4LTE | pdb_00004lte

Structure of Cysteine-free Human Insulin Degrading Enzyme in Complex with Macrocyclic Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4LTE/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-07-23 Released: 2014-05-21 
• Deposition Author(s): Foda, Z.H., Seeliger, M.A., Saghatelian, A., Liu, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones.

Maianti, J.P., McFedries, A., Foda, Z.H., Kleiner, R.E., Du, X.Q., Leissring, M.A., Tang, W.J., Charron, M.J., Seeliger, M.A., Saghatelian, A., Liu, D.R.

(2014) Nature 511: 94-98

• PubMed: 24847884 
• DOI: https://doi.org/10.1038/nature13297
• Primary Citation Related Structures: 
  4LTE


• PubMed Abstract: 
  

  Despite decades of speculation that inhibiting endogenous insulin degradation might treat type-2 diabetes, and the identification of IDE (insulin-degrading enzyme) as a diabetes susceptibility gene, the relationship between the activity of the zinc metalloprotein IDE and glucose homeostasis remains unclear. Although Ide(-/-) mice have elevated insulin levels, they exhibit impaired, rather than improved, glucose tolerance that may arise from compensatory insulin signalling dysfunction. IDE inhibitors that are active in vivo are therefore needed to elucidate IDE's physiological roles and to determine its potential to serve as a target for the treatment of diabetes. Here we report the discovery of a physiologically active IDE inhibitor identified from a DNA-templated macrocycle library. An X-ray structure of the macrocycle bound to IDE reveals that it engages a binding pocket away from the catalytic site, which explains its remarkable selectivity. Treatment of lean and obese mice with this inhibitor shows that IDE regulates the abundance and signalling of glucagon and amylin, in addition to that of insulin. Under physiological conditions that augment insulin and amylin levels, such as oral glucose administration, acute IDE inhibition leads to substantially improved glucose tolerance and slower gastric emptying. These findings demonstrate the feasibility of modulating IDE activity as a new therapeutic strategy to treat type-2 diabetes and expand our understanding of the roles of IDE in glucose and hormone regulation.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.
Department of Pharmacological Sciences, Stony Brook University, 1 Circle Road, Stony Brook, New York 11794, USA.
Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, 3204 Biological Sciences III, Irvine, California 92697, USA.
Ben-May Department for Cancer Research, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.
1] Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 228.6 kDa 
• Atom Count: 16,216 
• Modeled Residue Count: 1,912 
• Deposited Residue Count: 1,962 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	978	Homo sapiens	Mutation(s): 14  Gene Names: IDE EC: 3.4.24.56
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens) Explore P14735  Go to UniProtKB:  P14735
PHAROS:  P14735 GTEx:  ENSG00000119912

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrocyclic Inhibitor	C [auth M], D [auth N]	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
LYN	I [auth M], K [auth N]	2,6-DIAMINO-HEXANOIC ACID AMIDE C6 H16 N3 O HKXLAGBDJVHRQG-YFKPBYRVSA-O
FUM	J [auth M], L [auth N]	FUMARIC ACID C4 H4 O4 VZCYOOQTPOCHFL-OWOJBTEDSA-N
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 261.973	α = 90
b = 261.973	β = 90
c = 90.775	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
autoPROC	data scaling
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Foda, Z.H., Seeliger, M.A., Saghatelian, A., Liu, D.R.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-06-25
  Changes: Database references
• Version 1.2: 2014-07-23
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.0: 2024-04-24
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary