NF-κB p65 (RelA) homodimer uses distinct mechanisms to recognize DNA targets

Abstract Background: The NF-κB family of dimeric transcription factors regulates the expression of several genes by binding to a variety of related DNA sequences. One of these dimers, p65(RelA), regulates a subclass of these targets. We have shown previously that p65 binds to the 5′-GGAA T TTTC-3′ sequence asymmetrically. In that complex one subunit base specifically interacts with the preferred 5′ half site and the other subunit binds non-specifically to the 3′ half site. Results: Here we describe the crystal structures of two new p65–DNA complexes. One complex contains a pseudosymmetric 5′-GGAA T TTCC-3′ DNA sequence taken from the enhancer of the gene encoding interleukin 8 (IL-8) and the other contains the asymmetric 5′-GGAA T TCCC-3′ target DNA taken from the enhancer of the gene encoding type VII collagen. As expected, the global positioning of the dimer on both DNA targets is roughly symmetric, however, the hydrogen-bonding patterns at the protein–DNA interfaces differ significantly. One of the p65 monomers in complex with the asymmetric DNA binds to an extra base pair located immediately upstream of the 5′-GGAA-3′ half site. We also show that p65 binds to these targets with almost equal affinity and that different residues have variable roles in binding different κB targets. Conclusions: Taken together, these structures reveal that p65 exhibits the unique capability to specifically bind DNA targets of variable lengths from four to ten base pairs. Also, the small protein segment Arg41–Ser42–Ala43 is at least partially responsible for flexibility in DNA-binding modes.