2OXT

Crystal structure of Meaban virus nucleoside-2'-O-methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase

Mastrangelo, E.Bollati, M.Milani, M.Selisko, B.Peyrane, F.Canard, B.Grard, G.de Lamballerie, X.Bolognesi, M.

(2007) Protein Sci. 16: 1133-1145

  • DOI: 10.1110/ps.072758107

  • PubMed Abstract: 
  • Viral methyltransferases are involved in the mRNA capping process, resulting in the transfer of a methyl group from S-adenosyl-L-methionine to capped RNA. Two groups of methyltransferases (MTases) are known: (guanine-N7)-methyltransferases (N7MTases) ...

    Viral methyltransferases are involved in the mRNA capping process, resulting in the transfer of a methyl group from S-adenosyl-L-methionine to capped RNA. Two groups of methyltransferases (MTases) are known: (guanine-N7)-methyltransferases (N7MTases), adding a methyl group onto the N7 atom of guanine, and (nucleoside-2'-O-)-methyltransferases (2'OMTases), adding a methyl group to a ribose hydroxyl. We have expressed and purified two constructs of Meaban virus (MV; genus Flavivirus) NS5 protein MTase domain (residues 1-265 and 1-293, respectively). We report here the three-dimensional structure of the shorter MTase construct in complex with the cofactor S-adenosyl-L-methionine, at 2.9 angstroms resolution. Inspection of the refined crystal structure, which highlights structural conservation of specific active site residues, together with sequence analysis and structural comparison with Dengue virus 2'OMTase, suggests that the crystallized enzyme belongs to the 2'OMTase subgroup. Enzymatic assays show that the short MV MTase construct is inactive, but the longer construct expressed can transfer a methyl group to the ribose 2'O atom of a short GpppAC(5) substrate. West Nile virus MTase domain has been recently shown to display both N7 and 2'O MTase activity on a capped RNA substrate comprising the 5'-terminal 190 nt of the West Nile virus genome. The lack of N7 MTase activity here reported for MV MTase may be related either to the small size of the capped RNA substrate, to its sequence, or to different structural properties of the C-terminal regions of West Nile virus and MV MTase-domains.


    Organizational Affiliation

    Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, 20133-Milano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE-2'-O-METHYLTRANSFERASE
A, B, C, D
265Meaban virusMutation(s): 0 
Find proteins for A0EKU1 (Meaban virus)
Go to UniProtKB:  A0EKU1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.231 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 82.977α = 90.00
b = 82.977β = 90.00
c = 170.202γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance