Crystal structure of the refolded DENV3 methyltransferase

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

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This is version 1.2 of the entry. See complete history


Refolding of a fully functional flavivirus methyltransferase revealed that S-adenosyl methionine but not S-adenosyl homocysteine is copurified with flavivirus methyltransferase.

Brecher, M.B.Li, Z.Zhang, J.Chen, H.Lin, Q.Liu, B.Li, H.

(2015) Protein Sci 24: 117-128

  • DOI: https://doi.org/10.1002/pro.2594
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Methylation of flavivirus RNA is vital for its stability and translation in the infected host cell. This methylation is mediated by the flavivirus methyltransferase (MTase), which methylates the N7 and 2'-O positions of the viral RNA cap by using S-adenosyl-l-methionine (SAM) as a methyl donor. In this report, we demonstrate that SAM, in contrast to the reaction by-product S-adenosyl-l-homocysteine, which was assumed previously, is copurified with the Dengue (DNV) and West Nile virus MTases produced in Escherichia coli (E. coli). This endogenous SAM can be removed by denaturation and refolding of the MTase protein. The refolded MTase of DNV serotype 3 (DNV3) displays methylation activity comparable to native enzyme, and its crystal structure at 2.1 Å is almost identical to that of native MTase. We characterized the binding of Sinefungin (SIN), a previously described SAM-analog inhibitor of MTase function, to the native and refolded DNV3 MTase by isothermal titration calorimetry, and found that SIN binds to refolded MTase with more than 16 times the affinity of SIN binding to the MTase purified natively. Moreover, we show that SAM is also copurified with other flavivirus MTases, indicating that purification by refolding may be a generally applicable tool for studying flavivirus MTase inhibition.

  • Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Albany, New York, 12208.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nonstructural protein NS5
A, B
267dengue virus type 3Mutation(s): 0 
Gene Names: NS5
Find proteins for C1KBQ3 (dengue virus type 3)
Explore C1KBQ3 
Go to UniProtKB:  C1KBQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1KBQ3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.688α = 79.11
b = 48.386β = 78.75
c = 68.073γ = 69.71
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description