Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.33 kDa 
• Atom Count: 1,747 
• Modelled Residue Count: 135 
• Deposited Residue Count: 135 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3BS1

Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with a Novel Mode of Binding

• PDB DOI: 10.2210/pdb3BS1/pdb
• NDB: PD1057

• Classification: transcription regulator
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-21 Released: 2008-04-08 
• Deposition Author(s): Sidote, D.J., Barbieri, C., Wu, T., Stock, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding.

Sidote, D.J., Barbieri, C.M., Wu, T., Stock, A.M.

(2008) Structure 16: 727-735

• PubMed: 18462677 
• DOI: 10.1016/j.str.2008.02.011
• Primary Citation of Related Structures:  
  3BS1


• PubMed Abstract: 
  

The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 A resolution. The structure establishes a 10-stranded beta fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design.

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Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine and Department of Biochemistry, Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 679 Hoes Lane, Piscataway, NJ 08854, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Accessory gene regulator protein A	C [auth A]	103	Staphylococcus aureus	Mutation(s): 0  Gene Names: agrA, agr
UniProt
Find proteins for P0A0I7 (Staphylococcus aureus) Explore P0A0I7  Go to UniProtKB:  P0A0I7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DAP*DAP*DGP*(BRU)P*DAP*DT)-3')	A [auth B]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DAP*DAP*(BRU)P*DAP*DCP*DTP*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DTP*DAP*DA)-3')	B [auth C]	16	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.938	α = 90
b = 47.938	β = 90
c = 100.112	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Sidote, D.J., Barbieri, C., Wu, T., Stock, A.M.

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance