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PDBsum entry 2wc0

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protein ligands metals Protein-protein interface(s) links
Hydrolase/hormone PDB id
2wc0
Jmol
Contents
Protein chains
953 a.a. *
21 a.a. *
20 a.a. *
Ligands
DIO ×8
Metals
_ZN ×2
Waters ×360
* Residue conservation analysis
PDB id:
2wc0
Name: Hydrolase/hormone
Title: Crystal structure of human insulin degrading enzyme in complex with iodinated insulin
Structure: Insulin-degrading enzyme. Chain: a, b. Fragment: residues 42-1019. Synonym: insulin protease, insulysin, insulinase. Engineered: yes. Mutation: yes. Insulin a chain. Chain: c, e. Fragment: residues 90-110.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606
Resolution:
2.80Å     R-factor:   0.172     R-free:   0.220
Authors: M.Manolopoulou,Q.Guo,E.Malito,A.B.Schilling,W.J.Tang
Key ref:
M.Manolopoulou et al. (2009). Molecular Basis of Catalytic Chamber-assisted Unfolding and Cleavage of Human Insulin by Human Insulin-degrading Enzyme. J Biol Chem, 284, 14177-14188. PubMed id: 19321446 DOI: 10.1074/jbc.M900068200
Date:
06-Mar-09     Release date:   24-Mar-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14735  (IDE_HUMAN) -  Insulin-degrading enzyme
Seq:
Struc:
 
Seq:
Struc:
1019 a.a.
953 a.a.*
Protein chains
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
21 a.a.
Protein chains
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
20 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.4.24.56  - Insulysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Degradation of insulin, glucagon and other polypeptides. No action on proteins.
      Cofactor: Zinc
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   12 terms 
  Biological process     metabolic process   19 terms 
  Biochemical function     catalytic activity     21 terms  

 

 
DOI no: 10.1074/jbc.M900068200 J Biol Chem 284:14177-14188 (2009)
PubMed id: 19321446  
 
 
Molecular Basis of Catalytic Chamber-assisted Unfolding and Cleavage of Human Insulin by Human Insulin-degrading Enzyme.
M.Manolopoulou, Q.Guo, E.Malito, A.B.Schilling, W.J.Tang.
 
  ABSTRACT  
 
Insulin is a hormone vital for glucose homeostasis, and insulin-degrading enzyme (IDE) plays a key role in its clearance. IDE exhibits a remarkable specificity to degrade insulin without breaking the disulfide bonds that hold the insulin A and B chains together. Using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to obtain high mass accuracy, and electron capture dissociation (ECD) to selectively break the disulfide bonds in gas phase fragmentation, we determined the cleavage sites and composition of human insulin fragments generated by human IDE. Our time-dependent analysis of IDE-digested insulin fragments reveals that IDE is highly processive in its initial cleavage at the middle of both the insulin A and B chains. This ensures that IDE effectively splits insulin into inactive N- and C-terminal halves without breaking the disulfide bonds. To understand the molecular basis of the recognition and unfolding of insulin by IDE, we determined a 2.6-A resolution insulin-bound IDE structure. Our structure reveals that IDE forms an enclosed catalytic chamber that completely engulfs and intimately interacts with a partially unfolded insulin molecule. This structure also highlights how the unique size, shape, charge distribution, and exosite of the IDE catalytic chamber contribute to its high affinity ( approximately 100 nm) for insulin. In addition, this structure shows how IDE utilizes the interaction of its exosite with the N terminus of the insulin A chain as well as other properties of the catalytic chamber to guide the unfolding of insulin and allowing for the processive cleavages.
 
  Selected figure(s)  
 
Figure 3.
Structure of insulin-bound IDE. A, global view of the structure of insulin-bound IDE-CF-E111Q monomer. IDE domains 1–4 (IDE-D1 to IDE-D4) are colored green, blue, yellow, and red, respectively. Insulin A and B chains are colored magenta and cyan, respectively. The zinc ion is colored gray. B, composite omit map of insulin contoured at 1.5σ. C, electrostatic surface representation of insulin and IDE. The molecular surface is color-coded as calculated by Adaptive Poisson-Boltzmann Solver. The molecular surface is colored as calculated by Adaptive Poisson-Boltzmann Solver (51) (<–6 kT in red, 0 kT in white, and >+6 kT in blue). The interaction surface between the N- and C-terminal domains of IDE and insulin is marked by yellow dashed lines based on the contact residues displayed using CCP4 molecular graphics (30).
Figure 4.
Characterization of the IDE-insulin interaction. A, details of the interaction between insulin and IDE. Additional hydrogen bond networks are shown in the three right panels for clarity. IDE and insulin are colored as in Fig. 3. B, comparison of insulin in its free T-state form (PDB code 1G7A) and IDE-bound form. C, comparison of surface charge distribution of the partially unfolded insulin in insulin-bound IDE with T-state insulin modeled into the catalytic chamber of IDE. Surface representation of the substrate binding chamber of IDE was generated by the software Voidoo (31). The outer surface of IDE and the substrate chamber are colored pale green and dark green. The electrostatic surface representations of the IDE-bound insulin and T-state insulin models are calculated by Adaptive Poisson-Boltzmann Solver. D, comparison of IDE-bound insulin structure with the solution structures of insulin Ala^A2-DKP. Insulin Ala^A2-DKP has an Ile to Ala mutation in A2 residue of insulin-DKP, which is an engineered monomeric insulin. Left shows the comparison of IDE-bound insulin (colored in red and salmon for insulin A and B chain, respectively) with an exemplary NMR structure of insulin Ala^A2-DKP (PDB code 1K3M; colored in green and lime green for insulin A and B chain, respectively), and an exemplary NMR structure of insulin-DKP (PDB code 2JMN; colored in blue and light blue for insulin A and B chain, respectively). For a fair comparison, solution structures of insulin Ala^A2-DKP and insulin-DKP are also shown in the middle and right, respectively.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 14177-14188) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20498699 M.A.Leissring, E.Malito, S.Hedouin, L.Reinstatler, T.Sahara, S.O.Abdul-Hay, S.Choudhry, G.M.Maharvi, A.H.Fauq, M.Huzarska, P.S.May, S.Choi, T.P.Logan, B.E.Turk, L.C.Cantley, M.Manolopoulou, W.J.Tang, R.L.Stein, G.D.Cuny, and D.J.Selkoe (2010).
Designed inhibitors of insulin-degrading enzyme regulate the catabolism and activity of insulin.
  PLoS One, 5, e10504.
PDB code: 3e4a
20959807 M.Ren, Q.Guo, L.Guo, M.Lenz, F.Qian, R.R.Koenen, H.Xu, A.B.Schilling, C.Weber, R.D.Ye, A.R.Dinner, and W.J.Tang (2010).
Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme.
  EMBO J, 29, 3952-3966.
PDB codes: 2x69 2x6g 2x6l
19896952 Q.Guo, M.Manolopoulou, Y.Bian, A.B.Schilling, and W.J.Tang (2010).
Molecular basis for the recognition and cleavages of IGF-II, TGF-alpha, and amylin by human insulin-degrading enzyme.
  J Mol Biol, 395, 430-443.
PDB codes: 2wk3 3e4z 3e50 3hgz
19808678 L.A.Ralat, M.Ren, A.B.Schilling, and W.J.Tang (2009).
Protective role of Cys-178 against the inactivation and oligomerization of human insulin-degrading enzyme by oxidation and nitrosylation.
  J Biol Chem, 284, 34005-34018.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.