Molecular mechanism of IKK catalytic dimer docking to NF-κB substrates

• Published in: Nature communications 2024-09, Vol.15
• Main Authors: Li, Changqing, Moro, Stefano, Shostak, Kateryna, O’reilly, Francis J, Donzeau, Mariel, Graziadei, Andrea, Mcewen, Alastair G, Desplancq, Dominique, Poussin-Courmontagne, Pierre, Bachelart, Thomas, Fiskin, Mert, Berrodier, Nicolas, Pichard, Simon, Brillet, Karl, Orfanoudakis, Georges, Poterszman, Arnaud, Torbeev, Vladimir, Rappsilber, Juri, Davey, Norman E, Chariot, Alain, Zanier, Katia
• Format: Article
• Language: English
• Subjects: Life Sciences
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-52076-0

The inhibitor of κB (IκB) kinase (IKK) is a central regulator of NF-κB signaling. All IKK complexes contain hetero-or homodimers of the catalytic IKKβ and/or IKKα subunits. Here, we identify a YDDΦxΦ motif, which is conserved in substrates of canonical (IκBα, IκBβ) and alternative (p100) NF-κB pathways, and which mediates docking to catalytic IKK dimers. We demonstrate a quantitative correlation between docking affinity and IKK activity related to IκBα phosphorylation/degradation. Furthermore, we show that phosphorylation of the motif's conserved tyrosine, an event previously reported to promote IκBα accumulation and inhibition of NF-κB gene expression, suppresses the docking interaction. Results from integrated structural analyzes indicate that the motif binds to a groove at the IKK dimer interface. Consistently, suppression of IKK dimerization also abolishes IκBα substrate binding. Finally, we show that an optimized bivalent motif peptide inhibits NF-κB signaling. This work unveils a function for IKKα/β dimerization in substrate motif recognition.Nuclear factor κB (NF-κB) signaling plays a central role in the regulation of cellular inflammatory, immune, and apoptotic responses 1 . Under homeostatic conditions, NF-κB dimers are sequestered in the cytoplasm by interaction with inhibitor of κB (IκB) proteins or with the NF-κB precursor proteins p100 and p105. Receptor stimulation of the 'canonical' NF-κB pathway activates the inhibitor of κB (IκB) kinase (IKK), which, in turn, phosphorylates IκB proteins. This results in the ubiquitin-mediated degradation of IκB and subsequent nuclear translocation of p65/p50 NF-κB dimers 2 . Stimulation of the 'alternative' NF-κB pathway leads instead to IKK-mediated phosphorylation of p100, which triggers partial degradation of p100 into the mature p52 NF-κB subunit 2 .Different IKK complexes (collectively referred to as IKKs hereafter) exist in cells and exhibit variable subunit composition. The core of the canonical IKK complex comprises a heterodimer of the catalytic IKKα/1 and IKKβ/2 subunits (named IKKα and IKKβ hereafter) and two copies of the regulatory NEMO subunit 3-5 . Whereas IKKα contributes to kinase activation by phosphorylating the IKKβ activation loop 6 , the IKKβ subunit directly phosphorylates a phospho-dependent D p SGxx p S/T βTrCP degron motif (where pS or pT are phosphoserine