3C0K

Crystal Structure of a ribosomal RNA methyltranferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes

Sunita, S.Tkaczuk, K.L.Purta, E.Kasprzak, J.M.Douthwaite, S.Bujnicki, J.M.Sivaraman, J.

(2008) J.Mol.Biol. 383: 652-666

  • DOI: 10.1016/j.jmb.2008.08.062

  • PubMed Abstract: 
  • Methylation is the most common RNA modification in the three domains of life. Transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to specific atoms of RNA nucleotides is catalyzed by methyltransferase (MTase) enzymes. The rRNA MTase Rl ...

    Methylation is the most common RNA modification in the three domains of life. Transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to specific atoms of RNA nucleotides is catalyzed by methyltransferase (MTase) enzymes. The rRNA MTase RlmI (rRNA large subunit methyltransferase gene I; previously known as YccW) specifically modifies Escherichia coli 23S rRNA at nucleotide C1962 to form 5-methylcytosine. Here, we report the crystal structure of RlmI refined at 2 A to a final R-factor of 0.194 (R(free)=0.242). The RlmI molecule comprises three domains: the N-terminal PUA domain; the central domain, which resembles a domain previously found in RNA:5-methyluridine MTases; and the C-terminal catalytic domain, which contains the AdoMet-binding site. The central and C-terminal domains are linked by a beta-hairpin structure that has previously been observed in several MTases acting on nucleic acids or proteins. Based on bioinformatics analyses, we propose a model for the RlmI-AdoMet-RNA complex. Comparative structural analyses of RlmI and its homologs provide insight into the potential function of several structures that have been solved by structural genomics groups and furthermore indicate that the evolutionary paths of RNA and DNA 5-methyluridine and 5-methylcytosine MTases have been closely intertwined.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UPF0064 protein yccW
A, B
396Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rlmI (yccW)
EC: 2.1.1.191
Find proteins for P75876 (Escherichia coli (strain K12))
Go to UniProtKB:  P75876
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.312α = 90.00
b = 80.875β = 98.91
c = 66.155γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
CBASSdata collection
HKL-2000data scaling
SnBphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance