1QVT

CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO THE DRUG PROFLAVINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein

Schumacher, M.A.Miller, M.C.Brennan, R.G.

(2004) EMBO J 23: 2923-2930

  • DOI: https://doi.org/10.1038/sj.emboj.7600288
  • Primary Citation of Related Structures:  
    1QVT, 1QVU

  • PubMed Abstract: 

    The structural basis of simultaneous binding of two or more different drugs by any multidrug-binding protein is unknown and also how this can lead to a noncompetitive, uncompetitive or cooperative binding mechanism. Here, we describe the crystal structure of the Staphylococcus aureus multidrug-binding transcription repressor, QacR, bound simultaneously to ethidium (Et) and proflavin (Pf). The structure underscores the plasticity of the multidrug-binding pocket and reveals an alternative, Pf-induced binding mode for Et. To monitor the simultaneous binding of Pf and Et to QacR, as well as to determine the effects on the binding affinity of one drug when the other drug is prebound, a novel application of near-ultraviolet circular dichroism (UVCD) was developed. The UVCD equilibrium-binding studies revealed identical affinities of Pf for QacR in the presence or absence of Et, but significantly diminished affinity of Et for QacR when Pf is prebound, findings that are readily explicable by their structures. The principles for simultaneous binding of two different drugs discerned here are likely employed by the multidrug efflux transporters.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator qacRA [auth B],
B [auth D],
C [auth A],
D [auth E]
194Staphylococcus aureusMutation(s): 0 
Gene Names: QACR OR SAVP031
UniProt
Find proteins for P0A0N4 (Staphylococcus aureus)
Explore P0A0N4 
Go to UniProtKB:  P0A0N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0N4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRL
Query on PRL

Download Ideal Coordinates CCD File 
W [auth A]PROFLAVIN
C13 H11 N3
WDVSHHCDHLJJJR-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
E [auth B]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
E [auth B],
EA [auth E],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth D],
K [auth D],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
X [auth E],
Y [auth E],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.3α = 90
b = 172.3β = 90
c = 94.75γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-02-26
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description