Minor groove structures

The polypeptide chain of the lac repressor subunit is arranged in four domains (Figure 8.21) an N-terminal DNA-hinding domain with a helix-turn-helix motif, a hinge helix which binds to the minor groove of DNA, a large core domain which binds the corepressor and has a structure very similar to the periplasmic arablnose-binding protein described in Chapter 4, and finally a C-terminal a helix which is involved in tetramerization. This a helix is absent in the PurR subunit structure otherwise their structures are very similar. 

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.)...

Schumacher, M.A., et al. Crystal structure of Lac 1 member, PurR, bound to DNA minor groove binding by a helices. Science 266 763-770, 1994. 

TBP binds in the minor groove and induces large structural changes in DNA... 

In conclusion, one important factor that contributes to the strong affinity of TBP proteins to TATA boxes is the large hydrophobic interaction area between them. Major distortions of the B-DNA structure cause the DNA to present a wide and shallow minor groove surface that is sterically complementary to the underside of the saddle structure of the TBP protein. The complementarity of these surfaces, and in addition the six specific hydrogen bonds between four side chains from TBP and four hydrogen bond acceptors from bases in the minor groove, are the main factors responsible for causing TBP to bind to TATA boxes 100,000-fold more readily than to a random DNA sequence. 

Thirty percent of the tumor-derived mutations are in L3, which contains the single most frequently mutated residue, Arg 248. Clearly the interaction between DNA and the specific side chain of an arginine residue inside the minor groove is of crucial importance for the proper function of p53. It is an open question whether this interaction is needed for the recognition of specific DNA sequences, or is required for the proper distortion of the DNA structure, or a combination of both. Other residues that are frequently mutated in this region participate in interactions with loop L2 and stabilize the structures of loops L2 and L3. Mutations of these residues presumably destabilize the structure so that efficient DNA binding can no longer take place. 

TBP-TATA box complexes are known A p sheet in TBP forms the DNA-binding site TBP binds in the minor groove and induces large structural changes in DNA The interaction area between TBP and the TATA box is mainly hydrophobic Functional implications of the distortion of DNA by TBP... 

Microwaves, electromagnetic spectrum and. 419 Mincralocorticoid, 1083 Minor groove (DNA), 1104-1105 Mitomycin C, structure of, 970 Mixed aldol reaction, 885-886 requirements for. 885-886 Mixed Claisen condensation reaction, 890-891... 

A high-resolution 1 1 solution NMR structure of lmPy-y9-lm-y9-lmPy-y9-Dp elucidated the role of /9-alanine in minor groove recognition (Fig. 3.7 b) [47]. The p residues allow both Im rings in the /9-lm-/9-lm subunit to adapt to the relatively large... 

Fig. 3.10 Recognition of the DNA minor groove with benzimidazole derivatives, (a) Structure of the dimeric core for Py-benzimi-dazole (Bi), Py-hydroxybenzimidazole (Hz) and Py-imidazopyridine (Ip) (left) in comparison with the five-membered ring system (right). H-bonding surfaces along the recogni-...

Baird, P.B. Dervan, and D C. Rees. Structural effects of DNA sequence on T-A recognition by hydroxypyrrole/pyr-role pairs in the minor groove. J. Mol. Biol. 2000, 295, 557-567. 

An analysis of the hydration structure of water molecules in the major and minor grooves in B-DNA has shown that there is a filament of water molecules connecting both the inter and the intra phosphate groups of the two strands of B-DNA. However, such a connectivity is absent in the case of Z-DNA confirming earlier MC simulation results. The probability density distributions of the counterions around DNA shows deep penetration of the counterions in Z-DNA compared to B-DNA. Further, these distributions suggest very limited mobility for the counterions and show well defined counter-ion pattern as originally suggested in the MC study. 

Figure 35-2. A diagrammatic representation of the Watson and Crick modei of the doubie-heiicai structure of the B form of DNA.The horizontai arrow indicates the width of the doubie heiix (20 A), and the verticai arrow indicates the distance spanned by one compiete turn of the doubie heiix (34 A). One turn of B-DNA in-ciudes ten base pairs (bp), so the rise is 3.4 A per bp. The centrai axis of the doubie heiix is indicated by the verticai rod. The short arrows designate the poiarity of the antiparaiiei strands. The major and minor grooves are depicted. (A,adenine C, cytosine G, guanine ...

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