3FZG | pdb_00003fzg

Structure of the 16S rRNA methylase ArmA

• PDB DOI: https://doi.org/10.2210/pdb3FZG/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-26 Released: 2009-08-11 
• Deposition Author(s): Schmitt, E., Galimand, M., Panvert, M., Courvalin, P., Mechulam, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

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 Biology 388: 570-582

• PubMed: 19303884 
• DOI: https://doi.org/10.1016/j.jmb.2009.03.034
• Primary Citation Related Structures: 
  3FRH, 3FRI, 3FZG


• 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 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. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.78 kDa 
• Atom Count: 1,913 
• Modeled Residue Count: 196 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16S rRNA methylase	A	200	Escherichia coli	Mutation(s): 0  Gene Names: armA, pMUR050_016 EC: 2.1.1.179
UniProt
Find proteins for Q6F5A0 (Escherichia coli) Explore Q6F5A0  Go to UniProtKB:  Q6F5A0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.11	α = 90
b = 90.08	β = 90
c = 65.94	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SOLVE	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Schmitt, E., Galimand, M., Panvert, M., Courvalin, P., Mechulam, Y.

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations