1ram
From Proteopedia
(New page: 200px<br /><applet load="1ram" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ram, resolution 2.700Å" /> '''A NOVEL DNA RECOGNI...) |
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| - | [[Image:1ram.jpg|left|200px]]<br /><applet load="1ram" size=" | + | [[Image:1ram.jpg|left|200px]]<br /><applet load="1ram" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ram, resolution 2.700Å" /> | caption="1ram, resolution 2.700Å" /> | ||
'''A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER'''<br /> | '''A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex | + | The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair. However, one of the subunits (subunit B) encounters a half site of 5'-GAAA-3'. The single base-pair change from G-C to A-T results in highly unfavorable interactions between this half site and the base contacting protein residues in subunit B, which leads to an 18 degrees rotation of the N-terminal terminal domain from its normal conformation. Remarkably, subunit B retains all the interactions with the sugar phosphate backbone of the DNA target. This mode of interaction allows the NF-kappa B p65 homodimer to recognize DNA targets containing only one cognate half site. Differences in the sequence of the other half site provide variations in conformation and affinity of the complex. |
==About this Structure== | ==About this Structure== | ||
| - | 1RAM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with DTT as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1RAM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=DTT:'>DTT</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RAM OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Chen, Y | + | [[Category: Chen, Y Q.]] |
[[Category: Ghosh, G.]] | [[Category: Ghosh, G.]] | ||
[[Category: Ghosh, S.]] | [[Category: Ghosh, S.]] | ||
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[[Category: transcription regulation]] | [[Category: transcription regulation]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:48:52 2008'' |
Revision as of 12:48, 21 February 2008
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A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER
Overview
The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair. However, one of the subunits (subunit B) encounters a half site of 5'-GAAA-3'. The single base-pair change from G-C to A-T results in highly unfavorable interactions between this half site and the base contacting protein residues in subunit B, which leads to an 18 degrees rotation of the N-terminal terminal domain from its normal conformation. Remarkably, subunit B retains all the interactions with the sugar phosphate backbone of the DNA target. This mode of interaction allows the NF-kappa B p65 homodimer to recognize DNA targets containing only one cognate half site. Differences in the sequence of the other half site provide variations in conformation and affinity of the complex.
About this Structure
1RAM is a Single protein structure of sequence from Mus musculus with as ligand. Full crystallographic information is available from OCA.
Reference
A novel DNA recognition mode by the NF-kappa B p65 homodimer., Chen YQ, Ghosh S, Ghosh G, Nat Struct Biol. 1998 Jan;5(1):67-73. PMID:9437432
Page seeded by OCA on Thu Feb 21 14:48:52 2008
