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Structures of human insulin-degrading enzyme reveal a new substrate recognition mechanism

Abstract

Insulin-degrading enzyme (IDE), a Zn2+-metalloprotease, is involved in the clearance of insulin and amyloid-β (refs 1–3). Loss-of-function mutations of IDE in rodents cause glucose intolerance and cerebral accumulation of amyloid-β, whereas enhanced IDE activity effectively reduces brain amyloid-β (refs 4–7). Here we report structures of human IDE in complex with four substrates (insulin B chain, amyloid-β peptide (1–40), amylin and glucagon). The amino- and carboxy-terminal domains of IDE (IDE-N and IDE-C, respectively) form an enclosed cage just large enough to encapsulate insulin. Extensive contacts between IDE-N and IDE-C keep the degradation chamber of IDE inaccessible to substrates. Repositioning of the IDE domains enables substrate access to the catalytic cavity. IDE uses size and charge distribution of the substrate-binding cavity selectively to entrap structurally diverse polypeptides. The enclosed substrate undergoes conformational changes to form β-sheets with two discrete regions of IDE for its degradation. Consistent with this model, mutations disrupting the contacts between IDE-N and IDE-C increase IDE catalytic activity 40-fold. The molecular basis for substrate recognition and allosteric regulation of IDE could aid in designing IDE-based therapies to control cerebral amyloid-β and blood sugar concentrations1,8,9.

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Figure 1: Overall structure of IDE-E111Q in complex with insulin B chain.
Figure 2: Interaction of IDE with its substrates.
Figure 3: Conformational switch of IDE.
Figure 4: Conformational changes and catalysis of IDE substrates.

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Acknowledgements

We thank the staff of APS SBC 19-ID and Biocars 14-BM-C, P. Li and Q. Guo for help with data collection; M. Manolopoulou for help with protein purification; H. Im for help with IDE enzymatic assays; D. Wolfgeher for help with mass spectrometry; E. Johnson for providing the synthetic Aβ(1–42) peptide; and R. Bourdeau for critically reading the manuscript. This research was supported by NIH and The University of Chicago Diabetes Center grants to W.T. Author Contributions W.T. designed the experiments and Y.S. conducted all experiments. W.T. and Y.S. analysed the results and co-wrote the paper. All authors discussed the results and commented on the manuscript.

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Correspondence to Wei-Jen Tang.

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Coordinates of the X-ray structures of the substrate-bound IDE have been deposited in the RCSB Protein Data Bank under accession code 2G54 (Zn2+-IDE–insulin-B-chain), 2G56 (Zn2+-free IDE–insulin-B-chain), 2G47 (IDE–Aβ(1–40)), 2G48 (IDE–amylin) and 2G49 (IDE–glucagon). Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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Supplementary Figures 1–16 and Supplementary Tables 1–2. (PDF 2833 kb)

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Shen, Y., Joachimiak, A., Rich Rosner, M. et al. Structures of human insulin-degrading enzyme reveal a new substrate recognition mechanism. Nature 443, 870–874 (2006). https://doi.org/10.1038/nature05143

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