Architecture of DNA-binding Domains in Proteins

This section briefly summarizes the characteristics of DNA-binding proteins from a structural point of view. Here, we are interested mainly in those aspects responsible for the binding to DNA. Several review articles and book chapters describe the architecture of such proteins and the three-dimensional structures of protein-DNA complexes in some detail [109-112], Table 18.2 lists the protein-DNA complexes for which X-ray crystal structures have been determined. In all of these DNA is found in the B-conformation. 

Helix-turn-helix eukaryotic engrailed homeodomain 2.8 [107] 

Another major structural motif found in DNA-binding proteins are zinc-mediated loops. So far, three classes of zinc modules have been recognized [111]. The common feature of these classes is the use of a zinc ion as a crosslink to stabilize a small 

Another class of DNA-binding proteins are the restriction endonucleases which cleave DNA at specific sites. The recognition motif found in the complex between DNA and Eco R1 features a helices as well, but the interaction mode differs considerably from those found in the helix-turn-helix and zinc-finger proteins. In the Eco RI complex, a parallel bundle of four a helices penetrates the major groove, whereby only the ends of the helices interact with the DNA [99, 100]. In addition, an extension of the polypeptide chain of one of these helices wraps around the DNA and makes several contacts to bases. 

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]. 

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