2ERC

CRYSTAL STRUCTURE OF ERMC' A RRNA-METHYL TRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of ErmC', an rRNA 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: 7103-7112

  • DOI: 10.1021/bi973113c

  • PubMed Abstract: 
  • The prevalent mechanism of bacterial resistance to erythromycin and other antibiotics of the macrolide-lincosamide-streptogramin B group (MLS) is methylation of the 23S rRNA component of the 50S subunit in bacterial ribosomes. This sequence-specific ...

    The prevalent mechanism of bacterial resistance to erythromycin and other antibiotics of the macrolide-lincosamide-streptogramin B group (MLS) is methylation of the 23S rRNA component of the 50S subunit in bacterial ribosomes. This sequence-specific methylation is catalyzed by the Erm group of methyltransferases (MTases). They are found in several strains of pathogenic bacteria, and ErmC is the most studied member of this class. The crystal structure of ErmC' (a naturally occurring variant of ErmC) from Bacillus subtilis has been determined at 3.0 A resolution by multiple anomalous diffraction phasing methods. The structure consists of a conserved alpha/beta amino-terminal domain which binds the cofactor S-adenosyl-l-methionine (SAM), followed by a smaller, alpha-helical RNA-recognition domain. The beta-sheet structure of the SAM-binding domain is well-conserved between the DNA, RNA, and small-molecule MTases. However, the C-terminal nucleic acid binding domain differs from the DNA-binding domains of other MTases and is unlike any previously reported RNA-recognition fold. A large, positively charged, concave surface is found at the interface of the N- and C-terminal domains and is proposed to form part of the protein-RNA interaction surface. ErmC' exhibits the conserved structural motifs previously found in the SAM-binding domain of other methyltransferases. A model of SAM bound to ErmC' is presented which is consistent with the motif conservation among MTases.


    Related Citations: 
    • Sequence and Properties of Pim13, a Macrolide-Lincosamide-Streptogramin B Resistance Plasmid from Bacillus Subtilis
      Monod, M.,Denoya, C.,Dubnau, D.
      (1986) J.Bacteriol. 167: 138
    • Substrate Requirements for Ermc' Methyltransferase Activity
      Zhong, P.,Pratt, S.D.,Edalji, R.P.,Walter, K.A.,Holzman, T.F.,Shivakumar, A.G.,Katz, L.
      (1995) J.Bacteriol. 177: 4327


    Organizational Affiliation

    Laboratory of Protein Crystallography, Department of Scientific Information, Analysis and Management, Abbott Laboratories, Abbott Park, Illinois 60064-3500, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RRNA METHYL TRANSFERASE
A, B
244Bacillus subtilisMutation(s): 0 
Gene Names: ermC'
EC: 2.1.1.184
Find proteins for P13956 (Bacillus subtilis)
Go to UniProtKB:  P13956
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.232 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 146.900α = 90.00
b = 146.900β = 90.00
c = 57.900γ = 120.00
Software Package:
Software NamePurpose
HKLdata reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
SHARPphasing
PHASESphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance