The Homeodomain

Whereas amino acid sequence comparisons suggested that the homeodomain would contain a helix-turn-helix motif, the 60-residue homeodomain forms a stable structure that can bind to DNA as a monomer. The recognition helix in the homeodomain is longer and makes more contacts with the DNA core than the recognition helices from bacterial regulatory proteins (fig. 31.18). 

Although an isolated homeodomain can fold correctly and bind DNA with a specificity similar to that of the intact proteins, it is believed that the precise DNA-binding specificity is modulated by other regions of the protein. Protein-protein interactions may also have a role in modulating many homeodomain-DNA interactions. For example, the 

The homeobox sequence found in three Drosophila regulatory proteins. The sequence of amino acids along the main, continuous line is that found in the Antp homeobox. At points where the sequence of ftz proteins is different, the differences are shown above the corresponding Antp proteins, and at points where the sequence of 

Kissinger, B. Liu, E. Martin-Bianco, T. B. Komberg, and C. O. Pabo, Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution A framework for understanding homeodomain-DNA interactions, Cell 63 579-590, November 2, 1990. Copyright Cell Press. Reprinted by permission.) 

We tentatively conclude that the asymmetrical interaction of the homeodomain protein with DNA gives it a versa- 

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The homeodomain frequently binds to DNA as a monomer, in contrast to procaryotic DNA-binding proteins containing tbe belix-turn-helix motif, which usually bind as dimers. In vitro tbe homeodomain binds specifically to... 

Fi re 9.9 Comparison of the hellx-tum-helix motifs in homeodomains (a) and X repressor (b). The recognition helix (red) of the homeodomain is longer than in the procaryotic repressor motif. In addition the first helix of the homeodomain [(green in (a)] is oriented differently. 

Residues 3, 5, 6, and 8 in the N-terminal arm lie in the minor groove and form contacts with either the edge of the bases or with the DNA backbone. Almost all homeodomains contain four conserved residues, Asn 51, Arg 53, Trp 48 and Phe 49, in the middle of the long recognition helix. The first two conserved polar residues interact with DNA. The second two are part of the hydrophobic core of the homeodomain, and are important for the accurate positioning of the recognition helix and the N-terminal arm with respect to... 

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 9.11 Amino acid sequences of homeodomains from four differenf franscription factors Anfp is from fhe Antennapedia gene in the fruitfly Drosophila, a2 is from the yeast Mat o2 gene, eng is from fhe engrailed gene in Drosophila and POU is from fhe POU homeodomain in the mammalian gene Oct-1. Residues colored green form the hydrophobic core of the homeodomain, blue form nonspecific interactions with the DNA backbone and red form contacts with the edges of the DNA bases.

Both domains of the POU region bind to DNA by the usual combination of non specific binding to the DNA backbone and specific binding to the bases. The contacts between the homeodomain and DNA are similar to those of the engrailed homeodomain (compare Figures 9.10b and 9.15a) and the... 

The paired box is another sequence motif that is very well conserved during evolution and is found in a number of genes known to be of developmental significance in lower organisms. The paired box encodes the 128-amino acid paired domain, which binds DNA(Chalapakis et al., 1991), and shows similarity, with a helix-tum-helix motif, to the homeodomain. 

Interestingly, Chisaka et al. (1992) targeted the Hox-1.6 gene in a different manner and observed some distinct phenotypic effects. Alternate RNA processing allows the Hox-1.6 gene to encode two different proteins, one with the homeodomain and one without it. The experiments... 

Gibson, G., Schier, A., LeMotte, P., and Gehring, W. J. (1990). The specificities of Sex combs reduced and Antennapedia are defined by a distinct portion of each protein that includes the homeodomain. Cell 62 1087-1103. 

An interesting case of regulation at the translation level was discovered on the example of the homeodomain protein bicoid (bed), which is important in Drosophila differentiation (Dubnau and Struhl, 1996). The bicoid protein is a transcriptional activator that binds a cognate DNA element and stimulates the transcription of the neighboring genes. Apart from its specific DNA-binding capabUity, the bicoid protein binds to 3 -, non-translating sequences of the mRNA of another homeodomain protein (caudal protein) to inhibit its translation. 

Several DNA-binding motifs have been described, but here we focus on two that play prominent roles in the binding of DNA by regulatory proteins the helix-tum-helix and the zinc finger. We also consider a type of DNA-binding domain—the homeodomain—found in some eukaryotic proteins. 

DNA-Binding Proteins that Regulate Transcription in Eukaryotes Are Often Asymmetrical The Homeodomain Zinc Finger Leucine Zipper Helix-Loop-Helix... 

The most striking difference between DNA-binding proteins in prokaryotes and eukaryotes has to do with the symmetry of the interaction. In prokaryotes the binding proteins almost always interact in a symmetrical fashion with the DNA. In eukaryotes most of the cases that have been examined so far involve proteins that interact in an asymmetrical fashion with the DNA. In many cases the regulatory proteins interact in multisubunit complexes that contain nonidentical subunits. Four different types of structural motifs are discussed The homeodomain, the zinc finger, the leucine zipper, and the helix-loop-helix. 

Hanes, S. D., and R. Brent, A genetic model for interaction of the homeodomain recognition helix with DNA. Science 251 426-430, 1991. 

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