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PDBsum entry 2hcs
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the RNA polymerase domain of the west nile virus non-Structural protein 5.
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Authors
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H.Malet,
M.P.Egloff,
B.Selisko,
R.E.Butcher,
P.J.Wright,
M.Roberts,
A.Gruez,
G.Sulzenbacher,
C.Vonrhein,
G.Bricogne,
J.M.Mackenzie,
A.A.Khromykh,
A.D.Davidson,
B.Canard.
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Ref.
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J Biol Chem, 2007,
282,
10678-10689.
[DOI no: ]
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PubMed id
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Abstract
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Viruses of the family Flaviviridae are important human and animal pathogens.
Among them, the Flaviviruses dengue (DENV) and West Nile (WNV) cause regular
outbreaks with fatal outcomes. The RNA-dependent RNA polymerase (RdRp) activity
of the non-structural protein 5 (NS5) is a key activity for viral RNA
replication. In this study, crystal structures of enzymatically active and
inactive WNV RdRp domains were determined at 3.0- and 2.35-A resolution,
respectively. The determined structures were shown to be mostly similar to the
RdRps of the Flaviviridae members hepatitis C and bovine viral diarrhea virus,
although with unique elements characteristic for the WNV RdRp. Using a reverse
genetic system, residues involved in putative interactions between the RNA-cap
methyltransferase (MTase) and the RdRp domain of Flavivirus NS5 were identified.
This allowed us to propose a model for the structure of the full-length WNV NS5
by in silico docking of the WNV MTase domain (modeled from our previously
determined structure of the DENV MTase domain) onto the RdRp domain. The
Flavivirus RdRp domain structure determined here should facilitate both the
design of anti-Flavivirus drugs and structure-function studies of the Flavivirus
replication complex in which the multifunctional NS5 protein plays a central
role.
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Figure 1.
FIGURE 1. Crystal structure of WNV POL1 and comparison with
HCV RdRp. A, stereo view of a ribbon representation of WNV POL1
in its front orientation. The palm, thumb, and fingers domains
and the priming loop are colored in green, red, dark blue, and
purple, respectively.  -Helices and  -sheets
are indicated. Insertions in WNV POL1 compared with HCV RdRp are
displayed in yellow, and major structural differences are shown
in orange. These and other figures were prepared with PyMOL. B,
ribbon representation of HCV RdRp in its front orientation (50)
(PDB code 1NB6). The color code is the same as in A. Insertions
in HCV RdRp compared with WNV are colored in yellow.
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Figure 3.
FIGURE 3. Divalent ion binding site in WNV POL. Stereo view
of the calcium/magnesium ion non-catalytic binding site. The
POL2 model is represented in green sticks and the corresponding
electronic density in blue. The Ca^2+ ion is shown as a green
sphere. The figure is centered on the aspartic acids of motifs A
and C colored in yellow. Coordination with Asp^536 (motif A) and
Asp^669 (motif C) are indicated by black dotted lines.
Corresponding aspartic acids of motifs A and C in Phi6 (Asp^324,
Asp^453, and Asp^454) (PDB code 1HI0) are represented in magenta
sticks. The position of the two ions in the catalytic position,
inferred from the Phi6 RdRp structure, is indicated in purple.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
10678-10689)
copyright 2007.
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