Molecular mechanisms of human IRE1 activation through dimerization and ligand binding

Joshi, Amar; Newbatt, Yvette; McAndrew, P.C.; Stubbs, Mark; Burke, Rosemary; Richards, Mark W.; Bhatia, Chitra; Caldwell, John; McHardy, T.; Collins, Ian; Bayliss, Richard

doi:10.18632/oncotarget.3864

Cited by 53 publications

(73 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The lack of IRE1a dimer structure here could be due to the compound either preventing dimerization or stabilizing a monomeric form of IRE1a. While it was previously suggested that dimerization/oligomerization occurs after autophosphorylation, recent crystal structures of dephosphorylated human IRE1a dimers demonstrate that dimerization can precede phosphorylation in both face-to-face and back-to-back configurations (Ali et al, 2011;Joshi et al, 2015). It should also be noted that this molecule shifted the aC-helix out.…”

Section: Discussionmentioning

confidence: 90%

“…Despite this, the imidazopyridine molecule, compound 3, interacts with the hinge and the activation loop (DFG-in) in a similar fashion as staurosporine (r.m.s. on Ca 5 0.9 Å) and behaves as a type I kinase inhibitor (Joshi et al, 2015). GSK2850163 and compound 3 do not occupy overlapping pockets.…”

Section: Discussionmentioning

confidence: 97%

“…Specifically, the IRE1a/XBP 1 pathway has shown to be overexpressed in a variety of human cancers, and activation of the pathway has been shown to be essential for the survival of highly secretory multiple myeloma cells, where the protein load is high (Feldman et al, 2005;Koong et al, 2006;Carrasco et al, 2007). These key findings, coupled with the possibility to modulate IRE1a activity via targeting two potentially druggable domains, has made IRE1a a very attractive target in drug discovery (Hetz et al, 2013;Harrington et al, 2014;Maly and Papa, 2014;Sanches et al, 2014;Joshi et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Here, no dimers were found with the inhibitor-bound structure, suggesting that the compound may either prevent dimerization or stabilize a monomeric IRE1a. The second report presented two back-to-back dimers of IRE1a, one in the apo form and one in an inhibitor-bound form (PDB ID 4Z7G and 4Z7H;Joshi et al, 2015). These structures are consistent with yeast Ire1 dimers, but are distinct in that the apo structure contains a twisted interface between the dimers across the RNase domains, which may represent an additional intermediate of IRE1a prior to full activation.…”

Section: Introductionmentioning

confidence: 87%

See 3 more Smart Citations

Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1αEndoribonuclease Activity

et al. 2015

View full text Add to dashboard Cite

Activation of the inositol-requiring enzyme-1 alpha (IRE1a) protein caused by endoplasmic reticulum stress results in the homodimerization of the N-terminal endoplasmic reticulum luminal domains, autophosphorylation of the cytoplasmic kinase domains, and conformational changes to the cytoplasmic endoribonuclease (RNase) domains, which render them functional and can lead to the splicing of X-box binding protein 1 (XBP 1) mRNA. Herein, we report the first crystal structures of the cytoplasmic portion of a human phosphorylated IRE1a dimer in complex with (R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro(4.5)decane-7-carboxamide, a novel, IRE1a-selective kinase inhibitor, and staurosporine, a broad spectrum kinase inhibitor. (R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro(4.5)decane-7-carboxamide inhibits both the kinase and RNase activities of IRE1a. The inhibitor interacts with the catalytic residues Lys599 and Glu612 and displaces the kinase activation loop to the DFG-out conformation. Inactivation of IRE1a RNase activity appears to be caused by a conformational change, whereby the aC helix is displaced, resulting in the rearrangement of the kinase domain-dimer interface and a rotation of the RNase domains away from each other. In contrast, staurosporine binds at the ATP-binding site of IRE1a, resulting in a dimer consistent with RNase active yeast Ire1 dimers. Activation of IRE1a RNase activity appears to be promoted by a network of hydrogen bond interactions between highly conserved residues across the RNase dimer interface that place key catalytic residues poised for reaction. These data implicate that the intermolecular interactions between conserved residues in the RNase domain are required for activity, and that the disruption of these interactions can be achieved pharmacologically by small molecule kinase domain inhibitors.

