|
Figure 3.
Figure 3. Orientation of the C-Terminal Domains of Dbh and
Dpo4 and Their Interactions with DNA
(A) Comparison of the
structures of apo-Dbh (left; PDB code 1K1Q, chain A [Silvian et
al., 2001]), Dbh ternary complex (middle), and Dpo4 ternary
complex (right; Ab-2A, PDB code 1S0O, chain B [Ling et al.,
2004]). Arrows indicate direction and magnitude of movement
needed to move the C-terminal domain of one structure to the
orientation found in the Dbh ternary complex structure. Rotation
axes are shown as black lines. Structures were aligned based on
the polymerase domains; Dbh (apo) and Dbh (ternary), rmsd 1.2
Å, 232 Cα atoms; Dbh(ternary) and Dpo4 (Ab-2A ternary),
rmsd 1.7 Å, 240 Cα atoms.
(B) Residues of the
C-terminal domain of Dbh that contact the DNA. Atoms in the
C-terminal domain of Dbh that are located within 3.8 Å of
the DNA are highlighted in white.
(C) Comparison of DNA
binding by the C-terminal domains in the ternary complexes of
the Dbh (top) and Dpo4 Ab-2a (bottom). The bulged base in Dbh
(C-3) and the bulged ribose in Dpo4 (Ab-2A) are highlighted in
red. The structures are oriented identically, by superimposition
of the polymerase domains as in (A), and are viewed from the
same direction. For clarity, only the DNA and C-terminal domains
are shown. Structures are colored as in Figure 1.
|
