7Z05

White Bream virus N7-Methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome.

Shannon, A.Sama, B.Gauffre, P.Guez, T.Debart, F.Vasseur, J.J.Decroly, E.Canard, B.Ferron, F.

(2022) Nucleic Acids Res 50: 11186-11198

  • DOI: https://doi.org/10.1093/nar/gkac876
  • Primary Citation of Related Structures:  
    7Z05, 7Z2J

  • PubMed Abstract: 

    The order Nidovirales is a diverse group of (+)RNA viruses, with a common genome organization and conserved set of replicative and editing enzymes. In particular, RNA methyltransferases play a central role in mRNA stability and immune escape. However, their presence and distribution in different Nidovirales families is not homogeneous. In Coronaviridae, the best characterized family, two distinct methytransferases perform methylation of the N7-guanine and 2'-OH of the RNA-cap to generate a cap-1 structure (m7GpppNm). The genes of both of these enzymes are located in the ORF1b genomic region. While 2'-O-MTases can be identified for most other families based on conservation of both sequence motifs and genetic loci, identification of the N7-guanine methyltransferase has proved more challenging. Recently, we identified a putative N7-MTase domain in the ORF1a region (N7-MT-1a) of certain members of the large genome Tobaniviridae family. Here, we demonstrate that this domain indeed harbors N7-specific methyltransferase activity. We present its structure as the first N7-specific Rossmann-fold (RF) MTase identified for (+)RNA viruses, making it remarkably different from that of the known Coronaviridae ORF1b N7-MTase gene. We discuss the evolutionary implications of such an appearance in this unexpected location in the genome, which introduces a split-off in the classification of Tobaniviridae.


  • Organizational Affiliation

    Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 1260White bream virusMutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for Q008X6 (White bream virus (isolate Blicca bjoerkna L./Germany/DF24/00))
Explore Q008X6 
Go to UniProtKB:  Q008X6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ008X6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.216α = 90
b = 49.787β = 97.72
c = 53.926γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateFranceFondation pour la Recherche Medical
Agence Nationale de la Recherche (ANR)FranceANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references