3HYW

3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone

Replaces:  3H28

Summary for 3HYW

• Entry DOI: 10.2210/pdb3hyw/pdb
• Related: 3HYV 3HYX
• Descriptor: Sulfide-quinone reductase, FLAVIN-ADENINE DINUCLEOTIDE, 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione, ... (8 entities in total)
• Functional Keywords: monotopic membrane protein, flavoprotein, polysulfur, oxidoreductase
• Biological source: AQUIFEX AEOLICUS
• Total number of polymer chains: 6
• Total formula weight: 299675.69

Authors

Marcia, M.,Ermler, U.,Peng, G.H.,Michel, H. (deposition date: 2009-06-23, release date: 2009-07-14, Last modification date: 2023-11-22)

Primary citation

Marcia, M.,Ermler, U.,Peng, G.H.,Michel, H.
The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration
Proc.Natl.Acad.Sci.USA, 106:9625-9630, 2009

PubMed Abstract: Sulfide:quinone oxidoreductase (SQR) is a flavoprotein with homologues in all domains of life except plants. It plays a physiological role both in sulfide detoxification and in energy transduction. We isolated the protein from native membranes of the hyperthermophilic bacterium Aquifex aeolicus, and we determined its X-ray structure in the "as-purified," substrate-bound, and inhibitor-bound forms at resolutions of 2.3, 2.0, and 2.9 A, respectively. The structure is composed of 2 Rossmann domains and 1 attachment domain, with an overall monomeric architecture typical of disulfide oxidoreductase flavoproteins. A. aeolicus SQR is a surprisingly trimeric, periplasmic integral monotopic membrane protein that inserts about 12 A into the lipidic bilayer through an amphipathic helix-turn-helix tripodal motif. The quinone is located in a channel that extends from the si side of the FAD to the membrane. The quinone ring is sandwiched between the conserved amino acids Phe-385 and Ile-346, and it is possibly protonated upon reduction via Glu-318 and/or neighboring water molecules. Sulfide polymerization occurs on the re side of FAD, where the invariant Cys-156 and Cys-347 appear to be covalently bound to polysulfur fragments. The structure suggests that FAD is covalently linked to the polypeptide in an unusual way, via a disulfide bridge between the 8-methyl group and Cys-124. The applicability of this disulfide bridge for transferring electrons from sulfide to FAD, 2 mechanisms for sulfide polymerization and channeling of the substrate, S(2-), and of the product, S(n), in and out of the active site are discussed.

PubMed: 19487671
DOI: 10.1073/pnas.0904165106

Experimental method

X-RAY DIFFRACTION (2 Å)