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TitleCrystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from .
Journal, issue, pagesJ Struct Biol X, Vol. 4, Page 100030, Year 2020
Publish dateJul 3, 2020
AuthorsYuta Sato / Takashi Yabuki / Naruhiko Adachi / Toshio Moriya / Takatoshi Arakawa / Masato Kawasaki / Chihaya Yamada / Toshiya Senda / Shinya Fushinobu / Takayoshi Wakagi /
PubMed AbstractSulfur 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 ...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 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 (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 (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.
External linksJ Struct Biol X / PubMed:32775998 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.73 - 2.24 Å
Structure data

30073

6m3x

EMDB-30073, PDB-6m3x:
Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Method: EM (single particle) / Resolution: 2.24 Å

EMDB-30362:
2.05 angstrom resolution structure determination of sulfur oxygenase reductase using 200kV cryo-EM
Method: EM (single particle) / Resolution: 2.05 Å

PDB-6m35:
Crystal structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

Chemicals

ChemComp-FE:
Unknown entry / Iron

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

Source
  • Sulfurisphaera tokodaii (archaea)
  • sulfurisphaera tokodaii (strain dsm 16993 / jcm 10545 / nbrc 100140 / 7) (archaea)
  • Sulfurisphaera tokodaii str. 7 (archaea)
KeywordsOXIDOREDUCTASE / spherical homo 24-mer

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