3KPK

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans, C160A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification.

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

(2010) J Mol Biol 398: 292-305

  • DOI: 10.1016/j.jmb.2010.03.018
  • Primary Citation of Related Structures:  
    3KPK, 3T31, 3T2Z

  • PubMed Abstract: 
  • Sulfide:quinone oxidoreductase from the acidophilic and chemolithotrophic bacterium Acidithiobacillus ferrooxidans was expressed in Escherichia coli and crystallized, and its X-ray molecular structure was determined to 2.3 A resolution for native unbound protein in space group P4(2)2(1)2 ...

    Sulfide:quinone oxidoreductase from the acidophilic and chemolithotrophic bacterium Acidithiobacillus ferrooxidans was expressed in Escherichia coli and crystallized, and its X-ray molecular structure was determined to 2.3 A resolution for native unbound protein in space group P4(2)2(1)2 . The decylubiquinone-bound structure and the Cys160Ala variant structure were subsequently determined to 2.3 A and 2.05 A resolutions, respectively, in space group P6(2)22 . The enzymatic reaction catalyzed by sulfide:quinone oxidoreductase includes the oxidation of sulfide compounds H(2)S, HS(-), and S(2-) to soluble polysulfide chains or to elemental sulfur in the form of octasulfur rings; these oxidations are coupled to the reduction of ubiquinone or menaquinone. The enzyme comprises two tandem Rossmann fold domains and a flexible C-terminal domain encompassing two amphipathic helices that are thought to provide for membrane anchoring. The second amphipathic helix unwinds and changes its orientation in the hexagonal crystal form. The protein forms a dimer that could be inserted into the membrane to a depth of approximately 20 A. It has an endogenous flavin adenine dinucleotide (FAD) cofactor that is noncovalently bound in the N-terminal domain. Several wide channels connect the FAD cofactor to the exterior of the protein molecule; some of the channels would provide access to the membrane. The ubiquinone molecule is bound in one of these channels; its benzoquinone ring is stacked between the aromatic rings of two conserved Phe residues, and it closely approaches the isoalloxazine moiety of the FAD cofactor. Two active-site cysteine residues situated on the re side of the FAD cofactor form a branched polysulfide bridge. Cys356 disulfide acts as a nucleophile that attacks the C4A atom of the FAD cofactor in electron transfer reaction. The third essential cysteine Cys128 is not modified in these structures; its role is likely confined to the release of the polysulfur product.


    Organizational Affiliation

    Group in Protein Structure and Function, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, 4-31 Medical Sciences Building, Edmonton, Alberta, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sulfide-quinone reductase, putativeA434Acidithiobacillus ferrooxidans ATCC 23270Mutation(s): 1 
Gene Names: AFE_1792
EC: 1.8.5.4
UniProt
Find proteins for B7JBP8 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455))
Explore B7JBP8 
Go to UniProtKB:  B7JBP8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
LMT
Query on LMT

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

Download Ideal Coordinates CCD File 
F [auth A]R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
 Ligand Interaction
H2S
Query on H2S

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.08α = 90
b = 150.08β = 90
c = 81.679γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance