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Crystal structure of inhibitor of κB kinase β

Abstract

Inhibitor of κB (IκB) kinase (IKK) phosphorylates IκB proteins, leading to their degradation and the liberation of nuclear factor κB for gene transcription. Here we report the crystal structure of IKKβ in complex with an inhibitor, at a resolution of 3.6 Å. The structure reveals a trimodular architecture comprising the kinase domain, a ubiquitin-like domain (ULD) and an elongated, α-helical scaffold/dimerization domain (SDD). Unexpectedly, the predicted leucine zipper and helix–loop–helix motifs do not form these structures but are part of the SDD. The ULD and SDD mediate a critical interaction with IκBα that restricts substrate specificity, and the ULD is also required for catalytic activity. The SDD mediates IKKβ dimerization, but dimerization per se is not important for maintaining IKKβ activity and instead is required for IKKβ activation. Other IKK family members, IKKα, TBK1 and IKK-i, may have a similar trimodular architecture and function.

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Figure 1: Structure of xIKKβ.
Figure 2: Inhibitor-bound xIKKβ kinase domain.
Figure 3: Interactions among the KD, ULD and SDD.
Figure 4: ULD–SDD restricts IKKβ specificity and ULD is required for catalytic activity.
Figure 5: Dimerization is critical for IKKβ activation but not for its activity.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 3QA8 and 3QAD.

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Acknowledgements

We thank K. Rajashankar and N. Sukumar for data collection at the NE-CAT of APS, B. Schwer for help with the kinase assay, P. Gaillard for help with the chemistry and G. Ahlsen, L. Shapiro and B. Honig for the ultracentrifugation experiments. This work was supported by the National Institutes of Health (H.W. and M.K.), the American Heart Association (G.X. and Y.-C.L.) and the Cancer Research Institute (Y.-C.L.). M.K. is an American Cancer Society Research Professor.

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G.X. cloned, expressed, purified, crystallized and determined the crystal structure of xIKKβ and performed experiments to determine Km. Y.-C.L. cloned, expressed, purified and crystallized hIKKβ and performed pull-down experiments and kinase assays using phospho-IκBα antibody. Q.L. expressed the hIKKβ mutants in insect cells. G.N. and X.W. performed transfection, immunoprecipitation and kinase assays and M.K. supervised these experiments. H.W. supervised the project. G.X and H.W. made the figures and wrote the manuscript.

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Correspondence to Hao Wu.

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Xu, G., Lo, YC., Li, Q. et al. Crystal structure of inhibitor of κB kinase β. Nature 472, 325–330 (2011). https://doi.org/10.1038/nature09853

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