4P71

Apo PheRS from P. aeuriginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability.

Abibi, A.Ferguson, A.D.Fleming, P.R.Gao, N.Hajec, L.I.Hu, J.Laganas, V.A.McKinney, D.C.McLeod, S.M.Prince, D.B.Shapiro, A.B.Buurman, E.T.

(2014) J Biol Chem 289: 21651-21662

  • DOI: 10.1074/jbc.M114.574061
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The antimicrobial activity of phenyl-thiazolylurea-sulfonamides against Staphylococcus aureus PheRS are dependent upon phenylalanine levels in the extracellular fluids. Inhibitor efficacy in animal models of infection is substantially diminished by d ...

    The antimicrobial activity of phenyl-thiazolylurea-sulfonamides against Staphylococcus aureus PheRS are dependent upon phenylalanine levels in the extracellular fluids. Inhibitor efficacy in animal models of infection is substantially diminished by dietary phenylalanine intake, thereby reducing the perceived clinical utility of this inhibitor class. The search for novel antibacterial compounds against Gram-negative pathogens led to a re-evaluation of this phenomenon, which is shown here to be unique to S. aureus. Inhibition of macromolecular syntheses and characterization of novel resistance mutations in Escherichia coli demonstrate that antimicrobial activity of phenyl-thiazolylurea-sulfonamides is mediated by PheRS inhibition, validating this enzyme as a viable drug discovery target for Gram-negative pathogens. A search for novel inhibitors of PheRS yielded three novel chemical starting points. NMR studies were used to confirm direct target engagement for phenylalanine-competitive hits. The crystallographic structure of Pseudomonas aeruginosa PheRS defined the binding modes of these hits and revealed an auxiliary hydrophobic pocket that is positioned adjacent to the phenylalanine binding site. Three viable inhibitor-resistant mutants were mapped to this pocket, suggesting that this region is a potential liability for drug discovery.


    Organizational Affiliation

    From the Departments of Biosciences and Ed.Buurman@astrazeneca.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylalanine--tRNA ligase beta subunitA, B792Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pheTPA2739
EC: 6.1.1.20
Find proteins for Q9I0A4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0A4 
Go to UniProtKB:  Q9I0A4
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phenylalanine--tRNA ligase alpha subunitC, D338Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pheSPA2740
EC: 6.1.1.20
Find proteins for Q9I0A3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I0A3 
Go to UniProtKB:  Q9I0A3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.78α = 90
b = 219.08β = 101.91
c = 107.13γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
Cootmodel building
MOLREPphasing
SCALEPACKdata scaling
ROVERSIrefinement
SHARFFrefinement
SMARTrefinement
VONRHEINrefinement
MATTHEWSrefinement
TRONRUDrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-03-25 
  • Released Date: 2014-06-25 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy