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Figure 4.
Figure 4 Model for a topoisomerase domain-DNA complex. (A)
Electrostatic surface representation of the topoisomerase
domain. The diagram shows that the topoisomerase has a large
positively charged groove in one face of the protein centered
around the active site. The insets correspond to 90° views of
the molecule and show that there are no additional large
positively charged regions in the protein. The electrostatic
potential was calculated with the program APBS (Baker et al,
2001), with a dielectric constant of 80 for the solvent and 20
for the protein. The surface is colored with a blue to red
gradient from +5 to -5 K[b]T/e. (B) The diagram shows a model of
the topoisomerase domain in complex with B-DNA. The coloring
scheme is the same as in Figure 1. To create the model, the
linker helix and the multiHhH domain were removed. DNA was
docked using the HTH motif of human Pax6-paired domain-DNA
complex (Xu et al, 1999), but replacing the DNA with a
canonical, straight B-DNA model. No attempts were made to
prevent steric clashes. In the model, the active site tyrosine
is ideally placed to interact with the phosphodiester backbone
and the other putative active site residues are also in the
vicinity of DNA. The model suggests a potential way for topo-61
to interact with DNA, making extensive interactions.
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