1QAM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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' METHYLTRANSFERASEA244Bacillus subtilisMutation(s): 0 
Gene Names: ermC'
EC: 2.1.1.48 (PDB Primary Data), 2.1.1.184 (UniProt)
Find proteins for P13956 (Bacillus subtilis)
Explore P13956 
Go to UniProtKB:  P13956
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.38α = 90
b = 81.38β = 90
c = 122.22γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description