1JIL

Crystal structure of S. aureus TyrRS in complex with SB284485


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors.

Qiu, X.Janson, C.A.Smith, W.W.Green, S.M.McDevitt, P.Johanson, K.Carter, P.Hibbs, M.Lewis, C.Chalker, A.Fosberry, A.Lalonde, J.Berge, J.Brown, P.Houge-Frydrych, C.S.Jarvest, R.L.

(2001) Protein Sci 10: 2008-2016

  • DOI: 10.1110/ps.18001
  • Primary Citation of Related Structures:  
    1JIL, 1JIK, 1JIJ, 1JII

  • PubMed Abstract: 
  • SB-219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl-tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl-tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital-acquired infections ...

    SB-219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl-tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl-tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital-acquired infections. The full-length enzyme yielded crystals that diffracted to 2.8 A resolution, but a truncated version of the enzyme allowed the resolution to be extended to 2.2 A. These inhibitors not only occupy the known substrate binding sites in unique ways, but also reveal a butyl binding pocket. It was reported that the Bacillus stearothermophilus TyrRS T51P mutant has much increased catalytic activity. The S. aureus enzyme happens to have a proline at position 51. Therefore, our structures may contribute to the understanding of the catalytic mechanism and provide the structural basis for designing novel antimicrobial agents.


    Organizational Affiliation

    GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA. xiayang_qui-1@sbphrd.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tyrosyl-tRNA synthetase A420Staphylococcus aureusMutation(s): 0 
EC: 6.1.1.1
Find proteins for A6QHR2 (Staphylococcus aureus (strain Newman))
Explore A6QHR2 
Go to UniProtKB:  A6QHR2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
485
Query on 485

Download Ideal Coordinates CCD File 
A
[2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (3,4,5-TRIHYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YL)- ACETIC ACID
C17 H24 N2 O8
KUCHJUZRDGYEDY-HRNUQJICSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
485IC50 :  4   nM  PDBBind
485IC50:  4   nM  Binding MOAD
485IC50:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66α = 90
b = 102.9β = 90
c = 139.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model