2FPO

Putative methyltransferase yhhF from Escherichia coli.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.

Lesnyak, D.V., Osipiuk, J., Skarina, T., Sergiev, P.V., Bogdanov, A.A., Edwards, A., Savchenko, A., Joachimiak, A., Dontsova, O.A.

(2007) J Biol Chem 282: 5880-5887

  • DOI: 10.1074/jbc.M608214200
  • Primary Citation of Related Structures:  
    2FPO

  • PubMed Abstract: 

    • N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966 ...

    N(2)-Methylguanine 966 is located in the loop of Escherichia coli 16 S rRNA helix 31, forming a part of the P-site tRNA-binding pocket. We found yhhF to be a gene encoding for m(2)G966 specific 16 S rRNA methyltransferase. Disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at G966. The modification could be rescued by expression of recombinant protein from the plasmid carrying the yhhF gene. Moreover, purified m(2)G966 methyltransferase, in the presence of S-adenosylomethionine (AdoMet), is able to methylate 30 S ribosomal subunits that were purified from yhhF knock-out strain in vitro. The methylation is specific for G966 base of the 16 S rRNA. The m(2)G966 methyltransferase was crystallized, and its structure has been determined and refined to 2.05A(.) The structure closely resembles RsmC rRNA methyltransferase, specific for m(2)G1207 of the 16 S rRNA. Structural comparisons and analysis of the enzyme active site suggest modes for binding AdoMet and rRNA to m(2)G966 methyltransferase. Based on the experimental data and current nomenclature the protein expressed from the yhhF gene was renamed to RsmD. A model for interaction of RsmD with ribosome has been proposed.

    Organizational Affiliation: 

    Department of Bioinformatics and Bioengineering, Moscow State University, Moscow 119992, Russia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
methylase yhhF
A, B, C, D, E, F
A, B, C, D, E, F
202Escherichia coli K-12Mutation(s): 3 
Gene Names: yhhF, rsmD, b3465, JW3430
EC: 2.1.1 (PDB Primary Data), 2.1.1.171 (UniProt)
UniProt
Find proteins for P0ADX9 (Escherichia coli (strain K12))
Explore P0ADX9 
Go to UniProtKB:  P0ADX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADX9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
I [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
J [auth C],
K [auth D],
L [auth E],
G [auth A],
H [auth B],
J [auth C],
K [auth D],
L [auth E],
M [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.504α = 90
b = 96.912β = 92.21
c = 193.961γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
SCALEPACKdata scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance