4OD7

Complex structure of Proteus mirablis DsbA (C30S) with a non-covalently bound peptide PWATCDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.597 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Dithiol Oxidase DsbA Enzyme from Proteus Mirabilis Bound Non-covalently to an Active Site Peptide Ligand.

Kurth, F.Duprez, W.Premkumar, L.Schembri, M.A.Fairlie, D.P.Martin, J.L.

(2014) J.Biol.Chem. 289: 19810-19822

  • DOI: 10.1074/jbc.M114.552380
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA ...

    The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA from Proteus mirabilis, a bacterial pathogen increasingly associated with multidrug resistance. PmDsbA exhibits the characteristic properties of a DsbA, including an oxidizing potential, destabilizing disulfide, acidic active site cysteine, and dithiol oxidase catalytic activity. We evaluated a peptide, PWATCDS, derived from the partner protein DsbB and showed by thermal shift and isothermal titration calorimetry that it binds to PmDsbA. The crystal structures of PmDsbA, and the active site variant PmDsbAC30S were determined to high resolution. Analysis of these structures allows categorization of PmDsbA into the DsbA class exemplified by the archetypal Escherichia coli DsbA enzyme. We also present a crystal structure of PmDsbAC30S in complex with the peptide PWATCDS. The structure shows that the peptide binds non-covalently to the active site CXXC motif, the cis-Pro loop, and the hydrophobic groove adjacent to the active site of the enzyme. This high-resolution structural data provides a critical advance for future structure-based design of non-covalent peptidomimetic inhibitors. Such inhibitors would represent an entirely new antibacterial class that work by switching off the DSB virulence assembly machinery.


    Organizational Affiliation

    From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein
A, B, C
190Proteus mirabilis (strain HI4320)Mutation(s): 1 
Gene Names: dsbA
Find proteins for B4EZ68 (Proteus mirabilis (strain HI4320))
Go to UniProtKB:  B4EZ68
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
(ACE)PWATCDS(NH2) Peptide
D, E, F
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, C
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
D, E, F
NON-POLYMERH2 N

--

ACE
Query on ACE
D, E, F
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.597 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 74.056α = 90.00
b = 74.056β = 90.00
c = 93.270γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Blu-Icedata collection
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description