2ZUQ

Crystal structure of DsbB-Fab complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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
Disulfide bond formation protein B
A, D
176Escherichia coli (strain K12)Gene Names: dsbB (roxB, ycgA)
Membrane protein
mpstruct
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab fragment light chain
B, E
239N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab fragment heavy chain
C, F
221N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UQ1
Query on UQ1

Download SDF File 
Download CCD File 
A, D
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.275 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 269.307α = 90.00
b = 51.480β = 106.89
c = 125.845γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MACSCIENCEdata collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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