3E9J

Structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.379 
  • R-Value Work: 0.337 
  • R-Value Observed: 0.339 

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This is version 1.2 of the entry. See complete history


Literature

Preparation and structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB.

Malojcic, G.Owen, R.L.Grimshaw, J.P.Glockshuber, R.

(2008) FEBS Lett 582: 3301-3307

  • DOI: 10.1016/j.febslet.2008.07.063
  • Primary Citation of Related Structures:  
    3E9J

  • PubMed Abstract: 
  • Disulfide bond formation is a critical step in the folding of many secretory proteins. In bacteria, disulfide bonds are introduced by the periplasmic dithiol oxidase DsbA, which transfers its catalytic disulfide bond to folding polypeptides. Reduced DsbA is reoxidized by ubiquinone Q8, catalyzed by inner membrane quinone reductase DsbB ...

    Disulfide bond formation is a critical step in the folding of many secretory proteins. In bacteria, disulfide bonds are introduced by the periplasmic dithiol oxidase DsbA, which transfers its catalytic disulfide bond to folding polypeptides. Reduced DsbA is reoxidized by ubiquinone Q8, catalyzed by inner membrane quinone reductase DsbB. Here, we report the preparation of a kinetically stable ternary complex between wild-type DsbB, containing all essential cysteines, Q8 and DsbA covalently bound to DsbB. The crystal structure of this trapped DsbB reaction intermediate exhibits a charge-transfer interaction between Q8 and the Cys44 in the DsbB reaction center providing experimental evidence for the mechanism of de novo disulfide bond generation in DsbB.


    Organizational Affiliation

    ETH Zurich, Institute of Molecular Biology and Biophysics, CH-8093 Zurich, Switzerland. mgoran@ethz.ch



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol/disulfide oxidoreductase DsbAA [auth B],
C [auth E]
189Escherichia coli K-12Mutation(s): 1 
Gene Names: dsbAdsfppfAb3860JW3832
EC: 1.8.4
Membrane Entity: Yes 
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Explore P0AEG4 
Go to UniProtKB:  P0AEG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEG4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol/disulfide oxidoreductase DsbBB [auth C],
D [auth F]
182Escherichia coli K-12Mutation(s): 2 
Gene Names: dsbBroxBycgAb1185JW5182
EC: 1.8.5
Membrane Entity: Yes 
UniProt
Find proteins for P0A6M2 (Escherichia coli (strain K12))
Explore P0A6M2 
Go to UniProtKB:  P0A6M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6M2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UQ1
Query on UQ1

Download Ideal Coordinates CCD File 
E [auth C],
F
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.379 
  • R-Value Work: 0.337 
  • R-Value Observed: 0.339 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.305α = 90
b = 103.105β = 91.16
c = 125.826γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CLARAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations