Major groove homeodomain binding

Figure 9.10 Schematic diagrams illustrating the complex between DNA (orange) and one monomer of the homeodomain. The recognition helix (red) binds in the major groove of DNA and provides the sequence-specific interactions with bases in the DNA. The N-terminus (green) binds in the minor groove on the opposite side of the DNA molecule and arginine side chains make nonspecific interactions with the phosphate groups of the DNA. (Adapted from C.R. Kissinger et al Cell 63 579-590, 1990.)...

Figure 9.14 The two domains of the POU region bind in tandem on opposite sides of the DNA double helix. Both the POU-specific domain and the POU homeodomain have a helix-turn-helix motif (blue and red) which binds to DNA with their recognition helices (red) in the major groove. The linker region that joins these domains is partly disordered. (Adapted from J.D. Klemm et al.. Cell 77 21-32, 1994.)...

Figure 31.5. Homeodomain structure. The structure of a heterodimer formed from two different DNA-binding domains, each based on a homeodomain. Notice that each homeodomain has a helix-turn-helix motif with one helix inserted into the major groove of DNA. [Drawn from lAKH.pdb,]... 

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