Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.76 kDa 
• Atom Count: 6587 
• Modelled Residue Count: 790 
• Deposited Residue Count: 792 
• Unique protein chains: 1

3C0K

Crystal Structure of a ribosomal RNA methyltranferase

• PDB DOI: 10.2210/pdb3C0K/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-21 Released: 2008-11-04 
• Deposition Author(s): Subramanian, S., Jayaraman, S., Bujnicki, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.194 

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

• PubMed: 18789337 
• DOI: 10.1016/j.jmb.2008.08.062
• Primary Citation of Related Structures:  
  3C0K


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0064 protein yccW	A, B	396	Escherichia coli K-12	Mutation(s): 0  Gene Names: rlmI, yccW, b0967, JW5898 EC: 2.1.1 (PDB Primary Data), 2.1.1.191 (UniProt)
UniProt
Find proteins for P75876 (Escherichia coli (strain K12)) Explore P75876  Go to UniProtKB:  P75876

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.312	α = 90
b = 80.875	β = 98.91
c = 66.155	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SnB	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-21 
• Released Date: 2008-11-04 
Deposition Author(s): Subramanian, S., Jayaraman, S., Bujnicki, J.

Revision History  

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