3UOU

Crystal structure of the Kunitz-type protease inhibitor ShPI-1 Lys13Leu mutant in complex with pancreatic elastase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional Structure of a Kunitz-type Inhibitor in Complex with an Elastase-like Enzyme.

Garcia-Fernandez, R.Perbandt, M.Rehders, D.Ziegelmuller, P.Piganeau, N.Hahn, U.Betzel, C.Chavez, M.A.Redecke, L.

(2015) J.Biol.Chem. 290: 14154-14165

  • DOI: 10.1074/jbc.M115.647586

  • PubMed Abstract: 
  • Elastase-like enzymes are involved in important diseases such as acute pancreatitis, chronic inflammatory lung diseases, and cancer. Structural insights into their interaction with specific inhibitors will contribute to the development of novel anti- ...

    Elastase-like enzymes are involved in important diseases such as acute pancreatitis, chronic inflammatory lung diseases, and cancer. Structural insights into their interaction with specific inhibitors will contribute to the development of novel anti-elastase compounds that resist rapid oxidation and proteolysis. Proteinaceous Kunitz-type inhibitors homologous to the bovine pancreatic trypsin inhibitor (BPTI) provide a suitable scaffold, but the structural aspects of their interaction with elastase-like enzymes have not been elucidated. Here, we increased the selectivity of ShPI-1, a versatile serine protease inhibitor from the sea anemone Stichodactyla helianthus with high biomedical and biotechnological potential, toward elastase-like enzymes by substitution of the P1 residue (Lys(13)) with leucine. The variant (rShPI-1/K13L) exhibits a novel anti-porcine pancreatic elastase (PPE) activity together with a significantly improved inhibition of human neuthrophil elastase and chymotrypsin. The crystal structure of the PPE·rShPI-1/K13L complex determined at 2.0 Å resolution provided the first details of the canonical interaction between a BPTI-Kunitz-type domain and elastase-like enzymes. In addition to the essential impact of the variant P1 residue for complex stability, the interface is improved by increased contributions of the primary and secondary binding loop as compared with similar trypsin and chymotrypsin complexes. A comparison of the interaction network with elastase complexes of canonical inhibitors from the chelonian in family supports a key role of the P3 site in ShPI-1 in directing its selectivity against pancreatic and neutrophil elastases. Our results provide the structural basis for site-specific mutagenesis to further improve the binding affinity and/or direct the selectivity of BPTI-Kunitz-type inhibitors toward elastase-like enzymes.


    Organizational Affiliation

    From the Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, 20146 Habana, Cuba.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chymotrypsin-like elastase family member 1
A
240Sus scrofaMutation(s): 0 
Gene Names: CELA1 (ELA1)
EC: 3.4.21.36
Find proteins for P00772 (Sus scrofa)
Go to Gene View: CELA1
Go to UniProtKB:  P00772
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Kunitz-type proteinase inhibitor SHPI-1
B
55Stichodactyla helianthusMutation(s): 1 
Find proteins for P31713 (Stichodactyla helianthus)
Go to UniProtKB:  P31713
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.750α = 90.00
b = 47.180β = 100.07
c = 42.680γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2015-06-17
    Type: Database references