Relevant bibliographies by topics / Oxidoreductases, X-Ray Crystallography

Academic literature on the topic 'Oxidoreductases, X-Ray Crystallography'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Oxidoreductases, X-Ray Crystallography"

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Gibson, Marcus I., Percival Yang-Ting Chen, Aileen C. Johnson, Elizabeth Pierce, Mehmet Can, Stephen W. Ragsdale, and Catherine L. Drennan. "One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography." Proceedings of the National Academy of Sciences 113, no. 2 (December 28, 2015): 320–25. http://dx.doi.org/10.1073/pnas.1518537113.

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Thiamine pyrophosphate (TPP)-dependent oxalate oxidoreductase (OOR) metabolizes oxalate, generating two molecules of CO2and two low-potential electrons, thus providing both the carbon and reducing equivalents for operation of the Wood−Ljungdahl pathway of acetogenesis. Here we present structures of OOR in which two different reaction intermediate bound states have been trapped: the covalent adducts between TPP and oxalate and between TPP and CO2. These structures, along with the previously determined structure of substrate-free OOR, allow us to visualize how active site rearrangements can drive catalysis. Our results suggest that OOR operates via a bait-and-switch mechanism, attracting substrate into the active site through the presence of positively charged and polar residues, and then altering the electrostatic environment through loop and side chain movements to drive catalysis. This simple but elegant mechanism explains how oxalate, a molecule that humans and most animals cannot break down, can be used for growth by acetogenic bacteria.
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Zhang, Yanfei, Maia M. Cherney, Matthew Solomonson, Jianshe Liu, Michael N. G. James, and Joel H. Weiner. "Preliminary X-ray crystallographic analysis of sulfide:quinone oxidoreductase fromAcidithiobacillus ferrooxidans." Acta Crystallographica Section F Structural Biology and Crystallization Communications 65, no. 8 (July 30, 2009): 839–42. http://dx.doi.org/10.1107/s1744309109027535.

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Barber, James. "Photosystem II: the engine of life." Quarterly Reviews of Biophysics 36, no. 1 (January 27, 2003): 71–89. http://dx.doi.org/10.1017/s0033583502003839.

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1. Introduction 712. Electron transfer in PS II 723. (Mn)4cluster and mechanism of water oxidation 734. Organization and structure of the protein subunits 755. Organization of chlorophylls and redox active cofactors 816. Implications arising from the structural models 827. Perspectives 848. Acknowledgements 869. Addendum 8610. References 87Photosystem II (PS II) is a multisubunit membrane protein complex, which uses light energy to oxidize water and reduce plastoquinone. High-resolution electron cryomicroscopy and X-ray crystallography are revealing the structure of this important molecular machine. Both approaches have contributed to our understanding of the organization of the transmembrane helices of higher plant and cyanobacterial PS II and both indicate that PS II normally functions as a dimer. However the high-resolution electron density maps derived from X-ray crystallography currently at 3·7/3·8 Å, have allowed assignments to be made to the redox active cofactors involved in the light-driven water–plastoquinone oxidoreductase activity and to the chlorophyll molecules that absorb and transfer energy to the reaction centre. In particular the X-ray work has identified density that can accommodate the four manganese atoms which catalyse the water-oxidation process. The Mn cluster is located at the lumenal surface of the D1 protein and approximately 7 Å from the redox active tyrosine residue (YZ) which acts an electron/proton transfer link to the primary oxidant P680.+. The lower resolution electron microscopy studies, however, are providing structural models of larger PS II supercomplexes that are ideal frameworks in which to incorporate the X-ray derived structures.
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Panicker, Lata, Hari Sharan Misra, and Subhash Chandra Bihani. "Purification, crystallization and preliminary crystallographic investigation of FrnE, a disulfide oxidoreductase fromDeinococcus radiodurans." Acta Crystallographica Section F Structural Biology Communications 70, no. 11 (October 25, 2014): 1540–42. http://dx.doi.org/10.1107/s2053230x14020330.

