4E51

Crystal structure of a histidyl-tRNA synthetase HisRS from Burkholderia thailandensis bound to histidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 

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:  

  • 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.


    Related Citations: 
    • Combining functional and structural genomics to sample the essential Burkholderia structome.
      Baugh, L.,Gallagher, L.A.,Patrapuvich, R.,Clifton, M.C.,Gardberg, A.S.,Edwards, T.E.,Armour, B.,Begley, D.W.,Dieterich, S.H.,Dranow, D.M.,Abendroth, J.,Fairman, J.W.,Fox, D.,Staker, B.L.,Phan, I.,Gillespie, A.,Choi, R.,Nakazawa-Hewitt, S.,Nguyen, M.T.,Napuli, A.,Barrett, L.,Buchko, G.W.,Stacy, R.,Myler, P.J.,Stewart, L.J.,Manoil, C.,Van Voorhis, W.C.
      (2013) Plos One 8: e53851


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,International Center for Genetic Engineering and Biotechnology, New Delhi, 110 067, India.,Berkeley Center for Structural Biology, Advanced Light Source, Berkeley, CA, 94720, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA. tedwards@be4.com.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA.,University of Washington, Seattle, WA, 98195-6423, USA.,University of Washington, Department of Medical Education and Biomedical Informatics & Department of Global Health, Seattle, WA, 98195, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA.,University of Washington, Department of Genome Sciences, Seattle, WA, 98195-5065, USA.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA. tedwards@be4.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine--tRNA ligase
A, B
467Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)Mutation(s): 0 
Gene Names: hisS
EC: 6.1.1.21
Find proteins for Q2SWE3 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264))
Go to UniProtKB:  Q2SWE3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HIS
Query on HIS

Download SDF File 
Download CCD File 
A, B
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 70.160α = 90.00
b = 116.360β = 90.00
c = 142.990γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references
  • Version 1.2: 2017-03-29
    Type: Database references