residue may be responsible for channelling the protons needed for the reduction. These results are compared with other data available for these enzymes, highlighting similarities and differences within laccases and multicopper oxidases.
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Affiliation(s)
- Isabel Bento
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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Duggan KC, Walters MJ, Musee J, Harp JM, Kiefer JR, Oates JA, Marnett LJ. Molecular basis for cyclooxygenase inhibition by the non-steroidal anti-inflammatory drug naproxen. J Biol Chem 2010; 285:34950-9. [PMID: 20810665 DOI: 10.1074/jbc.m110.162982] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Naproxen ((S)-6-methoxy-α-methyl-2-naphthaleneacetic acid) is a powerful non-selective non-steroidal anti-inflammatory drug that is extensively used as a prescription and over-the-counter medication. Naproxen exhibits gastrointestinal toxicity, but its cardiovascular toxicity may be reduced compared with other drugs in its class. Despite the fact that naproxen has been marketed for many years, the molecular basis of its interaction with cyclooxygenase (COX) enzymes is unknown. We performed a detailed study of naproxen-COX-2 interactions using site-directed mutagenesis, structure-activity analysis, and x-ray crystallography. The results indicate that each of the pendant groups of the naphthyl scaffold are essential for COX inhibition, and only minimal substitutions are tolerated. Mutation of Trp-387 to Phe significantly reduced inhibition by naproxen, a result that appears unique to this inhibitor. Substitution of S or CH(2) for the O atom of the p-methoxy group yielded analogs that were not affected by the W387F substitution and that exhibited increased COX-2 selectivity relative to naproxen. Crystallization and x-ray analysis yielded structures of COX-2 complexed to naproxen and its methylthio analog at 1.7 and 2.3 Å resolution, respectively. The combination of mutagenesis, structure analysis, and x-ray crystallography provided comprehensive information on the unique interactions responsible for naproxen binding to COX-2.
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Affiliation(s)
- Kelsey C Duggan
- AB Hancock Jr Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt Institute for Chemical Biology, the Center in Molecular Toxicology, Nashville, Tennessee 37232-0146
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Gabison L, Chiadmi M, El Hajji M, Castro B, Colloc'h N, Prangé T. Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:714-24. [DOI: 10.1107/s090744491001142x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 03/25/2010] [Indexed: 02/04/2023]
Abstract
Urate oxidase (uricase; EC 1.7.3.3; UOX) fromAspergillus flavuscatalyzes the oxidation of uric acid in the presence of molecular oxygen to 5-hydroxyisourate in the degradation cascade of purines; intriguingly, catalysis proceeds using neither a metal ion (Fe, Cuetc.) nor a redox cofactor. UOX is a tetrameric enzyme with four active sites located at the interface of two subunits; its structure was refined at atomic resolution (1 Å) using new crystal data in the presence of xanthine and at near-atomic resolution (1.3–1.7 Å) in complexes with the natural substrate (urate) and two inhibitors: 8-nitroxanthine and 8-thiouric acid. Three new features of the structural and mechanistic behaviour of the enzyme were addressed. Firstly, the high resolution of the UOX–xanthine structure allowed the solution of an old structural problem at a contact zone within the tetramer; secondly, the protonation state of the substrate was determined from both a halochromic inhibitor complex (UOX–8-nitroxanthine) and from the H-atom distribution in the active site, using the structures of the UOX–xanthine and the UOX–uric acid complexes; and thirdly, it was possible to extend the general base system, characterized by the conserved catalytic triad Thr–Lys–His, to a large water network that is able to buffer and shuttle protons back and forth between the substrate and the peroxo hole along the reaction pathway.
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Grocholski T, Koskiniemi H, Lindqvist Y, Mäntsälä P, Niemi J, Schneider G. Crystal structure of the cofactor-independent monooxygenase SnoaB from Streptomyces nogalater: implications for the reaction mechanism. Biochemistry 2010; 49:934-44. [PMID: 20052967 DOI: 10.1021/bi901985b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SnoaB is a cofactor-independent monooxygenase that catalyzes the conversion of 12-deoxynogalonic acid to nogalonic acid in the biosynthesis of the aromatic polyketide nogalamycin in Streptomyces nogalater. In vitro (18)O(2) experiments establish that the oxygen atom incorporated into the substrate is derived from molecular oxygen. The crystal structure of the enzyme was determined in two different space groups to 1.7 and 1.9 A resolution, respectively. The enzyme displays the ferredoxin fold, with the characteristic beta-strand exchange at the dimer interface. The crystal structures reveal a putative catalytic triad involving two asparagine residues, Asn18 and Asn63, and a water molecule, which may play important roles in the enzymatic reaction. Site-directed mutagenesis experiments, replacing the two asparagines individually by alanine, led to a 100-fold drop in enzymatic activity. Replacement of an invariant tryptophan residue in the active site of the enzyme by phenylalanine also resulted in an enzyme variant with about 1% residual activity. Taken together, our findings are most consistent with a carbanion mechanism where the deprotonated substrate reacts with molecular oxygen via one electron transfer and formation of a caged radical.
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Affiliation(s)
- Thadee Grocholski
- Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
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