As we have just seen, the β subunit of I-κB kinase is the point of convergence for extracellular signals transmitted through multiple receptors, including Toll-like and IL-1 receptors. Since the cytosolic domains of the Toll-like and IL-1 receptors have no enzyme activity, it was a mystery for many years how activation of these receptors led to phosphorylation and activation of the β subunit of I-κB kinase. Early work showed that the presence of IL-1 led to oligomerization of the two IL-1 receptor proteins and the binding of several proteins to its cytosolic domain, including TRAF6, an E3 ubiquitin ligase that synthesizes polyubiquitin chains. Since all polyubiquitinylation was then thought to signal degradation by proteasomes, researchers looked for ubiquitinylated target proteins that were quickly destroyed. Not finding these, scientists looked for other possible roles for polyubiquitin and soon found that, depending on the specific E3 ubiquitin ligase, ubiquitin forms multiple types of polymers that have different structures and biological functions.

The E3 ubiquitin ligase that ubiquitinylates I-κBα links the carboxyl terminus of one ubiquitin to lysine 48 (K48) on another; this poly-K48-linked ubiquitin targets the attached protein to the proteasome (see Figure 16-35a). The E3 ligase TRAF6, in contrast, links the carboxyl terminus of one ubiquitin to lysine 63 (K63) on another (see Figure 3-36). The resultant poly-K63 ubiquitin chain does not target proteins for degradation; rather, these ubiquitin chains act as scaffolds that bind proteins that have a poly-K63 ubiquitin-binding domain. One of these proteins is the protein kinase TAK1, which becomes activated by binding to the polyubiquitin chain; another is the NEMO subunit of I-κB kinase. Binding to poly-K63 ubiquitin thus brings the kinase and its target, the β subunit of I-κB kinase, into proximity so that TAK1 can phosphorylate and thereby activate this downstream kinase (Figure 16-35b). As noted above, this kinase then phosphorylates I-κBα. Thus different types of polyubiquitin chains participate in very different ways in transmitting the IL-1 signal to activation of the NF-κB transcription factors.