1JIK

Crystal structure of S. aureus TyrRS in complex with SB-243545


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.205 

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 synthetaseA420Staphylococcus aureusMutation(s): 0 
EC: 6.1.1.1
UniProt
Find proteins for A6QHR2 (Staphylococcus aureus (strain Newman))
Explore A6QHR2 
Go to UniProtKB:  A6QHR2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
545 (Subject of Investigation/LOI)
Query on 545

Download Ideal Coordinates CCD File 
B [auth A][2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]-(1,3,4,5-TETRAHYDROXY-4-HYDROXYMETHYL-PIPERIDIN-2-YL)- ACETIC ACID BUTYL ESTER
C21 H33 N3 O9
IPZUTNGJHRAITA-FULAYSDLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
545 PDBBind:  1JIK IC50: 0.2 (nM) from 1 assay(s)
BindingDB:  1JIK IC50: 0.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.205 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.62α = 90
b = 105.38β = 90
c = 140.58γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-GENdata reduction
XDSdata scaling
X-PLORphasing

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: 2017-10-04
    Changes: Refinement description