1JT0

Crystal structure of a cooperative QacR-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR.

Schumacher, M.A.Miller, M.C.Grkovic, S.Brown, M.H.Skurray, R.A.Brennan, R.G.

(2002) EMBO J. 21: 1210-1218

  • DOI: 10.1093/emboj/21.5.1210

  • PubMed Abstract: 
  • The Staphylococcus aureus multidrug-binding protein QacR represses transcription of the qacA multidrug transporter gene and is induced by multiple structurally dissimilar drugs. QacR is a member of the TetR/CamR family of transcriptional regulators, ...

    The Staphylococcus aureus multidrug-binding protein QacR represses transcription of the qacA multidrug transporter gene and is induced by multiple structurally dissimilar drugs. QacR is a member of the TetR/CamR family of transcriptional regulators, which share highly homologous N-terminal DNA-binding domains connected to seemingly non-homologous ligand-binding domains. Unlike other TetR members, which bind approximately 15 bp operators, QacR recognizes an unusually long 28 bp operator, IR1, which it appears to bind cooperatively. To elucidate the DNA-binding mechanism of QacR, we determined the 2.90 A resolution crystal structure of a QacR-IR1 complex. Strikingly, our data reveal that the DNA recognition mode of QacR is distinct from TetR and involves the binding of a pair of QacR dimers. In this unique binding mode, recognition at each IR1 half-site is mediated by a complement of DNA contacts made by two helix-turn-helix motifs. The inferred cooperativity does not arise from cross-dimer protein-protein contacts, but from the global undertwisting and major groove widening elicited by the binding of two QacR dimers.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97201-3098, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN QACA 5'REGION
A, B, C, D
194Staphylococcus aureusMutation(s): 2 
Gene Names: qacR
Find proteins for P0A0N4 (Staphylococcus aureus)
Go to UniProtKB:  P0A0N4
Entity ID: 1
MoleculeChainsLengthOrganism
QACA operatorE,F28N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.222 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 174.700α = 90.00
b = 174.700β = 90.00
c = 151.950γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance