3ZRD

Oxidised Thiol peroxidase (Tpx) from Yersinia pseudotuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Characterisation of Tpx from Yersinia Pseudotuberculosis Reveals Insights Into the Binding of Salicylidene Acylhydrazide Compounds.

Gabrielsen, M.Beckham, K.S.H.Feher, V.A.Zetterstrom, C.E.Wang, D.Muller, S.Elofsson, M.Amaro, R.E.Byron, O.Roe, A.J.

(2012) PLoS One 7: 32217

  • DOI: https://doi.org/10.1371/journal.pone.0032217
  • Primary Citation of Related Structures:  
    2XPD, 2XPE, 2YJH, 3ZRD, 3ZRE

  • PubMed Abstract: 

    Thiol peroxidase, Tpx, has been shown to be a target protein of the salicylidene acylhydrazide class of antivirulence compounds. In this study we present the crystal structures of Tpx from Y. pseudotuberculosis (ypTpx) in the oxidised and reduced states, together with the structure of the C61S mutant. The structures solved are consistent with previously solved atypical 2-Cys thiol peroxidases, including that for "forced" reduced states using the C61S mutant. In addition, by investigating the solution structure of ypTpx using small angle X-ray scattering (SAXS), we have confirmed that reduced state ypTpx in solution is a homodimer. The solution structure also reveals flexibility around the dimer interface. Notably, the conformational changes observed between the redox states at the catalytic triad and at the dimer interface have implications for substrate and inhibitor binding. The structural data were used to model the binding of two salicylidene acylhydrazide compounds to the oxidised structure of ypTpx. Overall, the study provides insights into the binding of the salicylidene acylhydrazides to ypTpx, aiding our long-term strategy to understand the mode of action of this class of compounds.


  • Organizational Affiliation

    Institute of Infection, Immunity and Immunology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THIOL PEROXIDASE
A, B
200Yersinia pseudotuberculosis YPIIIMutation(s): 0 
EC: 1.11.1.15
UniProt
Find proteins for A0A0H3B2F9 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII))
Explore A0A0H3B2F9 
Go to UniProtKB:  A0A0H3B2F9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3B2F9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.18α = 90
b = 62.56β = 90
c = 88γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description