1QAN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 

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, 1QAO, 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. 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ERMC' METHYLTRANSFERASEA244Bacillus subtilisMutation(s): 0 
Gene Names: ermC'
EC: 2.1.1.48 (PDB Primary Data), 2.1.1.184 (UniProt)
UniProt
Find proteins for P13956 (Bacillus subtilis)
Explore P13956 
Go to UniProtKB:  P13956
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
D [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH PDBBind:  1QAN Ki: 3.30e+4 (nM) from 1 assay(s)
Binding MOAD:  1QAN Ki: 3.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.21α = 90
b = 81.21β = 90
c = 122.11γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2017-02-08
    Changes: Structure summary
  • Version 1.4: 2017-10-04
    Changes: Refinement description