3G1Z

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

PDB DOI: https://doi.org/10.2210/pdb3G1Z/pdb

Classification: LIGASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-30 Released: 2009-03-10
Deposition Author(s): Singer, A.U., Evdokimova, E., Kudritska, M., Cuff, M.E., Edwards, A.M., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

PubMed: 20670890 Search on PubMedSearch on PubMed Central
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. 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

Macromolecule Content

Total Structure Weight: 75.21 kDa
Atom Count: 5,950
Modelled Residue Count: 626
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lysyl-tRNA synthetase	A, B	326	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: genX, poxA, STM4344, yjeA EC: 6.1.1.6
UniProt
Find proteins for Q9ZJ12 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q9ZJ12 Go to UniProtKB: Q9ZJ12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ZJ12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.239
R-Value Work: 0.181
R-Value Observed: 0.184
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33G1Z

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.901	α = 90
b = 68.905	β = 110.31
c = 73.27	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description