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PDBsum entry 4v0r
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References listed in PDB file
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Key reference
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Title
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A crystal structure of the dengue virus ns5 protein reveals a novel inter-Domain interface essential for protein flexibility and virus replication.
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Authors
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Y.Zhao,
T.S.Soh,
J.Zheng,
K.W.Chan,
W.W.Phoo,
C.C.Lee,
M.Y.Tay,
K.Swaminathan,
T.C.Cornvik,
S.P.Lim,
P.Y.Shi,
J.Lescar,
S.G.Vasudevan,
D.Luo.
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Ref.
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Plos Pathog, 2015,
11,
e1004682.
[DOI no: ]
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PubMed id
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Abstract
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Flavivirus RNA replication occurs within a replication complex (RC) that
assembles on ER membranes and comprises both non-structural (NS) viral proteins
and host cofactors. As the largest protein component within the flavivirus RC,
NS5 plays key enzymatic roles through its N-terminal methyltransferase (MTase)
and C-terminal RNA-dependent-RNA polymerase (RdRp) domains, and constitutes a
major target for antivirals. We determined a crystal structure of the
full-length NS5 protein from Dengue virus serotype 3 (DENV3) at a resolution of
2.3 Å in the presence of bound SAH and GTP. Although the overall molecular
shape of NS5 from DENV3 resembles that of NS5 from Japanese Encephalitis Virus
(JEV), the relative orientation between the MTase and RdRp domains differs
between the two structures, providing direct evidence for the existence of a set
of discrete stable molecular conformations that may be required for its
function. While the inter-domain region is mostly disordered in NS5 from JEV,
the NS5 structure from DENV3 reveals a well-ordered linker region comprising a
short 310 helix that may act as a swivel. Solution Hydrogen/Deuterium Exchange
Mass Spectrometry (HDX-MS) analysis reveals an increased mobility of the thumb
subdomain of RdRp in the context of the full length NS5 protein which correlates
well with the analysis of the crystallographic temperature factors.
Site-directed mutagenesis targeting the mostly polar interface between the MTase
and RdRp domains identified several evolutionarily conserved residues that are
important for viral replication, suggesting that inter-domain cross-talk in NS5
regulates virus replication. Collectively, a picture for the molecular origin of
NS5 flexibility is emerging with profound implications for flavivirus
replication and for the development of therapeutics targeting NS5.
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