Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 250.03 kDa 
• Atom Count: 16150 
• Residue Count: 2064 
• Unique protein chains: 2

4P71

Apo PheRS from P. aeuriginosa

• DOI: 10.2210/pdb4P71/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


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

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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 

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

• PubMed: 24936059 
• 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 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.

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Organizational Affiliation: 

From the Departments of Biosciences and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Phenylalanine--tRNA ligase beta subunit	A, B	792	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: pheT, PA2739 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Phenylalanine--tRNA ligase alpha subunit	C, D	338	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: pheS, PA2740 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

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 = 112.78	α = 90
b = 219.08	β = 101.91
c = 107.13	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
Coot	model building
MOLREP	phasing
SCALEPACK	data scaling
ROVERSI	refinement
SHARFF	refinement
SMART	refinement
VONRHEIN	refinement
MATTHEWS	refinement
TRONRUD	refinement

Structure Validation

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