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PDBsum entry 1qvu

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protein ligands Protein-protein interface(s) links
Transcription PDB id
1qvu
Jmol
Contents
Protein chains
186 a.a. *
Ligands
_ET
PRL
* Residue conservation analysis
PDB id:
1qvu
Name: Transcription
Title: Crystal structure of the multidrug binding transcriptional repressor qacr bound to two drugs: ethidium and proflavine
Structure: Transcriptional regulator qacr. Chain: b, d, a, e. Fragment: qacr. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Gene: qacr or savp031. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.96Å     R-factor:   0.223     R-free:   0.273
Authors: M.A.Schumacher,M.C.Miller,R.G.Brennan
Key ref:
M.A.Schumacher et al. (2004). Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein. EMBO J, 23, 2923-2930. PubMed id: 15257299 DOI: 10.1038/sj.emboj.7600288
Date:
28-Aug-03     Release date:   03-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A0N4  (QACR_STAAU) -  HTH-type transcriptional regulator QacR
Seq:
Struc:
188 a.a.
186 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   3 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1038/sj.emboj.7600288 EMBO J 23:2923-2930 (2004)
PubMed id: 15257299  
 
 
Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein.
M.A.Schumacher, M.C.Miller, R.G.Brennan.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Ribbon diagrams of the drug-binding pocket of QacR. (A) QacR -Pf binary complex. (B) QacR -Et binary complex (Schumacher et al, 2001). (C) QacR -Pf -Et ternary complex. For clarity, only key drug-binding residues are shown. Acidic residues involved in drug neutralization are colored red and all other residues are colored light blue. Carbon, nitrogen and oxygen atoms of the drug molecules are colored white, blue and red, respectively. These figures and Figures 2A, C and 3A, B were made with SwissPdbViewer (Guex and Peitsch, 1997) and rendered with POVRAY (POV-Ray, Persistence of Vision Raytracer, version 3.1 (www.povray.org)).
Figure 3.
Figure 3 The structure of the ternary QacR -Pf -Et structure. (A) Ribbon diagram of the QacR -Pf -Et ternary complex. The nine helices are labelled as are the N- and C-termini. The bound Et is shown as red sticks and the bound Pf as yellow sticks. (B) Superimposition of binary QacR -Et (red), binary QacR -Pf (yellow) and ternary QacR -Pf -Et (blue) complexes showing the reorientation of Et in the ternary complex.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2923-2930) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21328631 H.T.Lei, Z.Shen, P.Surana, M.D.Routh, C.C.Su, Q.Zhang, and E.W.Yu (2011).
Crystal structures of CmeR-bile acid complexes from Campylobacter jejuni.
  Protein Sci, 20, 712-723.
PDB codes: 3qps 3qqa
21264225 K.M.Peters, B.E.Brooks, M.A.Schumacher, R.A.Skurray, R.G.Brennan, and M.H.Brown (2011).
A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity.
  PLoS One, 6, e15974.
PDB code: 3pm1
19819701 D.A.Gutmann, A.Ward, I.L.Urbatsch, G.Chang, and H.W.van Veen (2010).
Understanding polyspecificity of multidrug ABC transporters: closing in on the gaps in ABCB1.
  Trends Biochem Sci, 35, 36-42.  
20804453 F.Husain, and H.Nikaido (2010).
Substrate path in the AcrB multidrug efflux pump of Escherichia coli.
  Mol Microbiol, 78, 320-330.  
20580544 H.Wade (2010).
MD recognition by MDR gene regulators.
  Curr Opin Struct Biol, 20, 489-496.  
19961541 R.Ernst, P.Kueppers, J.Stindt, K.Kuchler, and L.Schmitt (2010).
Multidrug efflux pumps: substrate selection in ATP-binding cassette multidrug efflux pumps--first come, first served?
  FEBS J, 277, 540-549.  
20212112 Y.Takatsuka, C.Chen, and H.Nikaido (2010).
Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli.
  Proc Natl Acad Sci U S A, 107, 6559-6565.  
19231985 H.Nikaido (2009).
Multidrug resistance in bacteria.
  Annu Rev Biochem, 78, 119-146.  
19820093 M.Bellinzoni, S.Buroni, F.Schaeffer, G.Riccardi, E.De Rossi, and P.M.Alzari (2009).
Structural plasticity and distinct drug-binding modes of LfrR, a mycobacterial efflux pump regulator.
  J Bacteriol, 191, 7531-7537.
