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This Sandbox is Reserved from 06/12/2018, through 30/06/2019 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1480 through Sandbox Reserved 1543.

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Dimer of TBK1

TBK1 stands for Tank Binding Kinase 1. This enzyme is a cytoplasmic serine-threonine kinase, coded by EC=2.7.11.1. It catalyzes the transfer of a phosphate group from an ATP onto a protein, in order to form a phosphoprotein and an ADP. Its primary sequence is 729 residues long. This homodimere is involved in several signalization pathways such as the inhibition of apoptosis, inflammatory response. Its substrates are NF-κ-B, various IRFs (interferon regulatory factors), DDX3X. It is involved in several complexes depending on the cell type and the stimuli.

Overall structureOverall structure

spinqualitylabelsall models TBK1 monomer (PDB entry 4IW0) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

ProtomerProtomer

Structure of the KD domain in TBK1.

Kinase domain : () from amino acid 9 to amino acid 310: the active site is at the interface of the N- and C-terminal lobes. Inactive conformation: the C-helix and key residue Glu55 displaced from the active site. Active conformation: a rotation of the C-helix allows a key salt-bridge interaction between conserved glutamic acid in the C-helix and an active-site lysine residue. The DFG (Asp-Phe-Gly) motif and Ser172 are involved in the regulation of the kinase activity.

Ubiquitin-like domain : () from amino acid 309 to amino acid 385: it contains five β strands which form a hydrophobic interface, giving the protein a high structural homology with ubiquitin.

The (between amino acid 408 and amino acid 651) and the (between amino acid 626 and amino acid 713) are responsible for the dimerization of the protomer. Together they form the scaffolding dimerization domain (SDD). This domain presents many alpha-helix.

: from amino acid 15 to amino acid 23. This is where is bound the ATP needed for the reaction catalyzed by TBK1. This domain is really close to the catalytic residue in the 3D shape of the enzyme.

The KD and the ULD interact with each other: the ULD with the C-lobe of the KD. There is a between Tyr325 in the ULD and Glu109 in the KD. Moreover in the ULD makes favourable electrostatic interactions with Glu109-KD.

DimerDimer

ULD and KD also contribute to dimerization thanks to several interactions with the SDD of the opposite subunit in the homodimer. There are several hydrogen bonds between the KD (N- and C-lobes) and the SDD of the opposite subunit: a is formed between Asp33 in the N-lobe and Lys589 in the SDD and the strands the β7-β8 in the C-love interact with the SDD. A “ ” sequence (residues 355–357) in the ULD interacts with the SDD: Glu355-ULD interacts with Arg444-SDD (salt bridge) and Trp445-SDD (hydrogen bonds).

Possible residue modificationsPossible residue modifications

Several residues of TBK1 can be modified, by phosphorylation or polyubiquitination.

Phosphorylation : belongs to the kinase domain and can be phosphorylated by TBK1 itself, or by another serine kinase. This phosphorylation modifies the conformation of the (residues L164-G199), making the binding of the substrate possible. When S172 is not phosphorylated, the can dock itself between two αhelix of the kinase domain of another promoter. Furthermore, an containing the residues between D167 and L173 occupies the active site of this other protomer. Therefore, the active domain is not available for the binding of the substrate. But when S172 is phosphorylated, it can bind itself on the kinase domain of its own protomer, as the HPD domain which docks in the kinase domain in an intramolecular way, coming closer to the domain. This liberates the active site of the other protomer, which can now bind a substrate.

When S172 isn't phosphorylated, the activation loop binds to the active site of another protomer, providing the phosphorylation of substrates.

When S172 is phosphorylated, the activation loop comes closer to the KD, thanks to the docking of HPD. One protomer is in blue, the other in orange.

Hypothecal diagram of the transactivation mechanism of TBK1.

The autophosphorylation between two subunit of a dimer is not really probable, since when the protein is dimeric, the two kinase domains are located at the opposite of one another. Therefore, the phosphorylation of Ser172 is done either by the concerned protomer, either by the kinase domain of another TBK1 dimer when TBK1 are involved in scaffolding complexes. S172 can also be phosphorylated by kinases such as IKKB (also known as IKBKB), and dephosphorylated by phosphatases such as PPM1B.

Polyubiquitination : Polyubiquitination in a Lys63 manner on helps the activation of the kinase. The same type of modification on is responsible for dimerization.

Type Lys48 polyubiquitination on Lys670 is done by DTX4 and is responsible for the degradation of the protein, since this type of polyubiquitination is recognized by the proteasome.

Signalling pathwaysSignalling pathways

Diagram of the IFN pathway.

Inflammatory responseInflammatory response

The inflammatory response begin with the formation of the complex TBK1-TANK-TRAF. That allows phosphorylation of IRF3, IRF7 and DDX3X. Then these phosphorylated proteins form homodimers and they are translocated into the nucleus, where they activate transcription of interferon regulatory factors (IFN). Interferons are proteins synthetized in response to recognition of pathogen. They can interact with viral replication and inhibit it.

Anti-apoptosisAnti-apoptosis

The complex TBK1-TANK-TRAF phosphorylates an inhibitor of NFkappaB, which inactivates it. This finally activates NFkappaB, an anti-apoptotic transcription factor.

DiseasesDiseases

Interaction with viral proteins :

TBK1 is the target of some viral proteins such as VP35 from Ebola virus , or the P protein from Borna virus. Those proteins inhibit TBK1. Normally, TBK1 is responsible for virus-induced phosphorylations that lead to the cellular antiviral state. Therefore, the inhibition of the kinase prevents the establishment of such a cellular state. Since TBK1 is involved into the virus entrance following reaction, targeting TBK1 is a great solution for the viruses to prevent the reactions from the cell.

Oncology :

In case of some cancers, the permanent activation of TBK1 may be responsible of the proliferation of the cancerous cells. Since the substrates of TBK1 are involved in the proliferation pathway when phosphorylated, this permanent activation is a reason of the non apoptosis state of cells, and therefore of their proliferation.

Additional 3D structures of TBK1Additional 3D structures of TBK1

4IW0, 4IWP, 4IWQ, 4IWO : mechanism of activation

4IM0, 4IM2, 4IM3 : global structure

4EFO : structure of the ULD

4EUT, 4EUU : structure of the kinase domain, with a phosphorylated S172 or an unphosphorylated one

See AlsoSee Also

Interferon regulatory factor IRF3 and IRF7, 2i4i : DDX3X, IKKB, 2p8e : PPM1B, DTX4, TANK,

ReferencesReferences

TBK1 in UniprotKB

Cell Reports, Volume 3, Issue 3, 747-758, 28 February 2013 [1]

ContributorsContributors

Léa Faivre , Gaëlle Gillet