1U3A

mutant DsbA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Intriguing conformation changes associated with the trans/cis isomerization of a prolyl residue in the active site of the DsbA C33A mutant

Ondo-Mbele, E., Vives, C., Kone, A., Serre, L.

(2005) J Mol Biol 347: 555-563

  • DOI: 10.1016/j.jmb.2005.01.049
  • Primary Citation of Related Structures:  
    1TI1, 1U3A

  • PubMed Abstract: 

    • Escherichia coli DsbA belongs to the thioredoxin family and catalyzes the formation of disulfide bonds during the folding of proteins in the bacterial periplasm. It active site (C30-P31-H32-C33) consists of a disulfide bridge that is transferred to newly translocated proteins ...

    Escherichia coli DsbA belongs to the thioredoxin family and catalyzes the formation of disulfide bonds during the folding of proteins in the bacterial periplasm. It active site (C30-P31-H32-C33) consists of a disulfide bridge that is transferred to newly translocated proteins. The work reported here refers to the DsbA mutant termed C33A that retains, towards reduced unfolded thrombin inhibitor, an activity comparable with the wild-type enzyme. Besides, C33A is also able to form a stable covalent complex with DsbB, the membrane protein responsible for maintaining DsbA in its active form. We have determined the crystal structure of C33A at 2.0 angstroms resolution. Although the general architecture of wt DsbA is conserved, we observe the trans/cis isomerization of P31 in the active site and further conformational changes in the so-called "peptide binding groove" region. Interestingly, these modifications involve residues that are specific to DsbA but not to the thioredoxin family fold. The C33A crystal structure exhibits as well a hydrophobic ligand bound close to the active site of the enzyme. The structural analysis of C33A may actually explain the peculiar behavior of this mutant in regards with its interaction with DsbB and thus provides new insights for understanding the catalytic cycle of DsbA.

    Organizational Affiliation: 

    Laboratoire des Protéines Membranaires, Institut de Biologie Structurale Jean-Pierre Ebel CEA/CNRS/UJF. 41, rue Jules Horowitz, 38027 Grenoble cedex 01, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol: disulfide interchange protein dsbAA,
B,
C [auth D],
D [auth E]		189Escherichia coliMutation(s): 1 
Gene Names: dsbA, ppfA
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE5
Query on PE5
Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]		3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.956α = 90
b = 82.282β = 98.74
c = 113.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2004-07-21 
  • Released Date: 2005-05-03 
    • Deposition Author(s): Serre, L.

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary