Structural Motifs of DNA-Binding Proteins

DNA-binding proteins contact their recognition sequences via defined structural elements, termed DNA-binding motifs (overview Pabo Sauer, 1992 Burley, 1994). DNA-binding motifs are often found in structural elements of the protein which can fold independently from the rest of the protein and therefore represent separate DNA-binding domains. They can, however, also occur within sequence elements which can not independently fold, but whose folding depends on the tertiary structure of the rest of the protein. 

The most common and well-characterized DNA-binding motifs can be characterized as described below. 

The helix-tum-helix motif (HTH motif) is - historically seen - the first DNA-binding motif whose structure could be solved in a complex with DNA. It is often found in bacterial repressors. Many eucaryotic DNA-binding proteins also utilize the helix-turn- 

The structures of two Zn-binding motifs are shown in Fig. 1.4. The zinc binding motifs play, above all, a structuring role by ensuring that a recognition helix is correctly oriented and stabilized. The zinc ion does not contact the DNA directly. 

This group of binding motifs displays as characteristic structural element an extended bundle of two a-helices that are wound around each other in the form of a coiled-coil . At their end is a basic region which mediates the DNA binding (review Ellenberger, 

---

Zinc finger is a common structural motif in DNA-binding proteins. It is a hairpin bend of the protein held together by the Zn atom. 

Reflect and Apply Give examples of the major structural motifs in DNA-binding proteins, and explain how they bind. 

Structural analysis indicates that the fos and jun proteins belong to a class of DNA-binding proteins that share the conserved structural motif known as the leucine zipper (see fig. 31.21). Thus, the dimerization of these two proteins is mediated by hydrophobic interaction between the leucine side chains of two leucine zipper domains. 

Fig. 6.4 Receptor-regulated SMADs (R-SMADs) have two homology regions, one at the amino- and one at the cartXM termini, MHl and MH2. They are linked by a proline-rich linker region. The iinker region is highly variable in size and sequence. It participates in the formation of homo-oligomeric structures and contains phosphorylation sites for the MAP kinase. Phosphorylation by the MAP kinase has a negative effect, because it prevents nuclear translocation of the SMADs. R-SMADs interact through the MH2 domain with the activated receptor I and are phosphorylated at the C-terminal SS(V/M)S motif, where S is serine V, valine and M, methionine. Both, MHl and MH2 domains are essential for DNA binding and the recruitment of DNA-binding proteins.

Here we introduce several common classes of DNA-binding proteins whose three-dimensional structures have been determined. In all these examples and many other transcription factors, at least one a helix Is Inserted Into a major groove of DNA. However, some transcription factors contain alternative structural motifs (e.g., P strands and loops) that Interact with DNA. 

A further class of DNA-binding proteins which use the a helix as a recognition element are the leucine zippers, but detailed structural information is so far only available for the protein itself, not for its DNA complex [118]. In still another recognition motif, the met repressor binds to DNA in the form of two highly intertwined monomers. The groove is contacted by an antiparallel P sheet with one strand of the sheet coming from each monomer [112,115]. 

Figure 8.3 The DNA-binding protein Cro from bacteriophage lambda contains 66 amino acid residues that fold into three a helices and three P strands, (a) A plot of the Ca positions of the first 62 residues of the polypeptide chain. The four C-terminal residues are not visible in the electron density map. (b) A schematic diagram of the subunit structure. a helices 2 and 3 that form the helix-turn-helix motif ate colored blue and red, respectively. The view is different from that in (a), [(a) Adapted from W.F. Anderson et al., Nature 290 754-758, 1981. (b) Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.]...

The presence of this common helix-turn-helix motif poised for DNA binding in lambda Cro and repressor provided considerable stimulus for further genetic and structural studies of these and other procaryotic DNA-binding proteins. All the results essentially supported the proposed mode of binding between these regulator proteins and DNA. 

Figure 9.8 Schematic diagram of the three-dimensional structure of the Antennapedia homeodomain. The structure is built up from three a helices connected by short loops. Helices 2 and 3 form a helix-turn-hellx motif (blue and red) similar to those in procaryotic DNA-binding proteins. (Adapted from Y.Q. Qian et al.. Cell 59 573-580, 1989.)...

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

Tab. 3.1 DNA-binding proteins that have been inhibited by polyamides. The known DNA binding motifs from NMR or crystal structure data are shown. Significant groove contacts and proposed mechanism of polyamide inhibition are also shown for each protein...

Zinc, in addition to its use as a Lewis acid in enzyme catalysis, plays a structural role in stabilizing protein molecules. It is also involved in a characteristic motif, termed zinc finger, in a number of eukaryotic DNA-binding proteins (that regulate the transcription of DNA into RNA), first described by Aaron Klug. 

---