1JII | pdb_00001jii

Crystal structure of S. aureus TyrRS in complex with SB-219383


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.335 (Depositor) 
  • R-Value Work: 
    0.269 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1JII

This is version 1.5 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: https://doi.org/10.1110/ps.18001
  • Primary Citation Related Structures: 
    1JII, 1JIJ, 1JIK, 1JIL

  • 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. 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

Macromolecule Content 

  • Total Structure Weight: 48.07 kDa 
  • Atom Count: 2,585 
  • Modeled Residue Count: 319 
  • Deposited Residue Count: 420 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
tyrosyl-tRNA synthetase420Staphylococcus aureusMutation(s): 0 
EC: 6.1.1.1
UniProt
Find proteins for A6QHR2 (Staphylococcus aureus (strain Newman))
Explore A6QHR2 
Go to UniProtKB:  A6QHR2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6QHR2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
383

Query on 383



Download:Ideal Coordinates CCD File
B [auth A][2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (2,4,5,8-TETRAHYDROXY-7-OXA-2-AZA-BICYCLO[3.2.1]OCT-3-YL)- ACETIC ACID
C17 H23 N3 O9
JOBDOAKLPNMGKV-OEUXZGCXSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.335 (Depositor) 
  • R-Value Work:  0.269 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.56α = 90
b = 98.45β = 90
c = 142.13γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-GENdata reduction
X-GENdata 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
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description