2ram | pdb_00002ram
A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER
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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
2RAM is a Single protein structure of sequence from Mus musculus with DTV 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
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