3HYW

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration

Marcia, M., Ermler, U., Peng, G.H., Michel, H.

(2009) Proc Natl Acad Sci U S A 106: 9625-9630

  • DOI: 10.1073/pnas.0904165106
  • Primary Citation of Related Structures:  
    3HYV, 3HYW, 3HYX

  • 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 ...

    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.

    Organizational Affiliation: 

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max von Laue Strasse 3, D-60438 Frankfurt am Main, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sulfide-quinone reductaseA, B, C, D, E, F430Aquifex aeolicusMutation(s): 0 
EC: 1.8.5 (PDB Primary Data), 1.8.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for O67931 (Aquifex aeolicus (strain VF5))
Explore O67931 
Go to UniProtKB:  O67931
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
 AA [auth C], BB [auth F], G [auth A], JA [auth D], Q [auth B], TA [auth E]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
LMT
Query on LMT
Download Ideal Coordinates CCD File 
 CA [auth C], DB [auth F], I [auth A], LA [auth D], S [auth B], VA [auth E]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
DCQ
Query on DCQ
Download Ideal Coordinates CCD File 
 BA [auth C], CB [auth F], H [auth A], KA [auth D], R [auth B], UA [auth E]2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
C19 H30 O4
VMEGFMNVSYVVOM-UHFFFAOYSA-N		 Ligand Interaction
PS9
Query on PS9
Download Ideal Coordinates CCD File 
 EA [auth C], FB [auth F], K [auth A], NA [auth D], OA [auth D], U [auth B], V [auth B], XA [auth E]octathiocane
S8
JLQNHALFVCURHW-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AB [auth E] , FA [auth C] , GA [auth C] , GB [auth F] , HA [auth C] , HB [auth F] , IA [auth C] , IB [auth F] , 
AB [auth E],  FA [auth C],  GA [auth C],  GB [auth F],  HA [auth C],  HB [auth F],  IA [auth C],  IB [auth F],  JB [auth F],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  PA [auth D],  QA [auth D],  RA [auth D],  SA [auth D],  W [auth B],  X [auth B],  Y [auth B],  YA [auth E],  Z [auth B],  ZA [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
H2S
Query on H2S
Download Ideal Coordinates CCD File 
 DA [auth C], EB [auth F], J [auth A], MA [auth D], T [auth B], WA [auth E]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS		A, B, C, D, E, FL-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.78α = 90
b = 154.01β = 90
c = 175.55γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance