2ZUP

Updated crystal structure of DsbB-DsbA complex from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.304 
  • R-Value Observed: 0.305 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB

Inaba, K.Murakami, S.Nakagawa, A.Iida, H.Kinjo, M.Ito, K.Suzuki, M.

(2009) EMBO J 28: 779-791

  • DOI: 10.1038/emboj.2009.21
  • Primary Citation of Related Structures:  
    2ZUP, 2ZUQ

  • PubMed Abstract: 
  • In the Escherichia coli system catalysing oxidative protein folding, disulphide bonds are generated by the cooperation of DsbB and ubiquinone and transferred to substrate proteins through DsbA. The structures solved so far for different forms of DsbB lack the Cys104-Cys130 initial-state disulphide that is directly donated to DsbA ...

    In the Escherichia coli system catalysing oxidative protein folding, disulphide bonds are generated by the cooperation of DsbB and ubiquinone and transferred to substrate proteins through DsbA. The structures solved so far for different forms of DsbB lack the Cys104-Cys130 initial-state disulphide that is directly donated to DsbA. Here, we report the 3.4 A crystal structure of a DsbB-Fab complex, in which DsbB has this principal disulphide. Its comparison with the updated structure of the DsbB-DsbA complex as well as with the recently reported NMR structure of a DsbB variant having the rearranged Cys41-Cys130 disulphide illuminated conformational transitions of DsbB induced by the binding and release of DsbA. Mutational studies revealed that the membrane-parallel short alpha-helix of DsbB has a key function in physiological electron flow, presumably by controlling the positioning of the Cys130-containing loop. These findings demonstrate that DsbB has developed the elaborate conformational dynamism to oxidize DsbA for continuous protein disulphide bond formation in the cell.


    Organizational Affiliation

    Division of Protein Chemistry, Post-Genome Science Center, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan. inaba-k@bioreg.kyushu-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein dsbAA189Escherichia 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Disulfide bond formation protein BB176Escherichia coli K-12Mutation(s): 3 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UQ1
Query on UQ1

Download Ideal Coordinates CCD File 
D [auth B]UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.304 
  • R-Value Observed: 0.305 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.5α = 90
b = 165.5β = 90
c = 65.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MACSCIENCEdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations