3UOU | pdb_00003uou

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

• PDB DOI: https://doi.org/10.2210/pdb3UOU/pdb

• Classification: HYDROLASE/Hydrolase Inhibitor
• Organism(s): Sus scrofa, Stichodactyla helianthus
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2011-11-17 Released: 2012-11-21 
• Deposition Author(s): Garcia-Fernandez, R., Perbandt, M., Rehders, D., Gonzalez-Gonzalez, Y., Chavez, M.A., Betzel, C., Redecke, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.211 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Models: experimental

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 Biological Chem 290: 14154-14165

• PubMed: 25878249 
• DOI: https://doi.org/10.1074/jbc.M115.647586
• Primary Citation Related Structures: 
  3UOU


• 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 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.

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Organizational Affiliation: 
• From the Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, 20146 Habana, Cuba.
the Institute of Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 22761 Hamburg, Germany, the Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany, and.
the Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany, and Institute of Biochemistry, University of Lübeck, c/o Deutsches Elektronen Synchrotron (DESY), 22603 Hamburg, Germany.
the Institute of Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 22761 Hamburg, Germany.
the Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany, and Institute of Biochemistry, University of Lübeck, c/o Deutsches Elektronen Synchrotron (DESY), 22603 Hamburg, Germany [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 33.45 kDa 
• Atom Count: 2,591 
• Modeled Residue Count: 294 
• Deposited Residue Count: 295 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsin-like elastase family member 1	A	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kunitz-type proteinase inhibitor SHPI-1	B	55	Stichodactyla helianthus	Mutation(s): 1
UniProt
Find proteins for P31713 (Stichodactyla helianthus) Explore P31713  Go to UniProtKB:  P31713

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], O [auth B], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.211 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.75	α = 90
b = 47.18	β = 100.07
c = 42.68	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Garcia-Fernandez, R., Perbandt, M., Rehders, D., Gonzalez-Gonzalez, Y., Chavez, M.A., Betzel, C., Redecke, L.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Database references
• Version 1.2: 2015-06-17
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary