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Figure 1.
Fig. 1. Monomer structure. (A) The MjDEAD monomer showing
the amino- and carboxyl-terminal domains (labeled N and C in
subsequent figures). The linker between the domains can be seen
in the middle of the figure. The orientation of the dimer in
this view (in this and subsequent figures) is depicted in an
Inset, with the equivalent domains colored blue, as in the main
figure. Fig. 1A, as well as Fig. 1C, Fig. 2 A and B, and Fig. 3
A and C were made with MOLSCRIPT (41) and RASTER 3D (42). (B)
The topological organization of the MjDEAD monomer, illustrating
the similarities of the two domains. The "RecA-like core"
stretches from  -strands 1
and 2 and 4-7 as numbered for the amino-terminal domain and
their connecting  -helices.
Sequence numbers at the edges of secondary structure elements
are indicated, as are those loop regions observed to bind the
nucleic acid backbone in some or all of known helicase complexes
with nucleic acid. The region of polypeptide equivalent to the
GG motif (motif 1B) also contacts nucleic acid in the HCV NS3
helicase. -Helix F
and -strand no.
7 (that pack against their symmetry-related counterparts to form
a dimer) are indicated. (C) Difference in the amino- and
carboxyl-terminal domain orientation relative to other proteins.
Superposition of only the amino-terminal domain with that of
other proteins reveals a structure "opened up" relative to the
others (blue domains). Independent superposition of the
carboxyl-terminal domain on a "closed" structure (in this case
the PcrA DNA and AMPPNP structure) leads to a closing of the
MjDEAD structure to a conformation more like that observed for
other helicases (blue amino-terminal domain and gold
carboxyl-terminal domain). Single-stranded (ss)DNA binds at the
top of the two domains in other helicases in this orientation.
We assume that this closed structure for MjDEAD will likewise
resemble the structure of the DNA/ATP bound form of this enzyme.
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