6A09

Salmonella Typhi YfdX in the P222 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.293 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Physiological Exploration ofSalmonellaTyphi YfdX Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence.

Lee, H.S.Lee, S.Kim, J.S.Lee, H.R.Shin, H.C.Lee, M.S.Jin, K.S.Kim, C.H.Ku, B.Ryu, C.M.Kim, S.J.

(2018) Front Microbiol 9: 3329-3329

  • DOI: 10.3389/fmicb.2018.03329
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • YfdX is a prokaryotic protein encoded by several pathogenic bacteria including <i>Salmonella enterica </i> serovar Typhi, which causes one of the most fatal infectious diseases, typhoid fever. YfdX is a product of the <i>yfdXWUVE </i> operon and is ...

    YfdX is a prokaryotic protein encoded by several pathogenic bacteria including Salmonella enterica serovar Typhi, which causes one of the most fatal infectious diseases, typhoid fever. YfdX is a product of the yfdXWUVE operon and is known to be under the control of EvgA, a regulator protein controlling the expression of several proteins involved in response to environmental stress, in Escherichia coli . Nevertheless, unlike other proteins encoded by the same operon, the structural and physiological aspects of YfdX have been poorly characterized. Here, we identified a previously unknown pH-dependent stoichiometric conversion of S . Typhi YfdX between dimeric and tetrameric states; this conversion was further analyzed via determining its structure by X-ray crystallography at high resolution and by small-angle X-ray scattering in a solution state and via structure-based mutant studies. Biologically, YfdX was proven to be critically involved in Salmonella susceptibility to two β-lactam antibiotics, penicillin G and carbenicillin, as bacterial growth significantly impaired by its deficiency upon treatment with each of the two antibiotics was recovered by chromosomal complementation. Furthermore, by using Galleria mellonella larvae as an in vivo model of Salmonella infection, we demonstrated that Salmonella virulence was remarkably enhanced by YfdX deficiency, which was complemented by a transient expression of the wild-type or dimeric mutant but not by that of the monomeric mutant. The present study work provides direct evidence regarding the participation of YfdX in Salmonella antibiotic susceptibility and in the modulation of bacterial virulence, providing a new insight into this pathogen's strategies for survival and growth.


    Organizational Affiliation

    Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, South Korea.,Department of Biotechnology, University of Science and Technology KRIBB School, Daejeon, South Korea.,Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea.,Department of Biology, Chungnam National University, Daejeon, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YfdX protein
A, B, C, D, E, F, G, H
185Salmonella typhimuriumMutation(s): 0 
Gene Names: SBOV30831 (yfdX)
Find proteins for A0A0D6IF67 (Salmonella typhimurium)
Go to UniProtKB:  A0A0D6IF67
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.293 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.180 
  • Space Group: P 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.395α = 90.00
b = 127.071β = 90.00
c = 170.384γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-13
    Type: Data collection, Database references