1JIL

Crystal structure of S. aureus TyrRS in complex with SB284485

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 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:  

  • 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 bacte ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tyrosyl-tRNA synthetase
A
420Staphylococcus aureus (strain Newman)Mutation(s): 0 
Gene Names: tyrS
EC: 6.1.1.1
Find proteins for A6QHR2 (Staphylococcus aureus (strain Newman))
Go to UniProtKB:  A6QHR2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
485
Query on 485
Download SDF File 
Download CCD File 
A
[2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (3,4,5-TRIHYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YL)- ACETIC ACID
SB-284485
C17 H24 N2 O8
KUCHJUZRDGYEDY-HRNUQJICSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
485IC50: 4 nM (100) BINDINGDB
485IC50: 4 nM BINDINGMOAD
485IC50: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.000α = 90.00
b = 102.900β = 90.00
c = 139.800γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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