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 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/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 2.3, 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfide-quinone reductase
A, B, C, D, E
A, B, C, D, E, F
430Aquifex 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67931
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / 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]
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
LMT
Query on LMT

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CA [auth C]
DB [auth F]
I [auth A]
LA [auth D]
S [auth B]
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
DCQ
Query on DCQ

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BA [auth C]
CB [auth F]
H [auth A]
KA [auth D]
R [auth B]
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
PS9
Query on PS9

Download Ideal Coordinates CCD File 
EA [auth C]
FB [auth F]
K [auth A]
NA [auth D]
OA [auth D]
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
SO4
Query on SO4

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AB [auth E]
FA [auth C]
GA [auth C]
GB [auth F]
HA [auth C]
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
H2S
Query on H2S

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DA [auth C]
EB [auth F]
J [auth A]
MA [auth D]
T [auth B]
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A, B, C, D, E
A, B, C, D, E, F
L-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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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: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-22
    Changes: Data collection