4I5Q

Crystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.962 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the periplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium and the mechanistic implications.

Jiao, L.Kim, J.S.Song, W.S.Yoon, B.Y.Lee, K.Ha, N.C.

(2013) J.Struct.Biol. 183: 1-10

  • DOI: 10.1016/j.jsb.2013.05.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The disulfide-bond isomerase DsbC plays a crucial role in the folding of bacterial proteins in the periplasmic space. DsbC has a V-shaped dimeric structure with two domains, and Cys98 in the C-terminal domain attacks inappropriate disulfide bonds in ...

    The disulfide-bond isomerase DsbC plays a crucial role in the folding of bacterial proteins in the periplasmic space. DsbC has a V-shaped dimeric structure with two domains, and Cys98 in the C-terminal domain attacks inappropriate disulfide bonds in substrate proteins due to its high nucleophilic activity. In this article, we present the crystal structure of DsbC from Salmonella enterica serovar Typhimurium. We evaluated the conserved residues Asp95 and Arg125, which are located close to Cys98. The mutation of Asp95 or Arg125 abolished the disulfide isomerase activity of DsbC in an in vitro assay using a protein substrate, and the R125A mutation significantly reduced the chaperone activity for the substrate RNase I in vivo. Furthermore, a comparative analysis suggested that the conformation of Arg125 varies depending on the packing or protein-protein interactions. Based on these findings, we suggest that Asp95 and Arg125 modulate the pKa of Cys98 during catalysis.


    Organizational Affiliation

    Department of Manufacturing Pharmacy and Research Institute for Drug Development, Pusan National University, Busan 609-735, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein DsbC
A, B
222Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: dsbC
Find proteins for P55890 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P55890
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.962 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.989α = 90.00
b = 78.526β = 90.00
c = 84.414γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
CCP4model building
PHENIXrefinement
CCP4phasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description