3BTI

crystal structure of QacR(E58Q) bound to berberine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

QacR-cation recognition is mediated by a redundancy of residues capable of charge neutralization

Peters, K.M.Schuman, J.T.Skurray, R.A.Brown, M.H.Brennan, R.G.Schumacher, M.A.

(2008) Biochemistry 47: 8122-8129

  • DOI: 10.1021/bi8008246
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Staphylococcus aureus multidrug binding protein QacR binds to a broad spectrum of structurally dissimilar cationic, lipophilic drugs. Our previous structural analyses suggested that five QacR glutamic acid residues are critical for charge neutral ...

    The Staphylococcus aureus multidrug binding protein QacR binds to a broad spectrum of structurally dissimilar cationic, lipophilic drugs. Our previous structural analyses suggested that five QacR glutamic acid residues are critical for charge neutralization and specification of certain drugs. For example, E57 and E58 interact with berberine and with one of the positively charged moieties of the bivalent drug dequalinium. Here we report the structural and biochemical effects of substituting E57 and E58 with alanine and glutamine. Unexpectedly, individual substitutions of these residues did not significantly affect QacR drug binding affinity. Structures of QacR(E57Q) and QacR(E58Q) bound to dequalinium indicated that E57 and E58 are redundant for charge neutralization. The most significant finding was that berberine was reoriented in the QacR multidrug binding pocket so that its positive charge was neutralized by side chain oxygen atoms and aromatic residues. Together, these data emphasize the remarkable versatility of the QacR multidrug binding pocket, illustrating that the capacity of QacR to bind myriad cationic drugs is largely governed by the presence in the pocket of a redundancy of polar, charged, and aromatic residues that are capable of electrostatic neutralization.


    Organizational Affiliation

    School of Biological Sciences, A12, University of Sydney, Sydney, NSW, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional regulator qacR
B, D, A, E
188Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 3 
Gene Names: qacR
Find proteins for P0A0N3 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P0A0N3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BER
Query on BER

Download SDF File 
Download CCD File 
A
BERBERINE
C20 H18 N O4
YBHILYKTIRIUTE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BERKd: 720 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 171.480α = 90.00
b = 171.480β = 90.00
c = 94.400γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
CNSphasing
d*TREKdata scaling
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance