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PDBsum entry 8ohm
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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 RNA helicase from genotype 1b hepatitis c virus. A feasible mechanism of unwinding duplex RNA.
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Authors
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H.S.Cho,
N.C.Ha,
L.W.Kang,
K.M.Chung,
S.H.Back,
S.K.Jang,
B.H.Oh.
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Ref.
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J Biol Chem, 1998,
273,
15045-15052.
[DOI no: ]
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PubMed id
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Abstract
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Crystal structure of RNA helicase domain from genotype 1b hepatitis C virus has
been determined at 2.3 A resolution by the multiple isomorphous replacement
method. The structure consists of three domains that form a Y-shaped molecule.
One is a NTPase domain containing two highly conserved NTP binding motifs.
Another is an RNA binding domain containing a conserved RNA binding motif. The
third is a helical domain that contains no beta-strand. The RNA binding domain
of the molecule is distinctively separated from the other two domains forming an
interdomain cleft into which single stranded RNA can be modeled. A channel is
found between a pair of symmetry-related molecules which exhibit the most
extensive crystal packing interactions. A stretch of single stranded RNA can be
modeled with electrostatic complementarity into the interdomain cleft and
continuously through the channel. These observations suggest that some form of
this dimer is likely to be the functional form that unwinds double stranded RNA
processively by passing one strand of RNA through the channel and passing the
other strand outside of the dimer. A "descending molecular see-saw"
model is proposed that is consistent with directionality of unwinding and other
physicochemical properties of RNA helicases.
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Figure 3.
Fig. 3. Interaction of the D^290ECH and the T322AT
sequence of HCV RNA helicase. Note Asp290, Glu291, and His293
that form a part of the active site cavity are on a loop
structure and point in the same direction. The backbones of the
DECH motif and TAT sequence are in cyan and magenta,
respectively, and the side chains are in green. The white dotted
line indicates the hydrogen bond between His293 and Thr322.
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Figure 7.
Fig. 7. A side view of "descending molecular see-saw"
model for the translocation of HCV RNA helicase along ssRNA. The
dimer (left) translocates along the ssRNA (right) by a rotation
of about 60° (with respect to the axis of the RNA double
helix) along an axis passing the front part of RNA binding
motif. The right figure represents a translocation of the dimer
by a half-turn of RNA with respect to the location of the dimer
on ssRNA in the left figure. For clear presentation of the
translational motion, the two figures are shown with
orientations different by 180° with respect to each step.
Figs. 1, 3, and 5 were produced using the program MOLSCRIPT,
Fig. 2 using the program O, Fig. 4 using the program GRASP, and
Figs. 6 and 7 using the program QUANTA.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1998,
273,
15045-15052)
copyright 1998.
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