PDB codes: 2v57 2wgb
19130905 M.D.Routh, C.C.Su, Q.Zhang, and E.W.Yu (2009).
Structures of AcrR and CmeR: insight into the mechanisms of transcriptional repression and multi-drug recognition in the TetR family of regulators.
  Biochim Biophys Acta, 1794, 844-851.  
19715704 P.Zou, and H.S.McHaourab (2009).
Alternating access of the putative substrate-binding chamber in the ABC transporter MsbA.
  J Mol Biol, 393, 574-585.  
19453279 T.Eicher, L.Brandstätter, and K.M.Pos (2009).
Structural and functional aspects of the multidrug efflux pump AcrB.
  Biol Chem, 390, 693-699.  
19678712 X.Z.Li, and H.Nikaido (2009).
Efflux-mediated drug resistance in bacteria: an update.
  Drugs, 69, 1555-1623.  
18535149 A.L.Davidson, E.Dassa, C.Orelle, and J.Chen (2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
  Microbiol Mol Biol Rev, 72, 317.  
18722384 C.J.Tsai, Z.E.Sauna, C.Kimchi-Sarfaty, S.V.Ambudkar, M.M.Gottesman, and R.Nussinov (2008).
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima.
  J Mol Biol, 383, 281-291.  
18154452 F.J.Sharom (2008).
ABC multidrug transporters: structure, function and role in chemoresistance.
  Pharmacogenomics, 9, 105-127.  
18591276 F.Long, C.Rouquette-Loughlin, W.M.Shafer, and E.W.Yu (2008).
Functional cloning and characterization of the multidrug efflux pumps NorM from Neisseria gonorrhoeae and YdhE from Escherichia coli.
  Antimicrob Agents Chemother, 52, 3052-3060.  
18042544 I.Lehner, D.Basting, B.Meyer, W.Haase, T.Manolikas, C.Kaiser, M.Karas, and C.Glaubitz (2008).
The Key Residue for Substrate Transport (Glu14) in the EmrE Dimer Is Asymmetric.
  J Biol Chem, 283, 3281-3288.  
18658145 K.J.Newberry, J.L.Huffman, M.C.Miller, N.Vazquez-Laslop, A.A.Neyfakh, and R.G.Brennan (2008).
Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion.
  J Biol Chem, 283, 26795-26804.
PDB codes: 3d6y 3d6z 3d70 3d71
18616285 K.M.Peters, J.T.Schuman, R.A.Skurray, M.H.Brown, R.G.Brennan, and M.A.Schumacher (2008).
QacR-cation recognition is mediated by a redundancy of residues capable of charge neutralization.
  Biochemistry, 47, 8122-8129.
PDB codes: 3bt9 3btc 3bti 3btj 3btl
18219120 U.Okada, K.Kondo, T.Hayashi, N.Watanabe, M.Yao, T.Tamura, and I.Tanaka (2008).
Structural and functional analysis of the TetR-family transcriptional regulator SCO0332 from Streptomyces coelicolor.
  Acta Crystallogr D Biol Crystallogr, 64, 198-205.
PDB code: 2zb9
18295794 V.M.Korkhov, and C.G.Tate (2008).
Electron crystallography reveals plasticity within the drug binding site of the small multidrug transporter EmrE.
  J Mol Biol, 377, 1094-1103.  
18842589 Z.E.Sauna, S.S.Bohn, R.Rutledge, M.P.Dougherty, S.Cronin, L.May, D.Xia, S.V.Ambudkar, and J.Golin (2008).
Mutations Define Cross-talk between the N-terminal Nucleotide-binding Domain and Transmembrane Helix-2 of the Yeast Multidrug Transporter Pdr5: POSSIBLE CONSERVATION OF A SIGNALING INTERFACE FOR COUPLING ATP HYDROLYSIS TO DRUG TRANSPORT.
  J Biol Chem, 283, 35010-35022.  
17644067 C.C.Su, D.J.Rutherford, and E.W.Yu (2007).
Characterization of the multidrug efflux regulator AcrR from Escherichia coli.
  Biochem Biophys Res Commun, 361, 85-90.  
17910961 C.C.Su, H.Nikaido, and E.W.Yu (2007).
Ligand-transporter interaction in the AcrB multidrug efflux pump determined by fluorescence polarization assay.
  FEBS Lett, 581, 4972-4976.  
17429392 C.F.Higgins (2007).
Multiple molecular mechanisms for multidrug resistance transporters.
  Nature, 446, 749-757.  
17588774 K.D.Koclega, M.Chruszcz, M.D.Zimmerman, M.Cymborowski, E.Evdokimova, and W.Minor (2007).
Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment.
