Figure 3.
Fig. 3. A two-metal mechanism for group I intron splicing. (A)
F[O]-F[C] omit map (active-site metals were not included in the
model) used to assign M[1] and M[2] positions, superimposed on
the refined structure. The native density (5 ) for each metal
is depicted in blue. The other residues are as labeled. In (A),
(B), and (D), the scissile bond, nucleophile, and leaving group
are shown in yellow. (B) Active-site coordination to M[1] and
M[2]. In this and (D), the active-site Mg2+ ions are shown as
large orange spheres, the predicted inner and outer sphere
ligands are shown as small orange spheres, and the
metal-to-metal distance is labeled. Orange lines indicate inner
sphere coordinations. Labels for the individual nucleotides are
as in Fig. 2A. All the coordinations depicted in Fig. 1B are
satisfied in this structure. (C) Model of the group I intron
transition state stabilized by a two-metal mechanism. (D)
Two-metal active-site coordination within the T7 DNA polymerase
(1). The incoming deoxy-nucleotide triphosphate (dNTP), the
primer oligonucleotide, and active-site aspartates are labeled.
The nucleophile was not present in the crystal structure but is
modeled here for comparison.
The above figure is reprinted
by permission from the AAAs:
Science
(2005,
309,
1587-1590)
copyright 2005.
) for each metal
is depicted in blue. The other residues are as labeled. In (A),
(B), and (D), the scissile bond, nucleophile, and leaving group
are shown in yellow. (B) Active-site coordination to M[1] and
M[2]. In this and (D), the active-site Mg2+ ions are shown as
large orange spheres, the predicted inner and outer sphere
ligands are shown as small orange spheres, and the
metal-to-metal distance is labeled. Orange lines indicate inner
sphere coordinations. Labels for the individual nucleotides are
as in Fig. 2A. All the coordinations depicted in Fig. 1B are
satisfied in this structure. (C) Model of the group I intron
transition state stabilized by a two-metal mechanism. (D)
Two-metal active-site coordination within the T7 DNA polymerase
(1). The incoming deoxy-nucleotide triphosphate (dNTP), the
primer oligonucleotide, and active-site aspartates are labeled.
The nucleophile was not present in the crystal structure but is
modeled here for comparison.