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In prokaryotes, Dsb proteins catalyze the formation of native disulfide bonds through an oxidative folding pathway and are part of the cell machinery that protects proteins from oxidative stress.Deinococcus radioduransis an extremophile which shows unparalleled resistance to ionizing radiation and oxidative stress. It has a strong mechanism to protect its proteome from oxidative damage. The genome ofDeinococcusshows the presence of FrnE, a Dsb protein homologue that potentially provides the bacterium with oxidative stress tolerance. Here, crystallization and preliminary X-ray crystallographic analysis of FrnE fromD. radioduransare reported. Diffraction-quality single crystals were obtained using the hanging-drop vapour-diffusion method with reservoir solution consisting of 100 mMsodium acetate pH 5.0, 10% PEG 8000, 15–20% glycerol. Diffraction data were collected on an Agilent SuperNova system using a microfocus sealed-tube X-ray source. The crystal diffracted to 1.8 Å resolution at 100 K. The space group of the crystal was found to beP21221, with unit-cell parametersa= 47.91,b= 62.94,c= 86.75 Å, α = β = γ = 90°. Based on Matthews coefficient analysis, one monomer per asymmetric unit is present in the crystal, with a solvent content of approximately 45%.
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IGARASHI, Noriyuki. "X-ray Crystallographic Structure of the Novel Multipleheme Enzyme, Hydroxylamine Oxidoreductase from Nitrosomonas Europaea." Nihon Kessho Gakkaishi 41, no. 5 (1999): 283–92. http://dx.doi.org/10.5940/jcrsj.41.283.

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Cherrier, Mickaël V., Xavier Vernède, Daphna Fenel, Lydie Martin, Benoit Arragain, Emmanuelle Neumann, Juan C. Fontecilla-Camps, Guy Schoehn, and Yvain Nicolet. "Oxygen-Sensitive Metalloprotein Structure Determination by Cryo-Electron Microscopy." Biomolecules 12, no. 3 (March 12, 2022): 441. http://dx.doi.org/10.3390/biom12030441.

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Metalloproteins are involved in key cell processes such as photosynthesis, respiration, and oxygen transport. However, the presence of transition metals (notably iron as a component of [Fe-S] clusters) often makes these proteins sensitive to oxygen-induced degradation. Consequently, their study usually requires strict anaerobic conditions. Although X-ray crystallography has been the method of choice for solving macromolecular structures for many years, recently electron microscopy has also become an increasingly powerful structure-solving technique. We have used our previous experience with cryo-crystallography to develop a method to prepare cryo-EM grids in an anaerobic chamber and have applied it to solve the structures of apoferritin and the 3 [Fe4S4]-containing pyruvate ferredoxin oxidoreductase (PFOR) at 2.40 Å and 2.90 Å resolution, respectively. The maps are of similar quality to the ones obtained under air, thereby validating our method as an improvement in the structural investigation of oxygen-sensitive metalloproteins by cryo-EM.
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Mano, Jun’ichi, Hye-Jin Yoon, Kozi Asada, Elena Babiychuk, Dirk Inzé, and Bunzo Mikami. "Crystallization and preliminary X-ray crystallographic analysis of NADPH: azodicarbonyl/quinone oxidoreductase, a plant ζ-crystallin." Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1480, no. 1-2 (July 2000): 374–76. http://dx.doi.org/10.1016/s0167-4838(00)00073-x.

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Kmita, Katarzyna, Christophe Wirth, Judith Warnau, Sergio Guerrero-Castillo, Carola Hunte, Gerhard Hummer, Ville R. I. Kaila, Klaus Zwicker, Ulrich Brandt, and Volker Zickermann. "Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I." Proceedings of the National Academy of Sciences 112, no. 18 (April 20, 2015): 5685–90. http://dx.doi.org/10.1073/pnas.1424353112.

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Mitochondrial proton-pumping NADH:ubiquinone oxidoreductase (respiratory complex I) comprises more than 40 polypeptides and contains eight canonical FeS clusters. The integration of subunits and insertion of cofactors into the nascent complex is a complicated multistep process that is aided by assembly factors. We show that the accessory NUMM subunit of complex I (human NDUFS6) harbors a Zn-binding site and resolve its position by X-ray crystallography. Chromosomal deletion of the NUMM gene or mutation of Zn-binding residues blocked a late step of complex I assembly. An accumulating assembly intermediate lacked accessory subunit N7BM (NDUFA12), whereas a paralog of this subunit, the assembly factor N7BML (NDUFAF2), was found firmly bound instead. EPR spectroscopic analysis and metal content determination after chromatographic purification of the assembly intermediate showed that NUMM is required for insertion or stabilization of FeS cluster N4.
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Otrelo-Cardoso, Ana, Márcia da Silva Correia, Viola Schwuchow, Dmitri Svergun, Maria Romão, Silke Leimkühler, and Teresa Santos-Silva. "Structural Data on the Periplasmic Aldehyde Oxidoreductase PaoABC from Escherichia coli: SAXS and Preliminary X-ray Crystallography Analysis." International Journal of Molecular Sciences 15, no. 2 (January 31, 2014): 2223–36. http://dx.doi.org/10.3390/ijms15022223.

