Figure 2.
Figure 2 Structural comparison of Dpo4 and T7 DNA polymerase.
(A) The replicating base pairs in three Dpo4 structures (T/dGTP,
T/dATP and Ab-2A) are shown as ball-and-stick models. The two
metal ions (A and B) are shown as green spheres. The A-metal ion
position differs in each structure. The conformation of the
triphosphate is denoted as 'chair-like' and 'goat tail-like'.
(B) Superposition of T/dATP, T/dGTP and Ab-2A structures. The C
traces,
DNA and nucleotide substrate are shown in stick models. A
zoom-in stereo view of the finger domain with the replicating
base pair and metal ions (outlined in gray) is shown on the
right. The colors representing each structure are indicated. (C)
Superposition of the metal ion coordination in Dpo4 (Ab-2A,
yellow and brown colors) and T7 DNA polymerase (PDB: 1T7P, blue
and green colors) in a stereo view. The oxygen atoms of the
three conserved carboxylates and those involved in metal ion
coordination are highlighted in red. The metal ion coordination
is schematically drawn on the right. Red indicates ligands
conserved in both polymerases, light green in Dpo4 only and blue
in T7 only. The hypothesized 3'-OH of the primer strand is shown
in gray.
The above figure is reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2005,
24,
2957-2967)
copyright 2005.
traces,
DNA and nucleotide substrate are shown in stick models. A
zoom-in stereo view of the finger domain with the replicating
base pair and metal ions (outlined in gray) is shown on the
right. The colors representing each structure are indicated. (C)
Superposition of the metal ion coordination in Dpo4 (Ab-2A,
yellow and brown colors) and T7 DNA polymerase (PDB: 1T7P, blue
and green colors) in a stereo view. The oxygen atoms of the
three conserved carboxylates and those involved in metal ion
coordination are highlighted in red. The metal ion coordination
is schematically drawn on the right. Red indicates ligands
conserved in both polymerases, light green in Dpo4 only and blue
in T7 only. The hypothesized 3'-OH of the primer strand is shown
in gray.