4HT4

Molecular Basis of Vancomycin Resistance Transfer in Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.907 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus.

Edwards, J.S.Betts, L.Frazier, M.L.Pollet, R.M.Kwong, S.M.Walton, W.G.Ballentine, W.K.Huang, J.J.Habibi, S.Del Campo, M.Meier, J.L.Dervan, P.B.Firth, N.Redinbo, M.R.

(2013) Proc.Natl.Acad.Sci.USA 110: 2804-2809

  • DOI: 10.1073/pnas.1219701110
  • Primary Citation of Related Structures:  4HTE

  • PubMed Abstract: 
  • Multidrug-resistant Staphylococcus aureus infections pose a significant threat to human health. Antibiotic resistance is most commonly propagated by conjugative plasmids like pLW1043, the first vancomycin-resistant S. aureus vector identified in huma ...

    Multidrug-resistant Staphylococcus aureus infections pose a significant threat to human health. Antibiotic resistance is most commonly propagated by conjugative plasmids like pLW1043, the first vancomycin-resistant S. aureus vector identified in humans. We present the molecular basis for resistance transmission by the nicking enzyme in S. aureus (NES), which is essential for conjugative transfer. NES initiates and terminates the transfer of plasmids that variously confer resistance to a range of drugs, including vancomycin, gentamicin, and mupirocin. The NES N-terminal relaxase-DNA complex crystal structure reveals unique protein-DNA contacts essential in vitro and for conjugation in S. aureus. Using this structural information, we designed a DNA minor groove-targeted polyamide that inhibits NES with low micromolar efficacy. The crystal structure of the 341-residue C-terminal region outlines a unique architecture; in vitro and cell-based studies further establish that it is essential for conjugation and regulates the activity of the N-terminal relaxase. This conclusion is supported by a small-angle X-ray scattering structure of a full-length, 665-residue NES-DNA complex. Together, these data reveal the structural basis for antibiotic multiresistance acquisition by S. aureus and suggest novel strategies for therapeutic intervention.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicking enzyme
A
195Staphylococcus aureusGene Names: nes
Find proteins for Q53632 (Staphylococcus aureus)
Go to UniProtKB:  Q53632
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (28-MER)B28N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.907 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.229 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 63.226α = 90.00
b = 63.226β = 90.00
c = 313.756γ = 120.00
Software Package:
Software NamePurpose
RESOLVEphasing
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-31 
  • Released Date: 2013-01-30 
  • Deposition Author(s): Edwards, J.S.

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references
  • Version 1.2: 2013-03-06
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Advisory, Refinement description