4G4K | pdb_00004g4k

Structure of the Staphylococcus aureus AgrA LytTR Domain

• PDB DOI: https://doi.org/10.2210/pdb4G4K/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2012-07-16 Released: 2012-12-19 
• Deposition Author(s): Leonard, P.G., Bezar, I.F., Stock, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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

• PubMed: 23181972 
• DOI: https://doi.org/10.1021/bi3011785
• Primary Citation Related Structures: 
  4G4K


• 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.99 kDa 
• Atom Count: 1,974 
• Modeled Residue Count: 198 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Accessory gene regulator protein A	A, B	103	Staphylococcus aureus	Mutation(s): 0  Gene Names: agr, agrA
UniProt
Find proteins for P0A0I7 (Staphylococcus aureus) Explore P0A0I7  Go to UniProtKB:  P0A0I7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.414	α = 90
b = 45.894	β = 90
c = 112.138	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Leonard, P.G., Bezar, I.F., Stock, A.M.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description