3SX6

Crystal structure of sulfide:quinone oxidoreductase Cys356Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7955 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


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

Literature

Structure-activity characterization of sulfide:quinone oxidoreductase variants.

Cherney, M.M., Zhang, Y., James, M.N., Weiner, J.H.

(2012) J.Struct.Biol. 178: 319-328

  • DOI: 10.1016/j.jsb.2012.04.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Sulfide:quinone oxidoreductase (SQR) is a peripheral membrane protein that catalyzes the oxidation of sulfide species to elemental sulfur. The enzymatic reaction proceeds in two steps. The electrons from sulfides are transferred first to the enzyme c ...

    Sulfide:quinone oxidoreductase (SQR) is a peripheral membrane protein that catalyzes the oxidation of sulfide species to elemental sulfur. The enzymatic reaction proceeds in two steps. The electrons from sulfides are transferred first to the enzyme cofactor, FAD, which, in turn, passes them onto the quinone pool in the membrane. Several wild-type SQR structures have been reported recently. However, the enzymatic mechanism of SQR has not been fully delineated. In order to understand the role of the catalytically essential residues in the enzymatic mechanism of SQR we produced a number of variants of the conserved residues in the catalytic site including the cysteine triad of SQR from the acidophilic, chemolithotrophic bacterium Acidithiobacillus ferrooxidans. These were structurally characterized and their activities for each reaction step were determined. In addition, the crystal structures of the wild-type SQR with sodium selenide and gold(I) cyanide have been determined. Previously we proposed a mechanism for the reduction of sulfides to elemental sulfur involving nucleophilic attack of Cys356 on C(4A) atom of FAD. Here we also consider an alternative anionic radical mechanism by direct electron transfer from Cys356 to the isoalloxazine ring of FAD.

    Organizational Affiliation: 

    Department of Biochemistry, School of Translational Medicine, Faculty of Medicine and Dentistry, University of Alberta, 4-020J Katz Centre for Pharmacy and Health Research, Edmonton, Alberta, Canada T6G 2H7.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfide-quinone reductase, putative
A
437Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455)Mutation(s): 1 
EC: 1.8.5.4
Find proteins for B7JBP8 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455))
Go to UniProtKB:  B7JBP8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H2S
Query on H2S
Download SDF File 
Download CCD File 
A
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FAD
Query on FAD
Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
DCQ
Query on DCQ
Download SDF File 
Download CCD File 
A
2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
decylubiquinone
C19 H30 O4
VMEGFMNVSYVVOM-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT
Download SDF File 
Download CCD File 
A
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7955 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 149.828α = 90.00
b = 149.828β = 90.00
c = 81.513γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-06-13
    Type: Database references