3FRH

Structure of the 16S rRNA methylase RmtB, P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural bases for 16 S rRNA methylation catalyzed by ArmA and RmtB methyltransferases

Schmitt, E.Galimand, M.Panvert, M.Courvalin, P.Mechulam, Y.

(2009) J.Mol.Biol. 388: 570-582

  • DOI: 10.1016/j.jmb.2009.03.034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoglycosides are used extensively for the treatment of severe infections due to Gram-negative bacteria. However, certain species have become highly resistant after acquisition of genes for methyltransferases which catalyze post-transcriptional met ...

    Aminoglycosides are used extensively for the treatment of severe infections due to Gram-negative bacteria. However, certain species have become highly resistant after acquisition of genes for methyltransferases which catalyze post-transcriptional methylation of N7-G1405 in 16 S rRNA of 30 S ribosomal subunits. Inactivation of this enzymatic activity is therefore an important challenge for development of an effective therapy. The present work describes the crystallographic structures of methyltransferases RmtB and ArmA from clinical isolates. Together with biochemical experiments, the 3D structures indicate that the N-terminal domain specific for this family of methyltransferases is required for enzymatic activity. Site-directed mutagenesis has enabled important residues for catalysis and RNA binding to be identified. These high-resolution structures should underpin the design of potential inhibitors of these enzymes, which could be used to restore the activity of aminoglycosides against resistant pathogens.


    Organizational Affiliation

    Laboratoire de Biochimie, Ecole Polytechnique, Centre National de la Recherche Scientifique, Palaiseau Cedex, France. emma@botrytis.polytechnique.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
16S rRNA methylase
A
253Escherichia coliMutation(s): 0 
Gene Names: rmtB (RmtB)
EC: 2.1.1.179
Find proteins for Q763K9 (Escherichia coli)
Go to UniProtKB:  Q763K9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.856α = 90.00
b = 48.304β = 115.05
c = 54.558γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance