6M35

Crystal structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii

Summary for 6M35

• Entry DOI: 10.2210/pdb6m35/pdb
• Descriptor: Sulfur oxygenase/reductase, FE (III) ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: spherical homo 24-mer, oxidoreductase
• Biological source: Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
• Total number of polymer chains: 8
• Total formula weight: 288146.89

Authors

Sato, Y.,Yabuki, T.,Arakawa, T.,Yamada, C.,Fushinobu, S.,Wakagi, T. (deposition date: 2020-03-02, release date: 2020-07-15, Last modification date: 2023-11-29)

Primary citation

Sato, Y.,Yabuki, T.,Adachi, N.,Moriya, T.,Arakawa, T.,Kawasaki, M.,Yamada, C.,Senda, T.,Fushinobu, S.,Wakagi, T.
Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase fromSulfurisphaera tokodaii.
J Struct Biol X, 4:100030-100030, 2020

PubMed Abstract: 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.

PubMed: 32775998
DOI: 10.1016/j.yjsbx.2020.100030

Experimental method

X-RAY DIFFRACTION (1.73 Å)