Hox protein: Difference between revisions
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This observation can be explained based on a second crystal structure of an Scr-Exd-DNA ternary complex where the Hox-Exd hetrodimer is bound to a Hox consensus site, which is not specific to Scr. In this structure it is apparent that only <scene name='Sandbox_Reserved_169/Con/2'>Arg5 binds the minor groove</scene> and the remainder of the N-terminal linker is disordered (Figure 5).<br/> | This observation can be explained based on a second crystal structure of an Scr-Exd-DNA ternary complex where the Hox-Exd hetrodimer is bound to a Hox consensus site, which is not specific to Scr. In this structure it is apparent that only <scene name='Sandbox_Reserved_169/Con/2'>Arg5 binds the minor groove</scene> and the remainder of the N-terminal linker is disordered (Figure 5).<br/> | ||
[[Image:Cell2007-Fig4.jpg |thumb|left| | [[Image:Cell2007-Fig4.jpg |thumb|left|300px|Figure 6: Comparison of DNA shape of Scr specific in vivo site (left panel) vs. Hox consensus site (right panel). Elsevier/Cell Press has provided permission for usage of this figure<ref name="joshi"/>.]] | ||
Based on the comparison of the two crystal structures of a Scr-Exd-DNA ternary complexes (Figure 6), it was found that three N-terminal residues contact the minor groove of the Scr specific site ''fkh250'' (A) compared to only Arg5 binding the Hox consensus site ''fkh250con'' (B). In their protein-bound states, the shapes of both sites are distinct (dark gray, concave; green, convex surfaces). The distinct shapes of the two DNA binding sites, shown as minor groove width in the crystal structures of the complexes (blue plots), are already present when the protein is not bound to the DNA, with two minima in ''fkh250'' (C) vs. one minimum in ''fkh250con'' (D), as inferred by Monte Carlo simulations (green plots). Minor groove width (blue plots) and electrostatic potential (red plots) correlate and form two binding pockets in ''fkh250'' (E) and only a binding site for Arg5 in ''fkh250con'' (F).<br/> | Based on the comparison of the two crystal structures of a Scr-Exd-DNA ternary complexes (Figure 6), it was found that three N-terminal residues contact the minor groove of the Scr specific site ''fkh250'' (A) compared to only Arg5 binding the Hox consensus site ''fkh250con'' (B). In their protein-bound states, the shapes of both sites are distinct (dark gray, concave; green, convex surfaces). The distinct shapes of the two DNA binding sites, shown as minor groove width in the crystal structures of the complexes (blue plots), are already present when the protein is not bound to the DNA, with two minima in ''fkh250'' (C) vs. one minimum in ''fkh250con'' (D), as inferred by Monte Carlo simulations (green plots). Minor groove width (blue plots) and electrostatic potential (red plots) correlate and form two binding pockets in ''fkh250'' (E) and only a binding site for Arg5 in ''fkh250con'' (F).<br/> | ||