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Perturbations that derail the proper folding and assembly of proteins in the endoplasmic reticulum (ER) lead to misfolded protein accrual in the ER-a toxic condition known as ER stress. The unfolded protein response (UPR) is a signaling system evolved to detect and rectify ER stress. IRE1 is the most ancient member of the ER stress transducers and is conserved in all eukaryotes. In response to ER stress, IRE1 activates a UPR-dedicated transcription factor called X-box binding protein 1 (XBP1) in metazoans (or HAC1 in yeast) to bolster the productive capacity of the ER and purge misfolded proteins from the ER. To activate XBP1/HAC1, IRE1 cleaves XBP1/HAC1 mRNA twice to eliminate an inhibitory intron using a dormant nuclease function in its cytoplasmic effector region (IRE1(cyto)). Recent structural, molecular, and chemical biological approaches have greatly advanced our molecular understanding of how IRE1 transduces ER stress. Here we highlight a sampling of these advances with a bias toward structure and the insights they provide. We also propose a set of principles for IRE1 chemical modulation that may assist in the development of tools to better understand how IRE1 function contributes to health and disease and perhaps ultimately the development of new methods of therapeutic intervention., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Signaling in the most conserved branch of the endoplasmic reticulum (ER) unfolded protein response (UPR) is initiated by sequence-specific cleavage of the HAC1/XBP1 mRNA by the ER stress-induced kinase-endonuclease IRE1. We have discovered that the flavonol quercetin activates yeast IRE1's RNase and potentiates activation by ADP, a natural activating ligand that engages the IRE1 nucleotide-binding cleft. Enzyme kinetics and the structure of a cocrystal of IRE1 complexed with ADP and quercetin reveal engagement by quercetin of an unanticipated ligand-binding pocket at the dimer interface of IRE1's kinase extension nuclease (KEN) domain. Analytical ultracentrifugation and crosslinking studies support the preeminence of enhanced dimer formation in quercetin's mechanism of action. These findings hint at the existence of endogenous cytoplasmic ligands that may function alongside stress signals from the ER lumen to modulate IRE1 activity and at the potential for the development of drugs that modify UPR signaling from this unanticipated site., (Copyright 2010 Elsevier Inc. All rights reserved.)

Ire1 is an ancient transmembrane sensor of ER stress with dual protein kinase and ribonuclease activities. In response to ER stress, Ire1 catalyzes the splicing of target mRNAs in a spliceosome-independent manner. We have determined the crystal structure of the dual catalytic region of Ire1at 2.4 A resolution, revealing the fusion of a domain, which we term the KEN domain, to the protein kinase domain. Dimerization of the kinase domain composes a large catalytic surface on the KEN domain which carries out ribonuclease function. We further show that signal induced trans-autophosphorylation of the kinase domain permits unfettered binding of nucleotide, which in turn promotes dimerization to compose the ribonuclease active site. Comparison of Ire1 to a topologically disparate ribonuclease reveals the convergent evolution of their catalytic mechanism. These findings provide a basis for understanding the mechanism of action of RNaseL and other pseudokinases, which represent 10% of the human kinome.