3SX6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1016/j.jsb.2012.04.007
  • Primary Citation of Related Structures:  
    3SX6, 3SXI, 3SY4, 3SYI, 3SZ0, 3SZC, 3SZF, 3SZW, 3T0K, 3T14, 3T2K, 3T2Y

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfide-quinone reductase437Acidithiobacillus ferrooxidans ATCC 23270Mutation(s): 1 
Gene Names: AFE_1792
EC: 1.8.5.4
Membrane Entity: Yes 
UniProt
Find proteins for B7JBP8 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455))
Explore B7JBP8 
Go to UniProtKB:  B7JBP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7JBP8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
C [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
DCQ
Query on DCQ

Download Ideal Coordinates CCD File 
D [auth A]2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
C19 H30 O4
VMEGFMNVSYVVOM-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
H2S
Query on H2S

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TSY
Query on TSY
A
L-PEPTIDE LINKINGC3 H7 N O2 S3CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.828α = 90
b = 149.828β = 90
c = 81.513γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-06-13
    Changes: Database references
  • Version 2.0: 2024-03-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Structure summary