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Tu, Shih-Long, Nathan C. Rockwell, J. Clark Lagarias, and Andrew J. Fisher. "Insight into the Radical Mechanism of Phycocyanobilin−Ferredoxin Oxidoreductase (PcyA) Revealed by X-ray Crystallography and Biochemical Measurements†." Biochemistry 46, no. 6 (February 2007): 1484–94. http://dx.doi.org/10.1021/bi062038f.

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Dissertations / Theses on the topic "Oxidoreductases, X-Ray Crystallography"

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Gutierres, André Luís Teixeira. "Structural and functional studies on human enzymes involved in hydrogen sulfide breakdown." Master's thesis, 2016. http://hdl.handle.net/10362/19981.

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In human physiology, hydrogen sulfide (H2S), a small gaseous molecule that diffuses across aqueous and hydrophobic milieu, has been shown to team up with NO and CO as the third ‘gasotransmitter’. The still growing number of physiological processes shown to be regulated by H2S includes blood flow, cellular stress response, inflammation, immune defense, apoptosis and energy metabolism. Consequently, disturbed H2S metabolism is associated with numerous human pathologies, from cardiovascular and inflammatory disorders, to neurodegeneration and cancer. As any other reactive signaling molecule, H2S homeostasis requires a fine balance between its synthesis and breakdown. One of the enzymes involved in the synthesis of H2S in humans is cystathionine β-synthase (CBS), one key enzyme of the transsulfuration pathway. H2S breakdown relies on a mitochondrial pathway involving a sulfide:quinone oxidoreductase (SQR), a sulfur dioxygenase, Rhodanese, and a sulfite oxidase. O2-dependent H2S consumption may be primarily controlled by its efficient catabolism via SQR, which may be a key regulator in switching off H2S signaling by consuming it. Although numerous studies have focused on the functional analysis of H2S catabolism components, there is a paucity of structural data to support i) the understanding of functional/physiological data, and ii) the discovery and design of modulatory compounds with potential pharmacological interest. The aim of this dissertation was to characterize from a structural and functional viewpoint human enzymes involved in H2S metabolism, employing different biophysical methodologies. Recombinant human Rhodanese was expressed in Escherichia coli and purified with a yield of 2mg/L of culture. By a combination of DSF (Differential Scanning Fluorimetry), CD (Circular Dichroism) and SAXS (Small Angle X-ray Scattering) studies, it was observed that cysteine, thiosulfate and alliin affects Rhodanese structure. This information was used into crystallization trials but without getting any Rhodanese crystals. The recombinant human SQR expression and purification was unsuccessful, precluding any further studies, and being still under development. In parallel with work on the sulfide oxidizing unit, structural studies were carried out with recombinant human cystathionine β-synthase. In particular, the crystallographic structure of the disease-causing variant CBS P49L was obtained at 2.8 Å resolution, showing very subtle differences from the WT CBS structure. However, these do not completely explain the functional impact of this mutation and its pathogenicity.
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WOLFOVÁ, Julie. "Insight into the structure of tetrameric flavoprotein WrbA involved in oxidative-stress response." Doctoral thesis, 2012. http://www.nusl.cz/ntk/nusl-135814.

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This Ph.D. thesis addresses the structural characterization of the unique family of tetrameric flavoproteins WrbA, the role of which in the life of cells is still largely unknown but its enzymatic activity and expression properties implicate it in the cell protection against oxidative stress. Proteins of the WrbA family were proved to carry out two-electron reductions of quinones and in this way to prevent generation of the free radicals, similarly to other flavoproteins known as quinone oxidoreductases. Crystal structures of the liganded and unliganded forms of the prototypical WrbA from Escherichia coli were determined. Comparative analyses of these structures with the related flavoproteins were intended to identify and explain the defining structural features of the WrbA family and to clarify its structural and functional relationships to the other flavoproteins.
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