4RBR

Crystal structure of Repressor of Toxin (Rot), a central regulator of Staphylococcus aureus virulence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Functional Characterization of Repressor of Toxin (Rot), a Central Regulator of Staphylococcus aureus Virulence.

Killikelly, A.Benson, M.A.Ohneck, E.A.Sampson, J.M.Jakoncic, J.Spurrier, B.Torres, V.J.Kong, X.P.

(2015) J Bacteriol 197: 188-200

  • DOI: https://doi.org/10.1128/JB.02317-14
  • Primary Citation of Related Structures:  
    4RBR

  • PubMed Abstract: 

    Staphylococcus aureus is responsible for a large number of diverse infections worldwide. In order to support its pathogenic lifestyle, S. aureus has to regulate the expression of virulence factors in a coordinated fashion. One of the central regulators of the S. aureus virulence regulatory networks is the transcription factor repressor of toxin (Rot). Rot plays a key role in regulating S. aureus virulence through activation or repression of promoters that control expression of a large number of critical virulence factors. However, the mechanism by which Rot mediates gene regulation has remained elusive. Here, we have determined the crystal structure of Rot and used this information to probe the contribution made by specific residues to Rot function. Rot was found to form a dimer, with each monomer harboring a winged helix-turn-helix (WHTH) DNA-binding motif. Despite an overall acidic pI, the asymmetric electrostatic charge profile suggests that Rot can orient the WHTH domain to bind DNA. Structure-based site-directed mutagenesis studies demonstrated that R(91), at the tip of the wing, plays an important role in DNA binding, likely through interaction with the minor groove. We also found that Y(66), predicted to bind within the major groove, contributes to Rot interaction with target promoters. Evaluation of Rot binding to different activated and repressed promoters revealed that certain mutations on Rot exhibit promoter-specific effects, suggesting for the first time that Rot differentially interacts with target promoters. This work provides insight into a precise mechanism by which Rot controls virulence factor regulation in S. aureus.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, New York, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator rot
A, B
139Staphylococcus aureus subsp. aureus CN1Mutation(s): 0 
Gene Names: SAKOR_01705
UniProt
Find proteins for T1YAC1 (Staphylococcus aureus subsp. aureus CN1)
Explore T1YAC1 
Go to UniProtKB:  T1YAC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1YAC1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.56α = 85.45
b = 37.53β = 82.26
c = 63.91γ = 81.26
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations