Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 117; no. 9; pp. 4931 - 4941
• Main Authors: Abdella, Ryan, Aggarwal, Megha, Okura, Takashi, Lamb, Robert A., He, Yuan
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 03.03.2020
• Subjects: Animal diseases; Animal health; Antiviral agents; BASIC BIOLOGICAL SCIENCES; Biological Sciences; Catalytic Domain; Cryo-EM; Cryoelectron Microscopy; Crystallography; Crystallography, X-Ray; DNA-directed RNA polymerase; Domains; Enzymatic activity; Genome, Viral; Genomes; Methyltransferase; Methyltransferases - chemistry; Methyltransferases - genetics; Methyltransferases - metabolism; Models, Molecular; Nucleoproteins - chemistry; Nucleotides; Oligomerization; Parainfluenza; Parainfluenza Virus 5 - chemistry; Paramyxovirinae - enzymology; Paramyxovirinae - genetics; paramyxovirus; Phosphoproteins - chemistry; polymerase; Protein Binding; Protein Conformation; Protein Domains; Protein structure; replication; RNA polymerase; RNA viruses; RNA-directed RNA polymerase; Transcription; Viral Proteins - chemistry; Viral Proteins - metabolism; Viruses; X-ray crystallography; replication; transcription; Cryo-EM; polymerase; paramyxovirus
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1919837117

Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ∼250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L–P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. POD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5′ end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.