A structural guide to proteins of the NF-kappaB signaling module

Abstract

The prosurvival transcription factor NF-kappaB specifically binds promoter DNA to activate target gene expression. NF-kappaB is regulated through interactions with IkappaB inhibitor proteins. Active proteolysis of these IkappaB proteins is, in turn, under the control of the IkappaB kinase complex (IKK). Together, these three molecules form the NF-kappaB signaling module. Studies aimed at characterizing the molecular mechanisms of NF-kappaB, IkappaB, and IKK in terms of their three-dimensional structures have lead to a greater understanding of this vital transcription factor system.

Figure 1.

The NF-κB signaling module. NF-κB exists in the cytoplasm of resting cells by virtue of its noncovalent association with an IκB inhibitor protein. The IκB kinase (IKK) responds to diverse stimuli by catalyzing the phosphorylation-dependent 26 S proteasome-mediated degradation of complex-associated IκB. Active NF-κB accumulates in the nucleus where it binds with DNA sequence specificity in the promoter regions of target genes and activates their transcription.

Figure 2.

The NF-κB family. (A) The human genome encodes five polypeptides that assemble in various dimer combinations to form active NF-κB transcription factors. Each of the subunits contains the Rel homology region (RHR) near its amino terminus. The RHR consists of two folded domains, the amino-terminal domain (NTD) and the dimerization domain (DimD), that are joined by a short flexible linker and a carboxy-terminal flexible region that contains the nuclear localization signal (L). Three of the subunits, p65, c-Rel, and RelB, also contain a transcription activation domain (TAD) at their carboxy-terminal ends. RelB contains a predicted leucine zipper motif (LZ) amino-terminal to its RHR. The NF-κB subunits p50 and p52 lack transactivation domains and have glycine-rich regions (G). (B) A ribbon diagram representation of the RHR from p50 in its DNA-bound conformation. (C) The NF-κB p50:p65/RelA heterodimer bound to κB DNA. (D) Another view of the complex. (E) The NF-κB p50:p65/RelA heterodimer dimerization domains with key amino acid side chains labeled. (F) κB DNA from the NF-κB:DNA complex with key base-contacting amino acid residues labeled.

Figure 3.

The family of human IκB proteins. (A) IκB proteins are classified as in text. Classical IκB proteins possess ankyrin repeats (ANK) flanked by an amino-terminal signal response region and carboxy terminal PEST region. The signal response regions contain sites of phosphorylation by IKK (S), ubiquitination (K), and nuclear export (E). The NF-κB precursors serve as IκB proteins as well as the source of the mature p50 and p52 NF-κB subunits. (B) Ribbon diagram of the IκBα structure from the NF-κB:IκBα complex crystal structure. Individual ankyrin repeats are numbered, ANK 4 is colored magenta, and the PEST region is labeled. (C) Ribbon diagram of the NF-κB:IκBα complex. (D) Another view of the complex.

Figure 4.

Subunits of the human IKK complex. (A) Domain organization of IKK subunits. Catalytic subunits contain a kinase domain (KD), ubiquitin-like domain (U), leucine zipper (L), helix-loop-helix (H), serine-rich (S), and NEMO-binding motif (N). The NEMO/IKKγ subunit contains two predicted coiled-coil motifs (CC1 and ‐2), a leucine zipper (L), and a carboxy-terminal zinc-finger (ZF). (B) Ribbon diagram of the IKK2/IKKβ:NEMO/IKKγ complex. Individual polypeptides are labeled as well as some of the conserved hydrophobic amino acid side chains from IKK2/IKKβ. (C) Ribbon diagram of the NEMO/IKKγ:di-ubiquitin complex. (D) The NEMO/IKKγ carboxy-terminal zinc-finger motif structure.