Crystal structure of inhibitor of κB kinase β

Xu, Gang; Lo, Yu Chih; Li, Qiubai; Napolitano, Gennaro; Wu, Xuefeng; Jiang, Xuliang; Dréano, Michel; Karin, Michael; Wu, Hao

doi:10.1038/nature09853

Cited by 179 publications

(259 citation statements)

References 48 publications

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“…6C). Upon stimulations, IκBα is phosphorylated by the IκB kinase (IKK) (48), which is then recognized by the substrate receptor of the SCF for polyubiquitination, leading to subsequent proteasomal degradation. Degradation of IκBα releases NF-κB for nuclear translocation and activation of transcription.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure and versatile functional roles of the COP9 signalosome subunit 1

Lee

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) plays key roles in many biological processes, such as repression of photomorphogenesis in plants and protein subcellular localization, DNA-damage response, and NF-κB activation in mammals. It is an evolutionarily conserved eight-protein complex with subunits CSN1 to CSN8 named following the descending order of molecular weights. Here, we report the crystal structure of the largest CSN subunit, CSN1 from Arabidopsis thaliana (atCSN1), which belongs to the Proteasome, COP9 signalosome, Initiation factor 3 (PCI) domain containing CSN subunit family, at 2.7 Å resolution. In contrast to previous predictions and distinct from the PCI-containing 26S proteasome regulatory particle subunit Rpn6 structure, the atCSN1 structure reveals an overall globular fold, with four domains consisting of helical repeat-I, linker helix, helical repeat-II, and the C-terminal PCI domain. Our small-angle X-ray scattering envelope of the CSN1-CSN7 complex agrees with the EM structure of the CSN alone (apo-CSN) and suggests that the PCI end of each molecule may mediate the interaction. Fitting of the CSN1 structure into the CSN-Skp1-Cul1-Fbox (SCF) EM structure shows that the PCI domain of CSN1 situates at the hub of the CSN for interaction with several other subunits whereas the linker helix and helical repeat-II of CSN1 contacts SCF using a conserved surface patch. Furthermore, we show that, in human, the C-terminal tail of CSN1, a segment not included in our crystal structure, interacts with IκBα in the NF-κB pathway. Therefore, the CSN complex uses multiple mechanisms to hinder NF-κB activation, a principle likely to hold true for its regulation of many other targets and pathways.T he constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a more than 300-kDa complex that was first identified as a negative regulator of Constitutive Photomorphogenesis (COP) in plants (1, 2). In the subsequent years, the highly conserved protein complex was also found in fungi (3, 4), Caenorhabditis elegans (5), Drosophila melanogaster (6), and mammals (7,8). The most studied function of the CSN complex in eukaryotes is the regulation of protein degradation through two pathways, deneddylation (9-11) and deubiquitination (12, 13). In the deneddylation pathway, the CSN complex can influence the cullin-RING ligase activity by removing Nedd8, a ubiquitin-like protein, from a cullin (9, 14). On the other hand, the CSN complex can also suppress cullin activity through recruitment of the deubiquitination enzyme USP15 (12) or Ubp12p, the Schizosaccharomyces pombe ortholog of human USP15 (13). Other functions of the CSN complex identified in mammalian cells include regulating the phosphorylation of ubiquitin-proteasome pathway substrates through CSN-associated kinases (7,(15)(16)(17)(18). Overall, the CSN complex appears to be a key player in protein subcellular localization (19,20), DNA-damage response (21), NF-κB activation (22), development, and cell cycle control (23,24). Thus, the functions ...

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Section: Resultsmentioning

confidence: 99%

Crystal structure and versatile functional roles of the COP9 signalosome subunit 1

Lee

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…The kinase mutant adopts a conformation in which the phosphomimetic loop and the glycine-rich loop touch each other so that the protein substrate is excluded from binding. The high similarity in the conformations of this loop seen in all crystalline copies of xIKK␤ (13) suggests that this conformation also exists in solution rather than being the result of crystal lattice contacts only. It is possible that the S177E/ S181E mutant could sample the more productive, active conformations only when an ATP molecule is bound.…”

Section: Analysis Of Protein Constructs and Crystallization-twomentioning

confidence: 97%

“…The structure of xIKK␤ is no exception. The xIKK␤ activation loop harboring the S177E/S181E double mutation appears in yet another off conformation (13). In the structures of phosphorylated hIKK␤ and TBK1 (29,30), all three oxygens of the essential phosphate phospho-Ser-181 (phospho-Ser-172 in TBK1) interact with the cationic subsite of the kinase active site.…”

Section: Analysis Of Protein Constructs and Crystallization-twomentioning

confidence: 99%

“…The first crystal structures of an IKK␤, reported for the phosphomimetic mutant of Xenopus laevis IKK␤, xIKK␤(S177E/S181E), have greatly advanced our understanding of IKK (13). Similar structural elucidation of IKK␤ in an active phosphorylated state has been hampered by the inherent kinase heterogeneity due to phosphorylation.…”

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confidence: 99%

“…IKK␤ also has an additional ULD domain after the KD, which is absent in IKK␣. The novel ULD domain is required for the functional activity of IKK␤ and important for its substrate specificity (12,13).…”

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Crystal Structure of a Human IκB Kinase β Asymmetric Dimer

Liu

Misquitta

Olland

et al. 2013

Journal of Biological Chemistry

118

141

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Background: IB kinase ␤ is a key regulator in the NB signaling pathway. Results: Crystal structure of a human IKK␤ asymmetric dimer shows one kinase active site phosphorylated and in the active conformation and the other unphosphorylated and inactive. Conclusion: Depending on the phosphorylation state, IKK␤ can adopt distinct dimeric geometry. Significance: High resolution structure of hIKK␤ provides structural basis for its activation and potential use of inhibitor design.

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The NF‐κB regulator IκBβ exhibits different molecular interactivity and phosphorylation status from IκBα in an IKK2‐catalysed reaction

et al. 2020

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Activation of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-jB) transcription factor, a central player in immune response regulation, is based on phosphorylation of inhibitor of kappaB alpha (IjBa) by the Inhibitor of kappaB kinase (IKK) that triggers IjBa degradation. Although inhibitor of kappaB beta (IjBb) is structurally similar to IjBa, its precise characteristics remain undefined. Herein, we report that the molecular interactivity of IjBb with the kinase-active region of IKK subunit 2 (IKK2), as well as its phosphorylation status, differs markedly from those of IjBa. A mass spectrometry analysis revealed that IjBb phosphorylation sites are distributed in its C-terminal region, whereas IjBa phosphorylation sites are located in the N-terminal region. Furthermore, IKK2 phosphorylation sites in IjBb are found in a region distinct from typical degradation signals, such as phosphodegron and proline/glutamic acid/serine/threonine-rich sequence (PEST) motifs. Mutation of the IjBb phosphorylation sites enhances its resistance to homeostatic proteasomal degradation. These findings contribute a novel concept in NF-jB/IKK signalling research.

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Crystal structure of inhibitor of κB kinase β

Cited by 179 publications

References 48 publications

Crystal structure and versatile functional roles of the COP9 signalosome subunit 1

Crystal structure and versatile functional roles of the COP9 signalosome subunit 1

Crystal Structure of a Human IκB Kinase β Asymmetric Dimer

The NF‐κB regulator IκBβ exhibits different molecular interactivity and phosphorylation status from IκBα in an IKK2‐catalysed reaction

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