DNA binding site motif

Keywords Protein binding microarray DNA binding site motif ... 

Identification of the DNA Binding Site Motif from the Protein Binding Microarray Data... 

The two homologous repeats, each of 88 amino acids, at both ends of the TBP DNA-binding domain form two stmcturally very similar motifs. The two motifs each comprise an antiparallel p sheet of five strands and two helices (Figure 9.4). These two motifs are joined together by a short loop to make a 10-stranded p sheet which forms a saddle-shaped molecule. The loops that connect p strands 2 and 3 of each motif can be visualized as the stirmps of this molecular saddle. The underside of the saddle forms a concave surface built up by the central eight strands of the p sheet (see Figure 9.4a). Side chains from this side of the P sheet, as well as residues from the stirrups, form the DNA-binding site. No a helices are involved in the interaction area, in contrast to the situation in most other eucaryotic transcription factors (see below). 

The coiled-coil structure of the leucine zipper motif is not the only way that homodimers and heterodimers of transcription factors are formed. As we saw in Chapter 3 when discussing the RNA-binding protein ROP, the formation of a four-helix bundle structure is also a way to achieve dimerization, and the helix-loop-helix (HLH) family of transcription factors dimerize in this manner. In these proteins, the helix-loop-helix region is preceded by a sequence of basic amino acids that provide the DNA-binding site (Figure 10.23), and... 

Proteins with the helix-turn-helix or leucine zipper motifs form symmetric dimers, and their respective DNA binding sites are symmetric palindromes. In proteins with the zinc finger motif, the binding site is repeated two to nine times. These features allow for cooperative interactions between binding sites and enhance the degree and affinity of binding. 

The DNA binding site of Fur was predicted and then found to be in the N-terminal domain in an unusual helix-turn-helix motif (Holm et ah, 1994 Stojiljkovic and Hantke, 1995). The structure of Fur still remains to be determined and attempts to crystallize the protein have so far been unsuccessful. 

Discuss two main DNA-recognition motifs found in eukaryotic transcription factors. Describe their structures, indicate how they bind to DNA, and discuss how each specifically recognizes its DNA binding site. 

The crystal structure of TraR was the first reported structure among AHL receptor protein. 3-Oxo-C8-HSL—TraR complex forms a homodimer, which binds to DNA (tra box). TraR consists of two domains as LuxR. The N-terminal domain is an AHL-binding site and the C-terminal domain is a DNA-binding site with a helix-turn-helix motif (Figure 31).315... 

Gag knuckle this fold is composed of short ( 20 amino acids) Cys2His2 zinc fingers from retroviral gag proteins Motif a primary, secondary, or tertiary structural domain Palindromic DNA-binding site a DNA sequence that contains one inverted repeat composed of two half-sites of nucleotides... 

A study of the mechanism of repair and cytotoxicity of 5-fluorouracil demonstrated that base excision repair by UNG is the major repair mechanism, but that cytotoxicity resulted primarily from its incorporation into RNA. Using CD spectroscopy, a novel major groove binding motif has been identified in which Zn(II) ions stabilise DNA containing 5-fluoro-5-Iodouracil is frequently used as a crosslinking agent, and has been used to map DNA binding sites in the Tetrahymena telomerase and in the telomerase ribonucleoprotein. ... 

Figure 8.22 The lac repressor molecule is a V-shaped tetramer in which each arm is a dimer containing a DNA-hinding site. The helix-tum-helix motifs (red) of each dimer bind in two successive major grooves and the hinge helices (purple) bind adjacent to each other in the minor groove between the two major groove binding sites. The four subunits of the tetramer are held together by the four C-terminal helices (yellow) which form a four helix bundle. The bound DNA fragments are bent. (Adapted from M. Lewis et al., Science 271 1247-1254, 1996.)...

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