3HYX

3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


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
Find similar proteins by:  (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 (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
BA [auth C], DB [auth F], I [auth A], LA [auth D], S [auth B], VA [auth E]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
DA [auth C], FB [auth F], K [auth A], NA [auth D], U [auth B], XA [auth E]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
AUK (Subject of Investigation/LOI)
Query on AUK

Download Ideal Coordinates CCD File 
CA [auth C], EB [auth F], J [auth A], MA [auth D], T [auth B], WA [auth E]1-hydroxy-2-methyl-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]quinolin-4(1H)-one
C25 H33 N O2
FIHXCHBEHLCXEG-YEFHWUCQSA-N
 Ligand Interaction
PS9 (Subject of Investigation/LOI)
Query on PS9

Download Ideal Coordinates CCD File 
FA [auth C], HB [auth F], M [auth A], PA [auth D], W [auth B], ZA [auth E]octathiocane
S8
JLQNHALFVCURHW-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , AB [auth E] , BB [auth F] , CB [auth F] , G [auth A] , GA [auth C] , H [auth A] , HA [auth D] , 
AA [auth C], AB [auth E], BB [auth F], CB [auth F], G [auth A], GA [auth C], H [auth A], HA [auth D], IA [auth D], JA [auth D], KA [auth D], N [auth A], O [auth B], P [auth B], Q [auth B], QA [auth D], R [auth B], RA [auth E], SA [auth E], TA [auth E], UA [auth E], X [auth B], Y [auth C], Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
H2S
Query on H2S

Download Ideal Coordinates CCD File 
EA [auth C], GB [auth F], L [auth A], OA [auth D], V [auth B], YA [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: 2.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.18α = 90
b = 154.23β = 90
c = 176.53γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



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: Derived calculations, Version format compliance