Figure 28-14a

HTH-DNA Interactions:
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Figure 28-14b


X-ray structures of CAP–cAMP–dsDNA complexes. The dsDNA and cAMP in these twofold symmetric complexes are colored according to atom type with DNA C gray, cAMP C green, N blue, O red, and P orange. (a) CAP–cAMP in complex with a palindromic 30-bp self-complementary DNA initially viewed with its 2-fold axis horizontal. The protein is drawn in ribbon form with its identical subunits pink and blue and with their C-terminal domains in darker shades. The DNA is shown in stick form and the cAMP is drawn in space-filling form. Note the ~45 degree kink in the DNA between the 5th and 6th bases out from the center in both directions. This gives the DNA a 90 degree curvature about the protein. Click on the "Show HTH–DNA Interactions" button for a closer look at how CAP–cAMP's helix–turn–helix (HTH) motif interacts with its target DNA. Here the HTH motif is shown in cartoon form with its side chains that interact with the DNA in stick form colored according to atom type (C gray, N blue, O red, and S yellow). The DNA is also in stick form and similarly colored but with the C's of one strand green and those of the other strand cyan. In this view, the ~45 degree kink between the bases opposite the recognition helix is especially evident. (b) CAP–cAMP in complex with a 44-bp palindromic DNA and four αCTD subunits. The DNA, CAP, and cAMP are initially viewed and colored as in Part a with the DNA drawn in space-filling form. The αCTD subunits are drawn in ribbon form with the αCTDCAP,DNA light green and the αCTDDNA dark green. [Part a based on an X-ray structure by Thomas Steitz, Yale University. PDBid 1CGP. Part b based on an X-ray structure by Helen Berman and Richard Ebright, Rutgers University. PDBid 1LB2.]