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[[Image:Tbk1.jpg|400px|left|thumb| 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. | 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 structure= | =Overall structure= | ||
< | <Structure load='4IW0' size='500' frame='true' align='right' caption='TBK1 monomer (PDB entry 4IW0)' scene='56/568025/Vide/1' /> | ||
==Protomer== | ==Protomer== | ||
[[Image:Lobes.jpg|400px|left|thumb| Structure of the KD domain in TBK1. <ref name="transact" />]] | |||
'''Kinase domain :''' ( <scene name='56/568025/Kd/1'>KD</scene> ) from amino acid 9 to amino acid 310: the active site is at the interface of the N- and C-terminal lobes. | '''Kinase domain :''' (<scene name='56/568025/Kd/1'>KD</scene>) 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. | 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. | 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. | The DFG (Asp-Phe-Gly) motif and Ser172 are involved in the regulation of the kinase activity. | ||
'''Ubiquitin-like domain :''' ( <scene name='56/568025/Uld/ | '''Ubiquitin-like domain :''' (<scene name='56/568025/Uld/2'>ULD</scene>) 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 '''<scene name='56/568025/Lz/1'>leucine zipper</scene> ''' (between amino acid 408 and amino acid 651) and the '''coiled coil domain ''' (between amino acid | The '''<scene name='56/568025/Lz/1'>leucine zipper</scene> ''' (between amino acid 408 and amino acid 651) and the '''<scene name='56/568025/Coiledcoil/1'>coiled coil domain</scene>''' (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. | ||
'''ATP binding domain :''' 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. | '''<scene name='56/568025/Atp/1'>ATP binding domain</scene>:''' 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 | The KD and the ULD interact with each other: the ULD with the C-lobe of the KD. There is a <scene name='56/568025/Kd-ubl_interactions/2'>hydrogen bound</scene> between Tyr325 in the ULD and Glu109 in the KD. Moreover <scene name='56/568025/Kd-ubl_interactions/1'>Lys323</scene> in the ULD makes favourable electrostatic interactions with Glu109-KD. | ||
==Dimer== | ==Dimer== | ||
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 salt bridge 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 | There are several hydrogen bonds between the KD (N- and C-lobes) and the SDD of the opposite subunit: a | ||
<scene name='56/568025/33-589/2'>salt bridge</scene> 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 “ | |||
<scene name='56/568025/Egr-seq/1'>EGR</scene>” 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 modifications= | =Possible residue modifications= | ||
Several residues of TBK1 can be modified, by phosphorylation or polyubiquitination. | Several residues of TBK1 can be modified, by phosphorylation or polyubiquitination. | ||
'''Phosphorylation :''' <scene name='56/568025/Ser172/2'>Ser172</scene> belongs to the kinase domain and can be phosphorylated by TBK1 itself, or by another serine kinase. This phosphorylation modifies the conformation of the <scene name='56/568025/Activation_loop/1'>kinase activation loop</scene> (residues L164-G199), making the binding of the substrate possible. When S172 is not phosphorylated, the <scene name='56/568025/Hpd/1'>HPD motif</scene> can dock itself between two αhelix of the kinase domain of another promoter. Furthermore, an <scene name='56/568025/Helix/1'>helix</scene> 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 <scene name='56/568025/Dfg/1'>DFG</scene> domain. This liberates the active site of the other protomer, which can now bind a substrate. <ref name="transact">PMID:22619329</ref> | '''Phosphorylation :''' <scene name='56/568025/Ser172/2'>Ser172</scene> belongs to the kinase domain and can be phosphorylated by TBK1 itself, or by another serine kinase. This phosphorylation modifies the conformation of the <scene name='56/568025/Activation_loop/1'>kinase activation loop</scene> (residues L164-G199), making the binding of the substrate possible. When S172 is not phosphorylated, the <scene name='56/568025/Hpd/1'>HPD motif</scene> can dock itself between two αhelix of the kinase domain of another promoter. Furthermore, an <scene name='56/568025/Helix/1'>helix</scene> 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 <scene name='56/568025/Dfg/1'>DFG</scene> domain. This liberates the active site of the other protomer, which can now bind a substrate. <ref name="transact">PMID:22619329</ref> | ||
[[Image:Dimere.jpg|400px|left|thumb| When S172 isn't phosphorylated, the activation loop binds to the active site of another protomer, providing the phosphorylation of substrates. <ref name="transact" />]] | |||
[[Image:Activationloop2.jpg|400px|center|thumb| 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. <ref name="transact" />]] | |||
[[Image:transactivation.jpg|400px|left|thumb| Hypothecal diagram of the transactivation mechanism of TBK1. <ref name="transact" />]] | |||
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. <ref name="transact" /> | 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. <ref name="transact" /> | ||
S172 can also be phosphorylated by kinases such as IKKB (also known as IKBKB), and dephosphorylated by phosphatases such as PPM1B. | 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 | '''Polyubiquitination :''' Polyubiquitination in a Lys63 manner on | ||
<scene name='56/568025/K30/1'>Lys30</scene> helps the activation of the kinase. The same type of modification on <scene name='56/568025/K401/1'>Lys401</scene> is responsible for dimerization. Type Lys48 polyubiquitination on Lys670 is done by DTX4 and is responsible for the degradation of the protein. | <scene name='56/568025/K30/1'>Lys30</scene> helps the activation of the kinase. The same type of modification on <scene name='56/568025/K401/1'>Lys401</scene> 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 pathways = | = Signalling pathways = | ||
[[Image:IFN.jpg|400px|left|thumb| Diagram of the IFN pathway.]] | |||
== Inflammatory response == | == Inflammatory 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). | 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-apoptosis == | == Anti-apoptosis == | ||
The complex TBK1-TANK-TRAF phosphorylates an inhibitor of NFkappaB, which inactivates it. This finally activates NFkappaB, an anti-apoptotic transcription factor. | |||
= Diseases = | = Diseases = | ||