3KPK

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans, C160A mutant

Summary for 3KPK

• Entry DOI: 10.2210/pdb3kpk/pdb
• Related: 3kpg 3kpi
• Descriptor: Sulfide-quinone reductase, putative, FLAVIN-ADENINE DINUCLEOTIDE, DODECYL-BETA-D-MALTOSIDE, ... (6 entities in total)
• Functional Keywords: oxidoreductases, sulfide:quinone oxidoreductase, c160a mutant, oxidoreductase
• Biological source: Acidithiobacillus ferrooxidans ATCC 23270 (Ferrobacillus ferrooxidans (strain ATCC 23270))
• Total number of polymer chains: 1
• Total formula weight: 48872.99

Authors

Cherney, M.M.,Zhang, Y.,Solomonson, M.,Weiner, J.H.,James, M.N.G. (deposition date: 2009-11-16, release date: 2010-04-07, Last modification date: 2023-09-06)

Primary citation

Cherney, M.M.,Zhang, Y.,Solomonson, M.,Weiner, J.H.,James, M.N.
Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification.
J.Mol.Biol., 398:292-305, 2010

PubMed Abstract: Sulfide:quinone oxidoreductase from the acidophilic and chemolithotrophic bacterium Acidithiobacillus ferrooxidans was expressed in Escherichia coli and crystallized, and its X-ray molecular structure was determined to 2.3 A resolution for native unbound protein in space group P4(2)2(1)2 . The decylubiquinone-bound structure and the Cys160Ala variant structure were subsequently determined to 2.3 A and 2.05 A resolutions, respectively, in space group P6(2)22 . The enzymatic reaction catalyzed by sulfide:quinone oxidoreductase includes the oxidation of sulfide compounds H(2)S, HS(-), and S(2-) to soluble polysulfide chains or to elemental sulfur in the form of octasulfur rings; these oxidations are coupled to the reduction of ubiquinone or menaquinone. The enzyme comprises two tandem Rossmann fold domains and a flexible C-terminal domain encompassing two amphipathic helices that are thought to provide for membrane anchoring. The second amphipathic helix unwinds and changes its orientation in the hexagonal crystal form. The protein forms a dimer that could be inserted into the membrane to a depth of approximately 20 A. It has an endogenous flavin adenine dinucleotide (FAD) cofactor that is noncovalently bound in the N-terminal domain. Several wide channels connect the FAD cofactor to the exterior of the protein molecule; some of the channels would provide access to the membrane. The ubiquinone molecule is bound in one of these channels; its benzoquinone ring is stacked between the aromatic rings of two conserved Phe residues, and it closely approaches the isoalloxazine moiety of the FAD cofactor. Two active-site cysteine residues situated on the re side of the FAD cofactor form a branched polysulfide bridge. Cys356 disulfide acts as a nucleophile that attacks the C4A atom of the FAD cofactor in electron transfer reaction. The third essential cysteine Cys128 is not modified in these structures; its role is likely confined to the release of the polysulfur product.

PubMed: 20303979
DOI: 10.1016/j.jmb.2010.03.018

Experimental method

X-RAY DIFFRACTION (2.05 Å)