4EX5

Crystal structure of lysyl-tRNA synthetase LysRS from Burkholderia thailandensis bound to lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms.

Moen, S.O.Edwards, T.E.Dranow, D.M.Clifton, M.C.Sankaran, B.Van Voorhis, W.C.Sharma, A.Manoil, C.Staker, B.L.Myler, P.J.Lorimer, D.D.

(2017) Sci Rep 7: 223-223

  • DOI: 10.1038/s41598-017-00367-6
  • Primary Citation of Related Structures:  
    4EX5, 3SP1, 4E51, 4G6Z, 3TZE, 4GRI

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because ...

    Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because of this important biological function, aminoacyl-tRNA synthetases have been the focus of anti-infective drug development efforts and two aaRS inhibitors have been approved as drugs. Several researchers in the scientific community requested aminoacyl-tRNA synthetases to be targeted in the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure determination pipeline. Here we investigate thirty-one aminoacyl-tRNA synthetases from infectious disease organisms by co-crystallization in the presence of their cognate amino acid, ATP, and/or inhibitors. Crystal structures were determined for a CysRS from Borrelia burgdorferi bound to AMP, GluRS from Borrelia burgdorferi and Burkholderia thailandensis bound to glutamic acid, a TrpRS from the eukaryotic pathogen Encephalitozoon cuniculi bound to tryptophan, a HisRS from Burkholderia thailandensis bound to histidine, and a LysRS from Burkholderia thailandensis bound to lysine. Thus, the presence of ligands may promote aaRS crystallization and structure determination. Comparison with homologous structures shows conformational flexibility that appears to be a recurring theme with this enzyme class.


    Organizational Affiliation

    Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine--tRNA ligaseAB529Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: BTH_I1883lysS
EC: 6.1.1.6
Find proteins for Q2SXD6 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264))
Explore Q2SXD6 
Go to UniProtKB:  Q2SXD6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download CCD File 
A, B
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.22α = 90
b = 118.54β = 113.23
c = 94.54γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2017-03-29
    Changes: Database references