A novel DNA recognition mode by the NF-κB p65 homodimer

Abstract

The crystal structure of the NF-κB p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 Å 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° 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-κB 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.