4XQJ | pdb_00004xqj

Crystal structure of AgrA LytTR domain in complex with promoters

• PDB DOI: https://doi.org/10.2210/pdb4XQJ/pdb
• NAKB: 4XQJ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Staphylococcus aureus subsp. aureus COL, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-19 Released: 2016-04-06 
• Deposition Author(s): Gopal, B., Rajasree, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression.

Rajasree, K., Fasim, A., Gopal, B.

(2016) Biochem Biophys Rep 6: 124-134

• PubMed: 28955870 
• DOI: https://doi.org/10.1016/j.bbrep.2016.03.012
• Primary Citation Related Structures: 
  4XQJ, 4XQN, 4XQQ, 4XXE, 4XYO, 4XYQ


• PubMed Abstract: 
  

  The intracellular trigger for the quorum sensing response mechanism in Staphylococcus aureus involves the phosphorylation of the response regulator AgrA by the membrane anchored histidine kinase AgrC. AgrA activates transcription from three promoter sequences (P1-P3). The promoter strength, conditional association of AgrA with these promoter elements and temporal delay in AgrA-mediated changes in gene expression contribute to the diversity of the quorum sensing response in different S. aureus strains. AgrA promoters comprise of imperfect direct repeats of DNA with a consensus sequence- [TA][AC][CA]GTTN[AG][TG]. Here we describe crystal structures of the DNA-binding (LytTR) domain of AgrA with different cognate DNA sequences that reveal a hitherto unanticipated feature of AgrA-DNA interactions. AgrA promoter interactions are asymmetric with fewer interactions at the binding site proximal to the -35 promoter element. Biochemical assays to evaluate AgrA-promoter interactions suggests that phosphorylation induced dimerization of AgrA can compensate for the asymmetry in AgrA-DNA interactions. The structures also provide a basis to rationalize mutations that were noted to alter AgrA activity without affecting protein-DNA interactions. Put together, the structural data, gene expression and mutational analysis reveal that promoter strength and AgrA phosphorylation enable quorum-sensing triggered transcriptional changes leading to a transition from the persistent to virulent phenotype.

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Organizational Affiliation: 
• Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.37 kDa 
• Atom Count: 2,896 
• Modeled Residue Count: 246 
• Deposited Residue Count: 248 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Accessory gene regulator A	A, D	99	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: agrA, SACOL2026
UniProt
Find proteins for Q5HEG2 (Staphylococcus aureus (strain COL)) Explore Q5HEG2  Go to UniProtKB:  Q5HEG2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')	B, E	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')	C, F	13	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	CA [auth F], DA [auth F], EA [auth F], N [auth A], O [auth A], P [auth A], R [auth C], V [auth D], Y [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH	AA [auth F], BA [auth F], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], S [auth D], T [auth D], U [auth D], X [auth E]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CA	W [auth E], Z [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.225 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.03	α = 90
b = 92.87	β = 98.59
c = 45.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Gopal, B., Rajasree, K.

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description