4ye2 | pdb_00004ye2
The 1.35 structure of a viral RNase L antagonist reveals basis for the 2'-5'-oligoadenylate binding and enzyme activity.
Structural highlights
FunctionB3F2X4_ROTRH Counteracts the host innate immune response thanks to its phosphodiesterase that degrades the 5'-triphosphorylated, 2'-5' linked adenylate oligomers produced by the host cell IFN-inducible 2',5'-oligoadenylate synthetase (OAS). The host RNaseL is therefore not activated.[HAMAP-Rule:MF_04128] Multifunctional enzyme involved in mRNA capping. Catalyzes the formation of the 5' cap structure on the viral plus-strand transcripts. Specifically binds to GTP and displays guanylyltransferase and methyltransferase activities. Has affinity for ssRNA but not for dsRNA. Capping activity is non-specific and caps RNAs that initiate with either a G or an A residue. Together with VP1 polymerase, forms a VP1-VP3 complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are capped by VP3 and extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. DLPs probably have an RNA triphosphatase activity as well, whereas open cores do not.[HAMAP-Rule:MF_04128] Publication Abstract from PubMedSynthesis of 2' -5' -oligoadenylates (2-5A) by oligoadenylate synthetase (OAS) is an important innate cellular response that limits viral replication by activating the latent cellular ribonuclease, RNase L, to degrade single-stranded RNA. Some rotaviruses and coronaviruses antagonize the OAS/RNase L pathway through the activity of an encoded 2H phosphoesterase domain that cleaves 2-5A. These viral 2H phosphoesterases are phylogenetically related to the cellular A-kinase anchoring protein 7 (AKAP7) and share a core structure and an active site that contains two well-defined HPhi(S/T)Phi motifs, but their mechanism of substrate binding is unknown. Here we report the structures of a viral 2H phosphoesterase, the C-terminal domain (CTD) of the group A rotavirus VP3 protein, both alone and in complex with 2-5A. The domain forms a compact fold, with a concave beta-sheet that contains the catalytic cleft, but it lacks two alpha-helical regions and two beta-strands observed in AKAP7 and other 2H phosphoesterases. The co-crystal structure shows significant conformational changes in the "R-loop" upon ligand binding. Bioinformatics and biochemical analyses reveal that conserved residues and residues required for catalytic activity and substrate binding comprise the catalytic motifs and a region on one side of the binding cleft. We demonstrate that the VP3 CTD of group B rotavirus, but not that of group G, cleaves 2-5A. These findings suggest that the VP3 CTD is a streamlined version of a 2H phosphoesterase with a ligand-binding mechanism that is shared among 2H phosphodiesterases that cleave 2-5A. IMPORTANCE: The C-terminal domain (CTD) of rotavirus VP3 is a 2H phosphoesterase that cleaves 2' -5' -oligoadenylates (2-5A), potent activators of an important innate cellular antiviral pathway. 2H phosphoesterase superfamily proteins contain two conserved catalytic motifs and a proposed core structure. Here, we present structures of a viral 2H phosphoesterase, the rotavirus VP3 CTD, alone and in complex with its substrate, 2-5A. The domain lacks two alpha-helical regions and beta-strands present in other 2H phosphoesterases. A loop of the protein undergoes significant structural changes upon substrate binding. Together with our bioinformatics and biochemical findings, the crystal structures suggest that the RVA VP3 CTD domain is a streamlined version of a cellular enzyme that shares a ligand-binding mechanism with other 2H phosphodiesterases that cleave 2-5A, but differs from those of 2H phosphodiesterases that cleave other substrates. These findings may aid in the future design of antivirals targeting viral phosphodiesterases with cleavage specificity for 2-5A. Structural basis for 2' -5' -oligoadenylate binding and enzyme activity of a viral RNase L antagonist.,Ogden KM, Hu L, Jha BK, Sankaran B, Weiss SR, Silverman RH, Patton JT, Prasad BV J Virol. 2015 Apr 15. pii: JVI.00701-15. PMID:25878106[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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