2ZUP

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.304 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein dsbA
A
189Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: dsbA (dsf, ppfA)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oxidoreductases		Protein: 
DsbB-DsbA Periplasmic Oxidase Complex
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEG4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Disulfide bond formation protein B
B
176Escherichia coli (strain K12)Mutation(s): 3 
Gene Names: dsbB (roxB, ycgA)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oxidoreductases		Protein: 
DsbB-DsbA Periplasmic Oxidase Complex
Find proteins for P0A6M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6M2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UQ1
Query on UQ1
Download SDF File 
Download CCD File 
B
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.304 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 165.500α = 90.00
b = 165.500β = 90.00
c = 65.920γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
MACSCIENCEdata collection
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description