3LKZ

Structural and functional analyses of a conserved hydrophobic pocket of flavivirus methyltransferase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

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Literature

Structural and functional analyses of a conserved hydrophobic pocket of flavivirus methyltransferase.

Dong, H., Liu, L., Zou, G., Zhao, Y., Li, Z., Lim, S.P., Shi, P.Y., Li, H.

(2010) J Biol Chem 285: 32586-32595

  • DOI: https://doi.org/10.1074/jbc.M110.129197
  • Primary Citation of Related Structures:  
    3LKZ

  • PubMed Abstract: 

    The flavivirus methyltransferase (MTase) sequentially methylates the N7 and 2'-O positions of the viral RNA cap (GpppA-RNA → m(7)GpppA-RNA → m(7)GpppAm-RNA), using S-adenosyl-l-methionine (AdoMet) as a methyl donor. We report here that sinefungin (SIN), an AdoMet analog, inhibits several flaviviruses through suppression of viral MTase. The crystal structure of West Nile virus MTase in complex with SIN inhibitor at 2.0-Å resolution revealed a flavivirus-conserved hydrophobic pocket located next to the AdoMet-binding site. The pocket is functionally critical in the viral replication and cap methylations. In addition, the N7 methylation efficiency was found to correlate with the viral replication ability. Thus, SIN analogs with modifications that interact with the hydrophobic pocket are potential specific inhibitors of flavivirus MTase.

    • Organizational Affiliation: 

    Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 5
A, B
321West Nile virusMutation(s): 0 
Gene Names: Non-structural protein 5
UniProt
Find proteins for Q9Q6P4 (West Nile virus (strain NY-99))
Explore Q9Q6P4 
Go to UniProtKB:  Q9Q6P4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Q6P4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.363α = 112.01
b = 65.74β = 102.65
c = 77.119γ = 90.19
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description