Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii
| Autor: | Toshiya Senda, Shinya Fushinobu, Takatoshi Arakawa, Takayoshi Wakagi, Yuta Sato, Toshio Moriya, Naruhiko Adachi, Masato Kawasaki, Chihaya Yamada, Takashi Yabuki |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
SDS
sodium dodecyl sulfate Nonheme mononuclear iron center Sulfur metabolism chemistry.chemical_element Disproportionation Crystal structure AaSOR Acidianus ambivalens SOR CTF contrast transfer function Article HnSOR Halothiobacillus neapolitanus SOR RMSD root mean square deviation Structural Biology DTNB 5 5′-dithiobis(2-nitrobenzoic acid) SbSOR Sulfobacillus thermosulfidooxidans SOR StSOR Sulfurisphaera tokodaii SOR lcsh:QH301-705.5 PAGE polyacrylamide gel electrophoresis ComputingMethodologies_COMPUTERGRAPHICS SOR sulfur oxygenase reductase cryo-EM cryogenic electron microscopy X-ray crystallography biology Chemistry Thermophile TpSOR Thioalkalivibrio paradoxus SOR Resolution (electron density) Substrate (chemistry) Active site AqSOR Aquifex aeolicus SOR biology.organism_classification Sulfur pCMB p-chloromercuribenzoate Archaea Crystallography AtSOR Acidianus tengchongensis SOR lcsh:Biology (General) biology.protein SD standard deviation FSC Fourier shell correlation Cryogenic electron microscopy Acidianus |
| Zdroj: | Journal of Structural Biology: X Journal of Structural Biology: X, Vol 4, Iss, Pp 100030-(2020) |
| DOI: | 10.1101/2020.05.03.074773 |
| Popis: | Graphical abstract Highlights • Sulfur oxygenase reductase (SOR) was biochemically and structurally characterized. • High resolution structures of SOR were determined by crystallography and cryo-EM. • Twenty-four identical subunits of SOR form a hollow sphere. • Catalytic components exhibited different features in the crystal and cryo-EM structures. Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from Acidianus species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon Sulfurisphaera tokodaii (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5–13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of S. tokodaii (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM. |
| Databáze: | OpenAIRE |
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