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Probing the Solution Structure of IκB Kinase (IKK) Subunit γ and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit β by EPR Spectroscopy.

Bagnéris C, Rogala KB, Baratchian M, Zamfir V, Kunze MB, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CW - J. Biol. Chem. (2015)

Bottom Line: Because IKKγ functions as a scaffold, recruiting both vFLIP and the IKKα/β subunits, it has been proposed that binding of vFLIP could trigger a structural rearrangement in IKKγ conducive to activation.The coiled-coil comprises N- and C-terminal regions with distinct registers accommodated by a twist: this structural motif is exploited by vFLIP, allowing it to bind and subsequently activate the NF-κB pathway.In vivo assays confirm that NF-κB activation by vFLIP only requires the N-terminal region up to the transition between the registers, which is located directly C-terminal of the vFLIP binding site.

View Article: PubMed Central - PubMed

Affiliation: From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom.

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Comparison of the 3/5 model of IKKγ with crystal structures.A, 3/5 model (green) is overlaid with crystal structures of IKKγ fragments (magenta) with IKKβ, vFLIP, and diubiquitin (gray). Plots of the RMSDs of the positions of the non-hydrogenic atoms in the coiled-coil model structures (Registers 0–6) compared with those in the known crystal structures: (B) IKKγ + IKKβ (22); (C) IKKγ + vFLIP (12); (D) IKKγ ubiquitin binding region: apo (23) (blue), with diubiquitin (24) (magenta), and with Hiop (25) (green). The curves are fits to the RMSDs assuming a sinusoidal pattern that completes two oscillations within the heptad repeat.
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Figure 7: Comparison of the 3/5 model of IKKγ with crystal structures.A, 3/5 model (green) is overlaid with crystal structures of IKKγ fragments (magenta) with IKKβ, vFLIP, and diubiquitin (gray). Plots of the RMSDs of the positions of the non-hydrogenic atoms in the coiled-coil model structures (Registers 0–6) compared with those in the known crystal structures: (B) IKKγ + IKKβ (22); (C) IKKγ + vFLIP (12); (D) IKKγ ubiquitin binding region: apo (23) (blue), with diubiquitin (24) (magenta), and with Hiop (25) (green). The curves are fits to the RMSDs assuming a sinusoidal pattern that completes two oscillations within the heptad repeat.

Mentions: An overlay of the 3/5 hybrid with three crystal structures is presented in Fig. 7A. To obtain a metric of the deviation of the 7 models with crystal structures of IKKγ fragments, the root mean square deviations (RMSDs) of the positions of the non-hydrogenic atoms in these regions were calculated (Fig. 7, B–D). As expected the RMSDs follow a sinusoidal pattern covering two complete oscillations over 7 residues. The IKKγ + IKKβ crystal structure (PDB entry 3BRT (22), residues: 50–110) has the closest match with Register-4 followed by Register-0 (Fig. 7B) while the crystal structure of IKKγ + vFLIP (PDB entry 3CLC (12), residues: 195–250) has closest match with Register-3 followed by Register-6 (Fig. 7C). By contrast, crystal structures of the ubiquitin binding region both alone (PDB entry 2ZVN (24), residues: 270–330) and in complex with diubiquitin (PDB entry 3FX0 (23)) and Hiop (PDB entry 4OWF (25), residues: 255–335) have closest matches with Register-2 followed by Register-5 (Fig. 7D). Thus both 0/5 and 3/5 hybrid models that we constructed from the EPR data are consistent with crystal structures giving confidence that we have derived a realistic overall view of the structure of IKKγ in solution.


Probing the Solution Structure of IκB Kinase (IKK) Subunit γ and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit β by EPR Spectroscopy.

Bagnéris C, Rogala KB, Baratchian M, Zamfir V, Kunze MB, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CW - J. Biol. Chem. (2015)

Comparison of the 3/5 model of IKKγ with crystal structures.A, 3/5 model (green) is overlaid with crystal structures of IKKγ fragments (magenta) with IKKβ, vFLIP, and diubiquitin (gray). Plots of the RMSDs of the positions of the non-hydrogenic atoms in the coiled-coil model structures (Registers 0–6) compared with those in the known crystal structures: (B) IKKγ + IKKβ (22); (C) IKKγ + vFLIP (12); (D) IKKγ ubiquitin binding region: apo (23) (blue), with diubiquitin (24) (magenta), and with Hiop (25) (green). The curves are fits to the RMSDs assuming a sinusoidal pattern that completes two oscillations within the heptad repeat.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4505408&req=5

Figure 7: Comparison of the 3/5 model of IKKγ with crystal structures.A, 3/5 model (green) is overlaid with crystal structures of IKKγ fragments (magenta) with IKKβ, vFLIP, and diubiquitin (gray). Plots of the RMSDs of the positions of the non-hydrogenic atoms in the coiled-coil model structures (Registers 0–6) compared with those in the known crystal structures: (B) IKKγ + IKKβ (22); (C) IKKγ + vFLIP (12); (D) IKKγ ubiquitin binding region: apo (23) (blue), with diubiquitin (24) (magenta), and with Hiop (25) (green). The curves are fits to the RMSDs assuming a sinusoidal pattern that completes two oscillations within the heptad repeat.
Mentions: An overlay of the 3/5 hybrid with three crystal structures is presented in Fig. 7A. To obtain a metric of the deviation of the 7 models with crystal structures of IKKγ fragments, the root mean square deviations (RMSDs) of the positions of the non-hydrogenic atoms in these regions were calculated (Fig. 7, B–D). As expected the RMSDs follow a sinusoidal pattern covering two complete oscillations over 7 residues. The IKKγ + IKKβ crystal structure (PDB entry 3BRT (22), residues: 50–110) has the closest match with Register-4 followed by Register-0 (Fig. 7B) while the crystal structure of IKKγ + vFLIP (PDB entry 3CLC (12), residues: 195–250) has closest match with Register-3 followed by Register-6 (Fig. 7C). By contrast, crystal structures of the ubiquitin binding region both alone (PDB entry 2ZVN (24), residues: 270–330) and in complex with diubiquitin (PDB entry 3FX0 (23)) and Hiop (PDB entry 4OWF (25), residues: 255–335) have closest matches with Register-2 followed by Register-5 (Fig. 7D). Thus both 0/5 and 3/5 hybrid models that we constructed from the EPR data are consistent with crystal structures giving confidence that we have derived a realistic overall view of the structure of IKKγ in solution.

Bottom Line: Because IKKγ functions as a scaffold, recruiting both vFLIP and the IKKα/β subunits, it has been proposed that binding of vFLIP could trigger a structural rearrangement in IKKγ conducive to activation.The coiled-coil comprises N- and C-terminal regions with distinct registers accommodated by a twist: this structural motif is exploited by vFLIP, allowing it to bind and subsequently activate the NF-κB pathway.In vivo assays confirm that NF-κB activation by vFLIP only requires the N-terminal region up to the transition between the registers, which is located directly C-terminal of the vFLIP binding site.

View Article: PubMed Central - PubMed

Affiliation: From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom.

Show MeSH
Related in: MedlinePlus