4LLN

Crystal structure of S. aureus MepR-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR.

Birukou, I.Seo, S.M.Schindler, B.D.Kaatz, G.W.Brennan, R.G.

(2014) Nucleic Acids Res 42: 2774-2788

  • DOI: 10.1093/nar/gkt1215
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The multidrug efflux pump MepA is a major contributor to multidrug resistance in Staphylococcus aureus. MepR, a member of the multiple antibiotic resistance regulator (MarR) family, represses mepA and its own gene. Here, we report the structure of a ...

    The multidrug efflux pump MepA is a major contributor to multidrug resistance in Staphylococcus aureus. MepR, a member of the multiple antibiotic resistance regulator (MarR) family, represses mepA and its own gene. Here, we report the structure of a MepR-mepR operator complex. Structural comparison of DNA-bound MepR with 'induced' apoMepR reveals the large conformational changes needed to allow the DNA-binding winged helix-turn-helix motifs to interact with the consecutive major and minor grooves of the GTTAG signature sequence. Intriguingly, MepR makes no hydrogen bonds to major groove nucleobases. Rather, recognition-helix residues Thr60, Gly61, Pro62 and Thr63 make sequence-specifying van der Waals contacts with the TTAG bases. Removing these contacts dramatically affects MepR-DNA binding activity. The wings insert into the flanking minor grooves, whereby residue Arg87, buttressed by Asp85, interacts with the O2 of T4 and O4' ribosyl oxygens of A23 and T4. Mutating Asp85 and Arg87, both conserved throughout the MarR family, markedly affects MepR repressor activity. The His14':Arg59 and Arg10':His35:Phe108 interaction networks stabilize the DNA-binding conformation of MepR thereby contributing significantly to its high affinity binding. A structure-guided model of the MepR-mepA operator complex suggests that MepR dimers do not interact directly and cooperative binding is likely achieved by DNA-mediated allosteric effects.


    Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA, The John D. Dingell Department of Veterans Affairs Medical Center, B4333 JD Dingel VA Medical Center, 4646 John R, Detroit, MI 48201, USA and Department of Internal Medicine, Division of Infectious Diseases, Wayne State University School of Medicine, 5 Hudson, Harper University Hospital, 3990 John R, Detroit, MI 48201, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MepRA, B, C, D, I, J140Staphylococcus aureusMutation(s): 0 
Gene Names: 
Find proteins for Q5Y812 (Staphylococcus aureus)
Explore Q5Y812 
Go to UniProtKB:  Q5Y812
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
Palindromized mepR operator sequenceE, F, G, H, K, L24N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.343α = 90.61
b = 76.231β = 104.75
c = 109.41γ = 106.27
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description