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Molecular basis for specific viral RNA recognition and 2’-O ribose methylation by the dengue virus NS5 protein.

Lim, Siew Pheng, Soh, Sherryl, Shi, Pei-Yong, Zhao, Yongqian, Chung, Ka Yan, Swaminathan , Kunchithapadam , Vasudevan , Subhash G , Lescar, Julien and Luo, Dahai (2015) Molecular basis for specific viral RNA recognition and 2’-O ribose methylation by the dengue virus NS5 protein. Proceedings of the National Academy of Sciences.


Dengue virus (DENV) causes several hundred million human infections and more
than 20,000 deaths annually. Neither an efficacious vaccine conferring immunity against all
four circulating serotypes nor specific drugs are currently available to treat this emerging
global disease. Capping of the DENV RNA genome is an essential structural modification
that protects the RNA from degradation by 5’ exo-ribonucleases, ensures efficient expression
of viral proteins and allows escape from the host innate immune response. The large
flavivirus NS5 protein (105 kDa) has RNA methyl-transferase activities at its N terminal
region, which is responsible for capping the virus RNA genome. The methyl transfer
reactions are thought to occur sequentially using the strictly conserved flavivirus 5’ RNA
sequence as substrate (GpppAG-RNA), leading to the formation of the 5’ RNA cap: G0pppAGRNA
→m7G0pppAG-RNA (named “cap-0”) →m7G0pppAm2’-OG-RNA (named “cap-1”). To
elucidate how viral RNA is specifically recognized and methylated, we determined the
crystal structure of a ternary complex between the full-length NS5 protein from dengue virus,
an octameric cap-0 viral RNA substrate bearing the authentic DENV genomic sequence (5’-
m7G0pppA1G2U3U4G5U6U7-3’) and S-adenosyl-L-homocysteine (SAH), the by-product of the
methylation reaction. The structure provides for the first time a molecular basis for specific
adenosine 2’-O methylation, rationalizes mutagenesis studies targeting the K61-D146-K180-
E216 enzymatic tetrad as well as residues lining the RNA binding groove and offers novel
mechanistic and evolutionary insights into cap-1 formation by NS5, which underlies innate
immunity evasion by flaviviruses.

Item Type: Article
Date Deposited: 16 Jan 2016 00:45
Last Modified: 16 Jan 2016 00:45


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