Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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


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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.


  1. Duckworth, W. C., Bennett, R. G. & Hamel, F. G. Insulin degradation: progress and potential. Endocr. Rev. 19, 608–624 (1998)

    CAS  PubMed  Google Scholar 

  2. Kurochkin, I. V. Insulin-degrading enzyme: embarking on amyloid destruction. Trends Biochem. Sci. 26, 421–425 (2001)

    Article  CAS  Google Scholar 

  3. Bennett, R. G., Duckworth, W. C. & Hamel, F. G. Degradation of amylin by insulin-degrading enzyme. J. Biol. Chem. 275, 36621–36625 (2000)

    Article  CAS  Google Scholar 

  4. Farris, W. et al. Insulin-degrading enzyme regulates the levels of insulin, amyloid β-protein, and the β-amyloid precursor protein intracellular domain in vivo.. Proc. Natl Acad. Sci. USA 100, 4162–4167 (2003)

    Article  ADS  CAS  Google Scholar 

  5. Farris, W. et al. Partial loss-of-function mutations in insulin-degrading enzyme that induce diabetes also impair degradation of amyloid β-protein. Am. J. Pathol. 164, 1425–1434 (2004)

    Article  CAS  Google Scholar 

  6. Leissring, M. A. et al. Enhanced proteolysis of β-amyloid in APP transgenic mice prevents plaque formation, secondary pathology, and premature death. Neuron 40, 1087–1093 (2003)

    Article  CAS  Google Scholar 

  7. Miller, B. C. et al. Amyloid-β peptide levels in brain are inversely correlated with insulin activity levels in vivo.. Proc. Natl Acad. Sci. USA 100, 6221–6226 (2003)

    Article  ADS  CAS  Google Scholar 

  8. Selkoe, D. J. Clearing the brain’s amyloid cobwebs. Neuron 32, 177–180 (2001)

    Article  CAS  Google Scholar 

  9. Tanzi, R. E. & Bertram, L. Twenty years of the Alzheimer’s disease amyloid hypothesis: a genetic perspective. Cell 120, 545–555 (2005)

    Article  CAS  Google Scholar 

  10. Mirsky, I. A. & Broth-Kahn, R. H. The inactivation of insulin by tissue extracts. I. The distribution and properties of insulin inactivating extracts (insulinase). Arch. Biochem. 20, 1–9 (1949)

    CAS  PubMed  Google Scholar 

  11. Adames, N., Blundell, K., Ashby, M. N. & Boone, C. Role of yeast insulin-degrading enzyme homologs in propheromone processing and bud site selection. Science 270, 464–467 (1995)

    Article  ADS  CAS  Google Scholar 

  12. Fujita, A. et al. A yeast gene necessary for bud-site selection encodes a protein similar to insulin-degrading enzymes. Nature 372, 567–570 (1994)

    Article  ADS  CAS  Google Scholar 

  13. Perlman, R. K. & Rosner, M. R. Identification of zinc ligands of the insulin-degrading enzyme. J. Biol. Chem. 269, 33140–33145 (1994)

    CAS  PubMed  Google Scholar 

  14. Li, P., Kuo, W-L., Yousef, M., Rosner, M. R. & Tang, W-J. The C-terminal domain of human insulin degrading enzyme is required for the dimerization and substrate recognition. Biochem. Biophys. Res. Commun. 343, 1032–1037 (2006)

    Article  CAS  Google Scholar 

  15. Becker, A. B. & Roth, R. A. An unusual active site identified in a family of zinc metalloendopeptidases. Proc. Natl Acad. Sci. USA 89, 3835–3839 (1992)

    Article  ADS  CAS  Google Scholar 

  16. Maskos, K. in Handbook of Metalloproteins (eds Messerschmidt, A., Dode, W. & Cygler, M.) 190–198 (John Wiley & Sons, 2004)

  17. Lawrence, M. C. & Colman, P. M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946–950 (1993)

    Article  CAS  Google Scholar 

  18. Dombkowski, A. A. Disulfide by Design: a computational method for the rational design of disulfide bonds in proteins. Bioinformatics 19, 1852–1853 (2003)

    Article  CAS  Google Scholar 

  19. Song, E. S., Juliano, M. A., Juliano, L. & Hersh, L. B. Substrate activation of insulin-degrading enzyme (insulysin). A potential target for drug development. J. Biol. Chem. 278, 49789–49794 (2003)

    Article  CAS  Google Scholar 

  20. Chothia, C., Lesk, A. M., Dodson, G. G. & Hodgkin, D. C. Transmission of conformational change in insulin. Nature 302, 500–505 (1983)

    Article  ADS  CAS  Google Scholar 

  21. Sasaki, K., Dockerill, S., Adamiak, D. A., Tickle, I. J. & Blundell, T. X-ray analysis of glucagon and its relationship to receptor binding. Nature 257, 751–757 (1975)

    Article  ADS  CAS  Google Scholar 

  22. Braun, W., Wider, G., Lee, K. H. & Wuthrich, K. Conformation of glucagon in a lipid–water interphase by 1H nuclear magnetic resonance. J. Mol. Biol. 169, 921–948 (1983)

    Article  CAS  Google Scholar 

  23. Coles, M., Bicknell, W., Watson, A. A., Fairlie, D. P. & Craik, D. J. Solution structure of amyloid β-peptide(1–40) in a water–micelle environment. Is the membrane-spanning domain where we think it is?. Biochemistry 37, 11064–11077 (1998)

    Article  CAS  Google Scholar 

  24. Mascioni, A., Porcelli, F., Ilangovan, U., Ramamoorthy, A. & Veglia, G. Conformational preferences of the amylin nucleation site in SDS micelles: an NMR study. Biopolymers 69, 29–41 (2003)

    Article  CAS  Google Scholar 

  25. Sticht, H. et al. Structure of amyloid A4-(1–40)-peptide of Alzheimer’s disease. Eur. J. Biochem. 233, 293–298 (1995)

    Article  CAS  Google Scholar 

  26. Leissring, M. A. et al. Kinetics of amyloid β-protein degradation determined by novel fluorescence- and fluorescence polarization-based assays. J. Biol. Chem. 278, 37314–37320 (2003)

    Article  CAS  Google Scholar 

  27. Taylor, A. B. et al. Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. Structure 9, 615–625 (2001)

    Article  CAS  Google Scholar 

  28. Luciano, P. & Geli, V. The mitochondrial processing peptidase: function and specificity. Experientia 52, 1077–1082 (1996)

    Article  CAS  Google Scholar 

  29. La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement in the MIR and MAD methods. Methods Enzymol. 276, 472–494 (1997)

    Article  Google Scholar 

  30. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Wei-Jen Tang.

Ethics declarations

Competing interests

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 The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

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

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing