3BG4

The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor.

Kim, H.Chu, T.T.T.Kim, D.Y.Kim, D.R.Nguyen, C.M.T.Choi, J.Lee, J.R.Hahn, M.J.Kim, K.K.

(2008) J.Mol.Biol. 376: 184-192

  • DOI: 10.1016/j.jmb.2007.11.089

  • PubMed Abstract: 
  • Guamerin, a canonical serine protease inhibitor from Hirudo nipponia, was identified as an elastase-specific inhibitor and has potential application in various diseases caused by elevated elastase concentration. However, the application of guamerin i ...

    Guamerin, a canonical serine protease inhibitor from Hirudo nipponia, was identified as an elastase-specific inhibitor and has potential application in various diseases caused by elevated elastase concentration. However, the application of guamerin is limited because it also shows inhibitory activity against other proteases. To improve the selectivity of guamerin as an elastase inhibitor, it is essential to understand the binding mode of the inhibitor to elastase and to other proteases. For this purpose, we determined the crystal structure of guamerin in complex with chymotrypsin at 2.5 A resolution. The binding mode of guamerin on elastase was explored from the model structure of guamerin/elastase. Guamerin binds to the hydrophobic pocket of the protease in a substrate-like manner using its binding loop. In order to improve the binding selectivity of guamerin to elastase, several residues in the binding loop were mutated and the inhibitory activities of the mutants against elastase and chymotrypsin were monitored. The substitution of the Met36 residue for Ala in the P1 site increased the inhibitory activity against elastase up to 14-fold, while the same mutant showed 7-fold decreased activity against chymotrypsin compared to the wild-type guamerin. Furthermore, the M36A guamerin mutant more effectively protected endothelial cells against cell damage caused by elastase than the wild-type guamerin.


    Organizational Affiliation

    Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chymotrypsin A chain A
A
13Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00767 (Bos taurus)
Go to UniProtKB:  P00767
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chymotrypsin A chain B
B
131Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chymotrypsin A chain C
C
97Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Guamerin
D
57Hirudo nipponiaMutation(s): 0 
Find proteins for P46443 (Hirudo nipponia)
Go to UniProtKB:  P46443
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.274α = 90.00
b = 43.992β = 90.00
c = 122.570γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
EPMRphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance