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PDBsum entry 3hyw

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3hyw
Jmol
Contents
Protein chains
(+ 0 more) 429 a.a. *
Ligands
FAD ×6
DCQ ×5
LMT ×5
H2S ×6
PS9 ×8
SO4 ×24
DCQ-LMT
Waters ×1137
* Residue conservation analysis
PDB id:
3hyw
Name: Oxidoreductase
Title: 3-d x-ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium aquifex aeolicus in complex with decylubiquinone
Structure: Sulfide-quinone reductase. Chain: a, b, c, d, e, f. Synonym: sulfide:quinone oxidoreductase. Ec: 1.8.5.-
Source: Aquifex aeolicus. Organism_taxid: 63363. Strain: vf5
Resolution:
2.00Å     R-factor:   0.202     R-free:   0.236
Authors: M.Marcia,U.Ermler,G.H.Peng,H.Michel
Key ref:
M.Marcia et al. (2009). The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration. Proc Natl Acad Sci U S A, 106, 9625-9630. PubMed id: 19487671 DOI: 10.1073/pnas.0904165106
Date:
23-Jun-09     Release date:   14-Jul-09    
Supersedes: 3h28
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O67931  (O67931_AQUAE) -  Sulfide-quinone reductase
Seq:
Struc:
430 a.a.
429 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     nucleotide binding     2 terms  

 

 
DOI no: 10.1073/pnas.0904165106 Proc Natl Acad Sci U S A 106:9625-9630 (2009)
PubMed id: 19487671  
 
 
The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.
M.Marcia, U.Ermler, G.Peng, H.Michel.
 
  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.
 
  Selected figure(s)  
 
Figure 3.
Membrane-binding motifs of the SQR trimer. The membrane is indicated in gray. The overall trimer is in a cartoon semitransparent representation. The side chains of Arg-204 of all monomers are represented in cyan sticks to highlight the central trimerization contacts. Other residues and molecules are shown only for the 2 subunits in the foreground for better clarity of visualization. The FAD is in cyan mesh. The side chains of the residues and the molecules belonging to the different membrane-interacting motifs are shown as sticks. For sulfate groups a semitransparent surface is also shown. Different colors are attributed to the different structural motifs. In particular the N-terminal domain is dark green, the inner domain binding 1 sulfate ion and 1 MES molecule is light green, the 4 conserved lysines are dark blue, and the base of the trimer body is yellow. The distances were calculated from the plane of the sulfur atoms of the MES molecules, respectively, to the C[α] atom of Arg-204 and the C3B atom of the maltose head of DDM (chain A). An approximate value (40 Å) indicates the membrane thickness according to White and Wimley (23).
Figure 4.
Schematic representation of the distances (red dotted lines) between relevant Cys and FAD atoms in the catalytic site. Distances are in angstroms. The side chains of Cys-124, Cys-156, and Cys-347 are in a double conformation (-SHa/-SHb).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20419499 Y.B.Ma, Z.F.Zhang, M.Y.Shao, K.H.Kang, Z.Tan, and J.L.Li (2011).
Sulfide:quinone Oxidoreductase from Echiuran Worm Urechis unicinctus.
  Mar Biotechnol (NY), 13, 93.  
19769466 D.R.Linden, M.D.Levitt, G.Farrugia, and J.H.Szurszewski (2010).
Endogenous production of H2S in the gastrointestinal tract: still in search of a physiologic function.
  Antioxid Redox Signal, 12, 1135-1146.  
20077566 M.Marcia, U.Ermler, G.Peng, and H.Michel (2010).
A new structure-based classification of sulfide:quinone oxidoreductases.
  Proteins, 78, 1073-1083.  
20304090 P.D.Kiser, and K.Palczewski (2010).
Membrane-binding and enzymatic properties of RPE65.
  Prog Retin Eye Res, 29, 428-442.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.