4R8R

Dengue virus serotype 3 methyltransferase without a bound S-adenosyl methionine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine

Noble, C.G., Li, S.H., Dong, H., Chew, S.H., Shi, P.Y.

(2014) Antiviral Res 111C: 78-81

  • DOI: 10.1016/j.antiviral.2014.09.003
  • Primary Citation of Related Structures:  
    4R8R, 4R8S

  • PubMed Abstract: 

    • Flavivirus methyltransferase is a genetically-validated antiviral target. Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. This raises a possibility that SAM is an integral structural component required for the folding of dengue virus (DENV) methyltransferase ...

    Flavivirus methyltransferase is a genetically-validated antiviral target. Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. This raises a possibility that SAM is an integral structural component required for the folding of dengue virus (DENV) methyltransferase. Here we exclude this possibility by solving the crystal structure of DENV methyltransferase without SAM. The SAM ligand was removed from the enzyme through a urea-mediated denaturation-and-renaturation protocol. The crystal structure of the SAM-depleted enzyme exhibits a vacant SAM-binding pocket, with a conformation identical to that of the SAM-enzyme co-crystal structure. Functionally, equivalent enzymatic activities (N-7 methylation, 2'-O methylation, and GMP-enzyme complex formation) were detected for the SAM-depleted and SAM-containing recombinant proteins. These results clearly indicate that the SAM molecule is not an essential component for the correct folding of DENV methyltransferase. Furthermore, the results imply a potential antiviral approach to search for inhibitors that can bind to the SAM-binding pocket and compete against SAM binding. To demonstrate this potential, we have soaked crystals of DENV methyltransferase without a bound SAM with the natural product Sinefungin and show that preformed crystals are capable of binding ligands in this pocket.

    Organizational Affiliation: 

    Novartis Institute for Tropical Diseases, 10 Biopolis Road, 05-01 Chromos, Singapore 138670, Singapore. Electronic address: pei_yong.shi@novartis.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nonstructural protein NS5A, B267Dengue virus 3Mutation(s): 0 
EC: 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for C1KBQ3 (Dengue virus 3)
Explore C1KBQ3 
Go to UniProtKB:  C1KBQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1KBQ3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.082α = 90
b = 61.092β = 90
c = 182.35γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-09-02 
  • Released Date: 2014-10-15 
    • Deposition Author(s): Noble, C.G.

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release