RCSB PDB - 1L9K: dengue methyltransferase

 1L9K

dengue methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.275 

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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

An RNA cap (nucleoside-2'-O-) methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization

Egloff, M.P.Benarroch, D.Selisko, B.Romette, J.L.Canard, B.

(2002) EMBO J 21: 2757-2768

  • DOI: https://doi.org/10.1093/emboj/21.11.2757
  • Primary Citation of Related Structures:  
    1L9K, 2P1D

  • PubMed Abstract: 

    Viruses represent an attractive system with which to study the molecular basis of mRNA capping and its relation to the RNA transcription machinery. The RNA-dependent RNA polymerase NS5 of flaviviruses presents a characteristic motif of S-adenosyl-L-methionine-dependent methyltransferases at its N-terminus, and polymerase motifs at its C-terminus. The crystal structure of an N-terminal fragment of Dengue virus type 2 NS5 is reported at 2.4 A resolution. We show that this NS5 domain includes a typical methyltransferase core and exhibits a (nucleoside-2'-O-)-methyltransferase activity on capped RNA. The structure of a ternary complex comprising S-adenosyl-L-homocysteine and a guanosine triphosphate (GTP) analogue shows that 54 amino acids N-terminal to the core provide a novel GTP-binding site that selects guanine using a previously unreported mechanism. Binding studies using GTP- and RNA cap-analogues, as well as the spatial arrangement of the methyltransferase active site relative to the GTP-binding site, suggest that the latter is a specific cap-binding site. As RNA capping is an essential viral function, these results provide a structural basis for the rational design of drugs against the emerging flaviviruses.


  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Université Aix-Marseille I et II, ESIL, Campus de Luminy, F-13288 Marseille Cedex 09, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASE305dengue virus type 2Mutation(s): 7 
Gene Names: NS5 New Guinea C
EC: 2.7.7.48
UniProt
Find proteins for P12823 (Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969))
Explore P12823 
Go to UniProtKB:  P12823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12823
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.275 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.56α = 90
b = 111.56β = 90
c = 56.33γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CCP4data scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection