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Figure 4.
Figure 4. Nucleotide Binding by Cdc6A) Comparison of Cdc6
with various AAA^+ proteins. NSF-D2, Cdc6, and δ′ are shown
in ribbon representation and colored cyan, green/red, and gold.
Mg•ATP and Mg•ADP are shown bound to NSF-D2 and Cdc6,
respectively, as black ball-and-stick. Structural comparisons
between the AAA^+ regions of Cdc6, NSF-D2, and δ' can be made
by using the core regions with sequence similarity as an
additional guide: domain I of Cdc6 has an overall rmsd of 1.7
Å and 1.8 Å (spanning 100 and 79 residues) to
NSF-D2, and δ′, respectively; domain II of Cdc6 superposes
with the equivalent regions of NSF and δ' to 1.3 Å and
1.2 Å rmsd over 25 and 21 amino acids. Global rmsds
spanning both domains are similar to individual domain rmsds for
NSF-D2 and Cdc6 but are markedly different for cdc6 and δ′
(2.0 Å rmsd over 125 residues for NSF-D2 compared to 2.5
Å rmsd over 100 residues for δ′).(B) Stereogram view of
the nucleotide binding region. Secondary structure is shown as a
white coil. Residues within 4 Å of bound Mg•ADP are
shown as gray ball-and-stick and are labeled; the one exception
is His-167, which is part of the conserved sensor I motif but
lies 5 Å away from the β-phosphate group. ADP is colored
as magenta ball-and-stick, and the Mg^2+ ion and coordinating
waters are shown as black and red spheres, respectively.
Hydrogen bonds are shown as dashed lines. Backbone nitrogen
atoms are shown as blue spheres and are exaggerated in size for
emphasis.(A) and (B) generated by RIBBONS ([10]).
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