|
Figure 2.
Figure 2. Homology Modeling of DNA from the T7 DNAP Ternary
Complex onto the Molecular Surface of Dbh(A) Superposition of
the palm domains of Dbh (colored as in Figure 1A) and T7 DNAP
(colored in dark gray). The T7 DNAP catalytic aspartates (D475
and D654) and the residues that function as the steric gate
(E480) and bind the 3′ terminal phosphorous of the primer
strand (H704) are shown in stick representation, as are the
corresponding residues from Dbh (D7, D105, F12, and K153). The
Mg^2+ ions from the T7 DNAP ternary complex are shown as yellow
spheres. Cα atoms used in the superposition were 1–21,
77–95, 97–112, 118–137, and 138–153 from Dbh and
469–487, 614–632, 646–661, 662–681, and 689–704 from
T7 DNAP ternary complex (Protein Data Bank code 1T7P;
Doublié et al., 1998). Only the structurally aligned core
of the palm domains is shown.(B) View looking down onto the Dbh
active site. Primer and template DNA (light and dark gray,
respectively), incoming nucleotide, and magnesium ions (yellow
spheres) from the T7DNAP ternary complex structure
(Doublié et al., 1998) were modeled onto the molecular
surface of Dbh. Substrate molecules from the T7 DNAP ternary
complex structure were positioned onto the Dbh surface based on
the superposition of the palm domains shown in (A). The flexible
loop and N-terminal His[6]-tag are not shown in surface
representation and are, instead, shown with transparent and gray
lines, respectively. The molecular surface of Dbh was calculated
using a 1.4 Å radius probe in SPOCK (Christopher, 1998)
and is colored according to conserved motifs I-V as in Figure
1A.(C) Closer view of the active site with surface colored
according to electrostatic potential, with positively charged
areas in blue and negatively charged areas in red. The thumb
domain has been omitted for clarity, and the molecule has been
rotated slightly to show the surface of the nascent base pair
binding pocket more clearly. Surface areas contributed by some
of the residues discussed in the text are labeled
|
