crystal structure of QacR(E57Q) bound to Dequalinium

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/bi8008246
  • Primary Citation of Related Structures:  
    3BT9, 3BTC, 3BTI, 3BTJ, 3BTL

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator qacRA [auth B],
B [auth D],
C [auth A],
D [auth E]
188Staphylococcus aureus subsp. aureus Mu50Mutation(s): 3 
Gene Names: qacR
Find proteins for P0A0N3 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P0A0N3 
Go to UniProtKB:  P0A0N3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0N3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DEQ

Download Ideal Coordinates CCD File 
C30 H40 N4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B]
F [auth D]
G [auth D]
H [auth D]
I [auth D]
E [auth B],
F [auth D],
G [auth D],
H [auth D],
I [auth D],
J [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
U [auth E],
V [auth E],
W [auth E],
X [auth E],
Y [auth E]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
DEQ PDBBind:  3BT9 Kd: 1950 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.24α = 90
b = 171.24β = 90
c = 94.2γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description