1saa

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ATF-2 RECOGNITION SITE, NMR, 10 STRUCTURES

Overview

The effect of leucine zipper proteins binding to the DNA recognition site, is controversial. Results from crystallography, gel and solution methods, have led to opposite conclusions about the conformation of the DNA in the, complex. The role of the DNA binding site in the recognition process and, in the gene induction mediated by transcription factors needs to be, investigated further. In this article the self-complementary 16 bp, oligodeoxynucleotide (CATGTGACGTCACATG)2, which contains the cAMP response, element recognised by numerous transcription factors of the leucine zipper, family, has been examined free from proteins and in its interaction with, the mammalian activating transcription factor 2. The recognition process, has been investigated by circular dichroism analysis, which has revealed, conformational changes in both DNA and protein upon binding. The solution, structure of the 16mer, important in order to define the effects induced, by binding of leucine zipper proteins and the intrisic bending properties, of DNA, has been determined from NMR data using direct refinement against, NOE intensities, analysis of scalar coupling constants and restrained, molecular dynamics calculations. Final structures starting from the A and, B forms of DNA agreed to a pairwise root mean square deviation (r.m.s.d.), of 1.04 +/- 0.3 A (0.7 +/- 0.2 A to the average) for all atoms. The, terminal base pairs were less well determined, and the pairwise deviation, of the 12 core bp was 0.83 +/- 0.27 A (0.55 +/- 0.19 A to the average)., The final structures are within the B-family with an average helical twist, of 36+/-2 degrees. No significant intrinsic DNA bend is shown in the, activating transcription factor regulatory site. However, there are, substantial deviations from the canonical B-DNA (r.m.s.d. = 3.6 A) in the, core of the molecule, associated with relatively large base inclinations.

About this Structure

1SAA is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Solution structure of the ATF-2 recognition site and its interaction with the ATF-2 peptide., Conte MR, Lane AN, Bloomberg G, Nucleic Acids Res. 1997 Oct 1;25(19):3808-15. PMID:9380502

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