X-ray Structure of a NF-κB p50/RelB/DNA Complex Reveals Assembly of Multiple Dimers on Tandem κB Sites

Abstract

We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals distinctive features not observed for non-RelB complexes. For example, Lys274 of RelB is removed from the protein-DNA interface whereas the corresponding residues in all other subunits make base-specific contacts. This mode of binding suggests that RelB may allow the recognition of more diverse kappaB sequences. Complementary surfaces on RelB and p50, as revealed by the crystal contacts, are highly suggestive of assembly of multiple p50/RelB heterodimers on tandem kappaB sites in solution. Consistent with this model our in vitro binding experiments reveal optimal assembly of two wild-type p50/RelB heterodimers on tandem HIV kappaB DNA with 2 bp spacing but not by a mutant heterodimer where one of the RelB packing surface is altered. We suggest that multiple NF-kappaB dimers assemble at diverse kappaB promoters through direct interactions utilizing unique protein-protein interaction surfaces.

A single NFκB system for both canonical and non-canonical signaling

“…It suggests that nuclear accumulation of RelA, cRel and p50 in IKK2ca+ B cells can compensate for the loss of RelB:p52 activation in B cells deficient in BAFF-R signaling. Interestingly, analysis of crystal structure of RelB-containing dimers suggested that RelB may recognize a broader range of κB sequences than other dimers [93,94]. In sum, studies performed so far have not been able to reach a definite conclusion if different NFκB dimers activated by the non-canonical pathway have specific or overlapping gene activation functions.…”

A Structural Guide to Proteins of the NF- B Signaling Module

“…X-ray crystal structures of several additional NF-kB:DNA complexes have now been determined (Cramer et al 1997;Cramer et al 1999;Moorthy et al 2007;Panne et al 2007;Fusco et al 2009). Taken together, these structures suggest a model for how NF-kB dimers recognize kB DNA that contain significant deviations from the consensus sequence.…”

RelB is the NF-κB subunit downstream of NIK responsible for osteoclast differentiation

“…p52 can dimerize with both p65 and c-Rel (21), whose nuclear translocation are controlled by the classical NF-B pathway. Additionally, the RelB:p50 dimer is transcriptionally active and has been crystallized in complex with B DNA (22). As a DNA binding subunit, p52 bears a RHD, but does not have a transactivation domain, which is the region responsible for interactions with coactivators that may play a significant role in the selection of specific gene targets by NF-B complexes.…”