Structure of the human NF- Kappa B p52 homodimer-DNA complex at 2.1 angstrom resolution

The crystal structure of human NF- Kappa B p52 in its specific complex with the natural Kappa B DNA binding site MHC H-2 has been solved at 2.1 angstrom resolution. Whereas the overall structure resembles that of the NF- Kappa B p50-DNA complex, pronounced differences are observed within the 'insert region'. This sequence segment differs in length between different Rel proteins. Compared with NF- Kappa B p50, the compact alpha -helical insert region element is rotated away from the core of the N-terminal domain, opening up a mainly polar cleft. The insert region presents potential interaction surfaces to other proteins. The high resolution of the structure reveals many water molecules which mediate interactions in the protein-DNA interface. Additional complexity in Rel protein-DNA interaction comes from an extended interfacial water cavity that connects residues at the edge of the dimer interface to the central DNA bases. The observed water network might account for differences in binding specificity between NF- Kappa B p52 and NF- Kappa ,B p50 homodimers.