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Figure 5.
Fig. 5. Comparison of the β7-β8 hairpin conformations. (a)
A stereo view of superpositioned C^α traces of the
pyrrolysyladenylate-bound (black), the pyrrolysine/AMPPNP-bound
(green), AMPPNP-bound (yellow), and apo forms (red). The
locations of the C^α atoms for residues 377–387 are numbered,
with the same coloring as in each trace. (b and c) Stereo views
of the superposition of the pyrrolysyladenylate-bound (gray),
pyrrolysine/AMPPNP-bound (green), AMPPNP-bound (yellow), and apo
forms (vermilion). Val377, Gly378, and Asp379 (b), and Tyr384,
Gly385, Asp386, and Thr387 (c) are represented by ball-and-stick
models. d and e, A stereo view of the 2F[o] – F[c] electron
density map (contoured at 1.1 σ) around the β7-β8 regions.
(d) The AMPPNP-bound form. Direct hydrogen-bonding interactions
of Val402 with Asp386, and of Asp379 with Arg356, and the
water-mediated hydrogen-bonding interaction of Asp379 with
Thr387 are shown by pink, green, and orange dotted lines,
respectively. (e) The AMPPNP/pyrrolysine-bound form. Direct
hydrogen-bonding interactions of Val402 with Asp386, and of
Asp379 with Thr387 are shown by pink and orange dotted lines,
respectively. Gly385, Asp386, and Thr387 in each PylRS(c270)
form adopt the β8-open conformation, as shown in sky blue
circles. On the other hand, Gly378 and Asp379 adopt the β7-open
conformation in the AMPPNP-bound form and the β7-closed
conformation in the pyrrolysine/AMPPNP-bound form, as shown in
purple circles, respectively.
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