Recognition helices

Figure 8.8 The DNA-binding heiix-turn-helix motif in lambda Cro. Ca positions of the amino acids in this motif have been projected onto a plane and the two helices outlined. The second helix (red) is called the recognition helix because it is involved in sequence-specific recognition of DNA.

This model of Cro binding to DNA was arrived at by intuition and clever model building. Its validity was considerably strengthened when the same features were subsequently found in the DNA-binding domains of the lambda-repressor molecule. The helix-turn-helix motif with a recognition helix is present in the repressor, and moreover the repressor DNA-binding domains dimerize in the crystals in such a way that the recognition helices are separated by 34 A as in Cro. 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

Seguence-specific interaction between DNA and recognition helix allows recognition of OR regions... 

Structural studies of a repressor-DNA complex have shown that helices 4 and 5 form a helix-turn-helix motif and that side chains from the recognition helix 5 form water-mediated interactions with bases in the major groove. 

Figure 8.23 The helix-turn-helix motifs of the subunits of both the PurR and the lac repressor subunits bind to the major groove of DNA with the N-terminus of the second helix, the recognition helix, pointing into the groove. The two hinge helices of each arm of the V-shaped tetramer bind adjacent to each other in the minor groove of DNA, which is wide and shallow due to distortion of the B-DNA structure. (Adapted from M.A. Schumacher et al.. Science 266 763-770, 1994.)...

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 9.12 Schematic diagram of the structure of the heterodimeric yeast transcription factor Mat a2-Mat al bound to DNA. Both Mat o2 and Mat al are homeodomains containing the helix-turn-helix motif. The first helix in this motif is colored blue and the second, the recognition helix, is red. (a) The assumed structure of the Mat al homeodomain in the absence of DNA, based on Its sequence similarity to other homeodomains of known structure, (b) The structure of the Mat o2 homeodomain. The C-terminal tail (dotted) is flexible in the monomer and has no defined structure, (c) The structure of the Mat a 1-Mat a2-DNA complex. The C-terminal domain of Mat a2 (yellow) folds into an a helix (4) in the complex and interacts with the first two helices of Mat a2, to form a heterodimer that binds to DNA. (Adapted from B.J. Andrews and M.S. Donoviel, Science 270 251-253, 1995.)...

Three residues in the recognition helix provide the sequence-specific interactions with DNA... 

Figure 10.11 Sequence-specific interactions between DNA (yellow) and the recognition helix (red) of the glucocorticoid receptor. Three residues, Lys 461, Val 462 and Arg 466 make specific contacts with the edges of the bases In the major groove.

The two zinc ions fulfill important but different functions in the DNA-binding domains. The first zinc ion is important for DNA-bindlng because it properly positions the recognition helix the last two cysteine zinc ligands are part of this helix. The second zinc ion is important for dimerization since the five-residue loop between the first two cysteine zinc ligands is the main component of the dimer interaction area. 

Fig. 1.6. The Zn binding motif of the glncocorticoid receptor in complex with DNA. Shown is the complex of the dimeric DNA-binding domain of the glncocorticoid receptor with the cognate DNA element (Luisi et al., 1991). The Zn ions are shown as spheres. The two Zn ions are clearly non-eqnivalent. While one of the Zn ions aids in the fixation of the recognition helix in the major groove, the other correctly positions a strnctnral element for the dimerization of the monomers. MOLSCRIPT drawing (Kranhs, 1991).

Here two zinc ions are complexed by 6 Cys residues, whereby two of the Cys residues bind to both ligands (see Fig. 1.3 Fig. 1.4). The structure of GAL4 complexed with its recognition sequence indicates that the Zn ions mainly act to stabilize the small globular GAL4 protein and to orient the recognition helix correctly within the major groove. 

Fig. 1.12. Examples for the H-bonds in protein-nucleic add complexes. A) H-bond contacts of the X,-repressor in complex with its operator sequence. After Jordan Pabo, (1988). B) H-bonds in the complex between the Zinc fingers of Zif268 with the cognate recognition helix. Zif268 contacts the DNA with three Zn-fingers (finger 1-3 in Fig. 1.5). Shown are the H-bond contacts formed between the fingers and the base pairs of the recognition sequence. After Pavletich Pabo, (1991).

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