4FVU

Structural basis for the dsRNA specificity of the Lassa virus NP exonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for the dsRNA Specificity of the Lassa Virus NP Exonuclease.

Hastie, K.M.King, L.B.Zandonatti, M.A.Saphire, E.O.

(2012) Plos One 7: e44211-e44211

  • DOI: 10.1371/journal.pone.0044211

  • PubMed Abstract: 
  • Lassa virus causes hemorrhagic fever characterized by immunosuppression. The nucleoprotein of Lassa virus, termed NP, binds the viral genome. It also has an additional enzymatic activity as an exonuclease that specifically digests double-stranded RNA ...

    Lassa virus causes hemorrhagic fever characterized by immunosuppression. The nucleoprotein of Lassa virus, termed NP, binds the viral genome. It also has an additional enzymatic activity as an exonuclease that specifically digests double-stranded RNA (dsRNA). dsRNA is a strong signal to the innate immune system of viral infection. Digestion of dsRNA by the NP exonuclease activity appears to cause suppression of innate immune signaling in the infected cell. Although the fold of the NP enzyme is conserved and the active site completely conserved with other exonucleases in its DEDDh family, NP is atypical among exonucleases in its preference for dsRNA and its strict specificity for one substrate. Here, we present the crystal structure of Lassa virus NP in complex with dsRNA. We find that unlike the exonuclease in Klenow fragment, the double-stranded nucleic acid in complex with Lassa NP remains base-paired instead of splitting, and that binding of the paired complementary strand is achieved by "relocation" of a basic loop motif from its typical exonuclease position. Further, we find that just one single glycine that contacts the substrate strand and one single tyrosine that stacks with a base of the complementary, non-substrate strand are responsible for the unique substrate specificity. This work thus provides templates for development of antiviral drugs that would be specific for viral, rather than host exonucleases of similar fold and active site, and illustrates how a very few amino acid changes confer alternate specificity and biological phenotype to an enzyme.


    Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoprotein
A
243Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)Mutation(s): 1 
Gene Names: N
EC: 3.1.13.-
Find proteins for P13699 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Go to UniProtKB:  P13699
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*AP*GP*GP*GP*AP*G)-3')B8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*UP*CP*CP*CP*UP*CP*C)-3')C8synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 44.772α = 90.00
b = 84.311β = 90.00
c = 79.809γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-3000data reduction
PHENIXmodel building
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Structure summary
  • Version 1.2: 2018-03-14
    Type: Database references
  • Version 1.3: 2018-06-20
    Type: Data collection