Structural Biology

Dimerization as a Drug Target

Science Signaling  27 Apr 2010:
Vol. 3, Issue 119, pp. ec123
DOI: 10.1126/scisignal.3119ec123

Inositol-requiring enzyme 1 (IRE1) is an endoplasmic reticulum (ER) transmembrane protein with kinase and RNase activities that is critical in the unfolded protein response (UPR). Homologs of yeast IRE1 are also present in vertebrates. Unfolded proteins induce dimerization of IRE1 and trigger trans-autophosphorylation of the activation loop, which promotes ATP or ADP binding to the active site cleft of the kinase domain. Nucleotide binding stabilizes the dimer along an interface that includes the kinase domain and the RNase domain, known as the kinase extension nuclease (KEN) domain. The RNase portion of IRE1 then activates the transcription factor X-box binding protein 1 (XBP1) through alternative splicing. Wiseman et al. found that the flavonol quercetin increased the RNase activity of purified IRE1 toward a fluorescently labeled XBP1-based substrate in vitro. Coincubation of IRE1 with quercetin and ADP further increased IRE1 RNase activity over incubation with quercetin or ADP, suggesting that quercetin did not bind to the nucleotide binding site. An IRE1 construct (amino acids 658–1115) bound to ADP crystallizes as a dimer that contains two disordered regions encompassing parts of the activation loop and the KEN domain. In contrast, Wiseman et al. found that these regions were ordered in the crystal structure of IRE1(658-1115), ADP, and quercetin. Furthermore, a pair of quercetin molecules bound to the interface between the dimerized KEN domains, which the authors named the Q-site, and stabilized the IRE1 dimer. Purified forms of IRE1 with mutations in residues in the Q-site did not show increased RNase activity in response to quercetin. Mutations in Q-site residues Ser984 or Lys985 in IRE1 prevented quercetin from increasing the abundance of spliced XBP1 in mouse embryonic fibroblasts. The authors suggest that endogenous compounds might target the Q-site, and in the accompanying commentary, Shokat notes that drugs targeting the Q-site could be used to treat diseases associated with reduced abundance of spliced XBP1, such as inflammatory bowel disease.

R. L. Wiseman, Y. Zhang, K. P. K. Lee, H. P. Harding, C. M. Haynes, J. Price, F. Sicheri, D. Ron, Flavonol activation defines an unanticipated ligand-binding site in the kinase-RNase domain of IRE1. Mol. Cell 38, 291–304 (2010). [Online Journal]

K. M. Shokat, A drug-drug interaction crystallizes a new entry point into the UPR. Mol. Cell 38, 161–163 (2010). [Online Journal]