1saa
From Proteopedia
(New page: 200px<br /><applet load="1saa" size="450" color="white" frame="true" align="right" spinBox="true" caption="1saa" /> '''ATF-2 RECOGNITION SITE, NMR, 10 STRUCTURES''...) |
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| - | [[Image:1saa.gif|left|200px]]<br /><applet load="1saa" size=" | + | [[Image:1saa.gif|left|200px]]<br /><applet load="1saa" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1saa" /> | caption="1saa" /> | ||
'''ATF-2 RECOGNITION SITE, NMR, 10 STRUCTURES'''<br /> | '''ATF-2 RECOGNITION SITE, NMR, 10 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The effect of leucine zipper proteins binding to the DNA recognition site | + | 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== | ==About this Structure== | ||
| - | 1SAA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1SAA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SAA OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Bloomberg, G.]] | [[Category: Bloomberg, G.]] | ||
| - | [[Category: Conte, M | + | [[Category: Conte, M R.]] |
| - | [[Category: Lane, A | + | [[Category: Lane, A N.]] |
[[Category: aft-2]] | [[Category: aft-2]] | ||
[[Category: cre]] | [[Category: cre]] | ||
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[[Category: recognition]] | [[Category: recognition]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:59:27 2008'' |
Revision as of 12:59, 21 February 2008
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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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