NF-kB p52:RelB heterodimer recognizes two classes of kB sites with two distinct modes

The X-ray structure of the nuclear factor-jB (NF-jB) p52:RelB:jB DNA complex reveals a new recognition feature not previously seen in other NF-jB:jB DNA complexes. Arg 125 of RelB is in contact with an additional DNA base pair. Surprisingly, the p52:RelB R125A mutant heterodimer shows defects both in DNA binding and in transcriptional activity only to a subclass of jB sites. We found that the Arg 125-sensitive jB sites contain more contiguous and centrally located A:T base pairs than do the insensitive sites. A protein-induced kink observed in this complex, which used an AT-rich jB site, might allow the DNA contact by Arg 125; such a kink might not be possible in complexes with non-AT-rich jB sites. Furthermore, we show that the p52:RelB heterodimer binds to a broader spectrum of jB sites when compared with the p50:RelA heterodimer. We suggest that the p52:RelB heterodimer is more adaptable to complement seq-uence and structural variations in jB sites when compared with other NF-jB dimers