4G4K

Structure of the Staphylococcus aureus AgrA LytTR Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of a Hydrophobic Cleft in the LytTR Domain of AgrA as a Locus for Small Molecule Interactions That Inhibit DNA Binding.

Leonard, P.G.Bezar, I.F.Sidote, D.J.Stock, A.M.

(2012) Biochemistry 51: 10035-10043

  • DOI: 10.1021/bi3011785

  • PubMed Abstract: 
  • The AgrA transcription factor regulates the quorum-sensing response in Staphylococcus aureus, controlling the production of hemolysins and other virulence factors. AgrA binds to DNA via its C-terminal LytTR domain, a domain not found in humans but co ...

    The AgrA transcription factor regulates the quorum-sensing response in Staphylococcus aureus, controlling the production of hemolysins and other virulence factors. AgrA binds to DNA via its C-terminal LytTR domain, a domain not found in humans but common in many pathogenic bacteria, making it a potential target for antimicrobial development. We have determined the crystal structure of the apo AgrA LytTR domain and screened a library of 500 fragment compounds to find inhibitors of AgrA DNA binding activity. Using nuclear magnetic resonance, the binding site for five compounds has been mapped to a common locus at the C-terminal end of the LytTR domain, a site known to be important for DNA binding activity. Three of these compounds inhibit AgrA DNA binding. These results provide the first evidence that LytTR domains can be targeted by small organic compounds.


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ 08854-5635, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Accessory gene regulator protein A
A, B
103Staphylococcus aureusMutation(s): 0 
Gene Names: agrA (agr)
Find proteins for P0A0I7 (Staphylococcus aureus)
Go to UniProtKB:  P0A0I7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.414α = 90.00
b = 45.894β = 90.00
c = 112.138γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
RESOLVEphasing
StructureStudiodata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references