show abstract

Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 87%

See 2 more Smart Citations

Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1αEndoribonuclease Activity

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Tyr628, the β4--strand component of the R--spine equivalent to Nek7 Tyr97, is in the down position and forms a H--bond with the activation loop at Asp711 of the DFG--motif. In contrast, the human kinase--RNase domain crystallized in apo--form exhibited a pre--active kinase conformation, in which the R--spine and Lys--Glu salt bridges are assembled, but the unphosphorylated activation loop is disordered ( Figure 5B) [52]. Mutation of Tyr628 to phenylalanine increases the autophosphorylation rate, suggesting that the Tyr--down conformation captured in the structure of ADP--bound human IRE1 is a genuine autoinhibitory state [52].…”

Section: Tyr--down Autoinhibitory Mechanism In Ire1mentioning

confidence: 97%

The Ys and wherefores of protein kinase autoinhibition

Bayliss

Haq

Yeoh

2015

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Self Cite

View full text Add to dashboard Cite

Protein phosphorylation is a key reaction in the regulation of cellular events and is catalyzed by over 500 protein kinases in humans. The activities of protein kinases are strictly controlled through a diverse set of mechanisms. Structural studies have shown that the conformation adopted by kinases in their active state are highly similar, whereas inactive kinases can adopt a variety of conformations. Many kinases are maintained in a catalytically inactive state through autoinhibition. This involves a conformation of the kinase active site that is unable to support catalysis and requires activation through a signal such as binding of a regulatory protein. In this review, we briefly summarize some of the well--established autoinhibitory mechanisms and then focus on a relatively unexplored mode of autoinhibition that was first discovered in the Nek family of kinases and is also relevant to IRE1. This involves a tyrosine side--chain that blocks the active site and which must undergo a conformational change to enable kinase activity. We have termed this the Tyr--down autoinhibitory mechanism. We summarise the evidence for this mechanism and describe its role in kinase inhibitor design. Finally, we survey the kinome to identify other kinases with the potential to be governed by an autoinhibitory Tyr--down mechanism.

show abstract

Emerging roles of the αC‐β4 loop in protein kinase structure, function, evolution, and disease

2020

View full text Add to dashboard Cite

The faithful propagation of cellular signals in most organisms relies on the coordinated functions of a large family of protein kinases that share a conserved catalytic domain. The catalytic domain is a dynamic scaffold that undergoes large conformational changes upon activation. Most of these conformational changes, such as movement of the regulatory αC-helix from an "out"to "in" conformation, hinge on a conserved, but understudied, loop termed the αC-β4 loop, which mediates conserved interactions to tether flexible structural elements to the kinase core. We previously showed that the αC-β4 loop is a unique feature of eukaryotic protein kinases. Here, we review the emerging roles of this loop in kinase structure, function, regulation, and diseases. Through a kinome-wide analysis, we define the boundaries of the loop for the first time and show that sequence and structural variation in the loop correlate with conformational and regulatory variation. Many recurrent disease mutations map to the αC-β4 loop and contribute to drug resistance and abnormal kinase activation by relieving key auto-inhibitory interactions associated with αC-helix and interlobe movement. The αC-β4 loop is a hotspot for post-translational modifications, protein-protein interaction, and Hsp90 mediated folding. Our kinome-wide analysis provides insights for hypothesis-driven characterization of understudied kinases and the development of allosteric protein kinase inhibitors.

show abstract

Molecular mechanisms of human IRE1 activation through dimerization and ligand binding

Cited by 53 publications

References 44 publications

Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1αEndoribonuclease Activity

Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1αEndoribonuclease Activity

The Ys and wherefores of protein kinase autoinhibition

Emerging roles of the αC‐β4 loop in protein kinase structure, function, evolution, and disease

Contact Info

Product

Resources

About