  J Struct Biol, 159, 424-432.
PDB code: 1z77
17416591 M.E.Guazzaroni, M.T.Gallegos, J.L.Ramos, and T.Krell (2007).
Different modes of binding of mono- and biaromatic effectors to the transcriptional regulator TTGV: role in differential derepression from its cognate operator.
  J Biol Chem, 282, 16308-16316.  
17950313 M.Li, R.Gu, C.C.Su, M.D.Routh, K.C.Harris, E.S.Jewell, G.McDermott, and E.W.Yu (2007).
Crystal structure of the transcriptional regulator AcrR from Escherichia coli.
  J Mol Biol, 374, 591-603.
PDB code: 2qop
17159924 O.Lomovskaya, H.I.Zgurskaya, M.Totrov, and W.J.Watkins (2007).
Waltzing transporters and 'the dance macabre' between humans and bacteria.
  Nat Rev Drug Discov, 6, 56-65.  
17686491 R.Gu, C.C.Su, F.Shi, M.Li, G.McDermott, Q.Zhang, and E.W.Yu (2007).
Crystal structure of the transcriptional regulator CmeR from Campylobacter jejuni.
  J Mol Biol, 372, 583-593.
PDB code: 2qco
16352827 E.M.Hearn, M.R.Gray, and J.M.Foght (2006).
Mutations in the central cavity and periplasmic domain affect efflux activity of the resistance-nodulation-division pump EmhB from Pseudomonas fluorescens cLP6a.
  J Bacteriol, 188, 115-123.  
16823814 G.A.Ascoli, E.Domenici, and C.Bertucci (2006).
Drug binding to human serum albumin: abridged review of results obtained with high-performance liquid chromatography and circular dichroism.
  Chirality, 18, 667-679.  
16856936 O.Lewinson, J.Adler, N.Sigal, and E.Bibi (2006).
Promiscuity in multidrug recognition and transport: the bacterial MFS Mdr transporters.
  Mol Microbiol, 61, 277-284.  
16545467 R.A.Shilling, H.Venter, S.Velamakanni, A.Bapna, B.Woebking, S.Shahi, and H.W.van Veen (2006).
New light on multidrug binding by an ATP-binding-cassette transporter.
  Trends Pharmacol Sci, 27, 195-203.  
16407274 W.Terán, T.Krell, J.L.Ramos, and M.T.Gallegos (2006).
Effector-repressor interactions, binding of a single effector molecule to the operator-bound TtgR homodimer mediates derepression.
  J Biol Chem, 281, 7102-7109.  
16675700 Y.Yin, X.He, P.Szewczyk, T.Nguyen, and G.Chang (2006).
Structure of the multidrug transporter EmrD from Escherichia coli.
  Science, 312, 741-744.
PDB code: 2gfp
16282328 Z.Xu, B.A.O'Rourke, R.A.Skurray, and M.H.Brown (2006).
Role of transmembrane segment 10 in efflux mediated by the staphylococcal multidrug transport protein QacA.
  J Biol Chem, 281, 792-799.  
16166543 E.W.Yu, J.R.Aires, G.McDermott, and H.Nikaido (2005).
A periplasmic drug-binding site of the AcrB multidrug efflux pump: a crystallographic and site-directed mutagenesis study.
  J Bacteriol, 187, 6804-6815.
PDB codes: 1t9t 1t9u 1t9v 1t9w 1t9x 1t9y
16691487 F.J.Sharom, M.R.Lugo, and P.D.Eckford (2005).
New insights into the drug binding, transport and lipid flippase activities of the p-glycoprotein multidrug transporter.
  J Bioenerg Biomembr, 37, 481-487.  
15557318 J.Adler, and E.Bibi (2005).
Promiscuity in the geometry of electrostatic interactions between the Escherichia coli multidrug resistance transporter MdfA and cationic substrates.
  J Biol Chem, 280, 2721-2729.  
15767250 M.E.Guazzaroni, T.Krell, A.Felipe, R.Ruiz, C.Meng, X.Zhang, M.T.Gallegos, and J.L.Ramos (2005).
The multidrug efflux regulator TtgV recognizes a wide range of structurally different effectors in solution and complexed with target DNA: evidence from isothermal titration calorimetry.
  J Biol Chem, 280, 20887-20893.  
15870072 M.Klotzsche, C.Berens, and W.Hillen (2005).
A peptide triggers allostery in tet repressor by binding to a unique site.
  J Biol Chem, 280, 24591-24599.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.