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

• Published in: PloS one Vol. 7; no. 8; p. e44211
• Main Authors: Hastie, Kathryn M, King, Liam B, Zandonatti, Michelle A, Saphire, Erica Ollmann
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28.08.2012; Public Library of Science (PLoS)
• Subjects: Acids; Amino acid sequence; Antiviral agents; Binding sites; Biochemistry; Biology; Causes of; Crystal structure; Deoxyribonucleic acid; DNA; Double-stranded RNA; Drug development; Drugs; E coli; Enzymatic activity; Escherichia coli; Exonuclease; Exonucleases; Fever; Genetic aspects; Genomes; Glycine; Health aspects; Hemorrhage; Hemorrhagic fever; Hydrogen; Immune system; Immunology; Immunosuppression; Immunosuppressive agents; Infections; Innate immunity; Kinases; Lassa fever; Lassa Fever - genetics; Lassa Fever - metabolism; Lassa virus - genetics; Lassa virus - metabolism; Nucleoproteins - genetics; Nucleoproteins - metabolism; Phenotypes; Physiological aspects; Protection and preservation; Protein Conformation; Proteins; Relocation; Ribonucleic acid; RNA; RNA, Double-Stranded - genetics; RNA, Double-Stranded - metabolism; RNA, Viral - genetics; RNA, Viral - metabolism; Science; Signaling; Splitting; Substrate specificity; Substrates; Tyrosine; Viral infections; Viral proteins; Viruses; United States; La Jolla California; United States > US; California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0044211

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.