1GZ0 | pdb_00001gz0

23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.279 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

The Structure of the Rlmb 23S Rrna Methyltransferase Reveals a New Methyltransferase Fold with a Unique Knot

Michel, G., Sauve, V., Larocque, R., Li, Y., Matte, A., Cygler, M.

(2002) Structure 10: 1303

  • DOI: https://doi.org/10.1016/s0969-2126(02)00852-3
  • Primary Citation Related Structures: 
    1GZ0

  • PubMed Abstract: 

    In Escherichia coli, RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. The crystal structure of this 2'O-methyltransferase has been determined at 2.5 A resolution. RlmB consists of an N-terminal domain connected by a flexible extended linker to a catalytic C-terminal domain and forms a dimer in solution. The C-terminal domain displays a divergent methyltransferase fold with a unique knotted region, and lacks the classic AdoMet binding site features. The N-terminal domain is similar to ribosomal proteins L7 and L30, suggesting a role in 23S rRNA recognition. The conserved residues in this novel family of 2'O-methyltransferases cluster in the knotted region, suggesting the location of the catalytic and AdoMet binding sites.

    • Organizational Affiliation: 
    • Biotechnology Research Institute, National Research Council of Canada and Montreal Joint Centre for Structural Biology, Montreal, Quebec, Canada.

Macromolecule Content 

  • Total Structure Weight: 223.56 kDa 
  • Atom Count: 13,953 
  • Modeled Residue Count: 1,807 
  • Deposited Residue Count: 2,024 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
A, B, C, D, E
A, B, C, D, E, F, G, H
253Escherichia coliMutation(s): 0 
EC: 2.1.1 (PDB Primary Data), 2.1.1.185 (UniProt)
UniProt
Find proteins for P63177 (Escherichia coli (strain K12))
Explore P63177 
Go to UniProtKB:  P63177
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63177
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.279 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.478α = 90
b = 132.288β = 96.4
c = 90.71γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary