4LQE

Crystal Structure of MepB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases.

Agah, S.Poulos, S.Banchs, C.Faham, S.

(2014) Protein Sci. 23: 594-602

  • DOI: 10.1002/pro.2438

  • PubMed Abstract: 
  • The MepRAB operon in Staphylococcus aureus has been identified to play a role in drug resistance. Although the functions of MepA and MepR are known, little information is available on the function of MepB. Here we report the X-ray structure of MepB t ...

    The MepRAB operon in Staphylococcus aureus has been identified to play a role in drug resistance. Although the functions of MepA and MepR are known, little information is available on the function of MepB. Here we report the X-ray structure of MepB to 2.1 Å revealing its structural similarity to the PD-(D/E)XK family of endonucleases. We further show that MepB binds DNA and RNA, with a higher affinity towards RNA and single stranded DNA than towards double stranded DNA. Notably, the PD-(D/E)XK catalytic active site residues are not conserved in MepB. MepB's association with a drug resistance operon suggests that it plays a role in responding to antimicrobials. This role is likely carried out through MepB's interactions with nucleic acids.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MepB
A
160Staphylococcus aureus (strain Mu50 / ATCC 700699)N/A
Find proteins for A0A0H3JPI4 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  A0A0H3JPI4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.236 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 44.645α = 90.00
b = 91.139β = 90.00
c = 100.004γ = 90.00
Software Package:
Software NamePurpose
CRANKphasing
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-17 
  • Released Date: 2014-03-12 
  • Deposition Author(s): Faham, S., Agah, S.

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-05-07
    Type: Database references