2WHX

A second conformation of the NS3 protease-helicase from dengue virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Flexibility between the Protease and Helicase Domains of the Dengue Virus Ns3 Protein Conferred by the Linker Region and its Functional Implications.

Luo, D.Wei, N.Doan, D.N.Paradkar, P.N.Chong, Y.Davidson, A.D.Kotaka, M.Lescar, J.Vasudevan, S.G.

(2010) J.Biol.Chem. 285: 18817

  • DOI: 10.1074/jbc.M109.090936
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The dengue virus (DENV) NS3 protein is essential for viral polyprotein processing and RNA replication. It contains an N-terminal serine protease region (residues 1-168) joined to an RNA helicase (residues 180-618) by an 11-amino acid linker (169-179) ...

    The dengue virus (DENV) NS3 protein is essential for viral polyprotein processing and RNA replication. It contains an N-terminal serine protease region (residues 1-168) joined to an RNA helicase (residues 180-618) by an 11-amino acid linker (169-179). The structure at 3.15 A of the soluble NS3 protein from DENV4 covalently attached to 18 residues of the NS2B cofactor region (NS2B(18)NS3) revealed an elongated molecule with the protease domain abutting subdomains I and II of the helicase (Luo, D., Xu, T., Hunke, C., GrĂ¼ber, G., Vasudevan, S. G., and Lescar, J. (2008) J. Virol. 82, 173-183). Unexpectedly, using similar crystal growth conditions, we observed an alternative conformation where the protease domain has rotated by approximately 161 degrees with respect to the helicase domain. We report this new crystal structure bound to ADP-Mn(2+) refined to a resolution of 2.2 A. The biological significance for interdomain flexibility conferred by the linker region was probed by either inserting a Gly residue between Glu(173) and Pro(174) or replacing Pro(174) with a Gly residue. Both mutations resulted in significantly lower ATPase and helicase activities. We next increased flexibility in the linker by introducing a Pro(176) to Gly mutation in a DENV2 replicon system. A 70% reduction in luciferase reporter signal and a similar reduction in the level of viral RNA synthesis were observed. Our results indicate that the linker region has evolved to an optimum length to confer flexibility to the NS3 protein that is required both for polyprotein processing and RNA replication.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PROTEASE/NTPASE/HELICASE NS3
A
618Dengue virus type 4 (strain Thailand/0348/1991)Mutation(s): 0 
Find proteins for Q2YHF0 (Dengue virus type 4 (strain Thailand/0348/1991))
Go to UniProtKB:  Q2YHF0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SERINE PROTEASE SUBUNIT NS2B
C
14Dengue virus type 4 (strain Thailand/0348/1991)Mutation(s): 0 
Find proteins for Q2YHF0 (Dengue virus type 4 (strain Thailand/0348/1991))
Go to UniProtKB:  Q2YHF0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.420α = 90.00
b = 87.720β = 92.90
c = 75.779γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-07 
  • Released Date: 2010-04-07 
  • Deposition Author(s): Luo, D., Lescar, J.

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance