3G1Z

Structure of IDP01693/yjeA, a potential t-RNA synthetase from Salmonella typhimurium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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Literature

PoxA, yjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica.

Navarre, W.W., Zou, S.B., Roy, H., Xie, J.L., Savchenko, A., Singer, A., Edvokimova, E., Prost, L.R., Kumar, R., Ibba, M., Fang, F.C.

(2010) Mol Cell 39: 209-221

  • DOI: https://doi.org/10.1016/j.molcel.2010.06.021
  • Primary Citation of Related Structures:  
    3G1Z

  • PubMed Abstract: 

    • We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-beta-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered expression of multiple proteins, including several encoded on the SPI-1 pathogenicity island ...

    We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-beta-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered expression of multiple proteins, including several encoded on the SPI-1 pathogenicity island. PoxA mediates posttranslational modification of bacterial elongation factor P (EF-P), analogous to the modification of the eukaryotic EF-P homolog, eIF5A, with hypusine. The modification of EF-P is a mechanism of regulation whereby PoxA acts as an aminoacyl-tRNA synthetase that attaches an amino acid to a protein resembling tRNA rather than to a tRNA.

    Organizational Affiliation: 

    Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. william.navarre@utoronto.ca



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative lysyl-tRNA synthetaseA, B326Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: genX, poxA, STM4344, yjeA
EC: 6.1.1.6 (PDB Primary Data), 6.3.1 (UniProt)
UniProt
Find proteins for Q9ZJ12 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q9ZJ12 
Go to UniProtKB:  Q9ZJ12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZJ12
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.901α = 90
b = 68.905β = 110.31
c = 73.27γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-10-12
    Changes: Database references