1QAO

THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism.

Schluckebier, G.Zhong, P.Stewart, K.D.Kavanaugh, T.J.Abad-Zapatero, C.

(1999) J.Mol.Biol. 289: 277-291

  • DOI: 10.1006/jmbi.1999.2788
  • Primary Citation of Related Structures:  1QAM, 1QAN, 1QAQ

  • PubMed Abstract: 
  • The rRNA methyltransferase ErmC' transfers methyl groups from S -adenosyl-l-methionine to atom N6 of an adenine base within the peptidyltransferase loop of 23 S rRNA, thus conferring antibiotic resistance against a number of macrolide antibiotics. Th ...

    The rRNA methyltransferase ErmC' transfers methyl groups from S -adenosyl-l-methionine to atom N6 of an adenine base within the peptidyltransferase loop of 23 S rRNA, thus conferring antibiotic resistance against a number of macrolide antibiotics. The crystal structures of ErmC' and of its complexes with the cofactor S -adenosyl-l-methionine, the reaction product S-adenosyl-l-homocysteine and the methyltransferase inhibitor Sinefungin, respectively, show that the enzyme undergoes small conformational changes upon ligand binding. Overall, the ligand molecules bind to the protein in a similar mode as observed for other methyltransferases. Small differences between the binding of the amino acid parts of the different ligands are correlated with differences in their chemical structure. A model for the transition-state based on the atomic details of the active site is consistent with a one-step methyl-transfer mechanism and might serve as a first step towards the design of potent Erm inhibitors.


    Related Citations: 
    • Crystal structure of ErmC', an RNA methyltransferase which mediates antibiotic resistance in bacteria
      Bussiere, D.E.,Muchmore, S.W.,Dealwis, C.G.,Schluckebier, G.,Nienaber, V.L.,Edalji, R.P.,Walter, K.A.,Ladror, U.S.,Holzman, T.F.,Abad-Zapatero, C.
      (1998) Biochemistry 37: 7103


    Organizational Affiliation

    Abbott Laboratories, D46Y-AP 10, 100 Abbott Park Road, Abbott Park, IL, 60064, USA. gerd.schluckebier@abbott.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ERMC' METHYLTRANSFERASE
A
244Bacillus subtilisGene Names: ermC'
EC: 2.1.1.184
Find proteins for P13956 (Bacillus subtilis)
Go to UniProtKB:  P13956
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.460α = 90.00
b = 81.460β = 90.00
c = 121.570γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-08
    Type: Structure summary
  • Version 1.4: 2017-10-04
    Type: Refinement description