3P92

Human mesotrypsin complexed with bovine pancreatic trypsin inhibitor variant (BPTI-K15R/R17G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.115 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The P2' residue is a key determinant of mesotrypsin specificity: engineering a high-affinity inhibitor with anticancer activity.

Salameh, M.A.Soares, A.S.Hockla, A.Radisky, D.C.Radisky, E.S.

(2011) Biochem J 440: 95-105

  • DOI: https://doi.org/10.1042/BJ20110788
  • Primary Citation of Related Structures:  
    3P92, 3P95

  • PubMed Abstract: 

    PRSS3/mesotrypsin is an atypical isoform of trypsin, the up-regulation of which has been implicated in promoting tumour progression. Mesotrypsin inhibitors could potentially provide valuable research tools and novel therapeutics, but small-molecule trypsin inhibitors have low affinity and little selectivity, whereas protein trypsin inhibitors bind poorly and are rapidly degraded by mesotrypsin. In the present study, we use mutagenesis of a mesotrypsin substrate, APPI (amyloid precursor protein Kunitz protease inhibitor domain), and of a poor mesotrypsin inhibitor, BPTI (bovine pancreatic trypsin inhibitor), to dissect mesotrypsin specificity at the key P(2)' position. We find that bulky and charged residues strongly disfavour binding, whereas acidic residues facilitate catalysis. Crystal structures of mesotrypsin complexes with BPTI variants provide structural insights into mesotrypsin specificity and inhibition. Through optimization of the P(1) and P(2)' residues of BPTI, we generate a stable high-affinity mesotrypsin inhibitor with an equilibrium binding constant K(i) of 5.9 nM, a >2000-fold improvement in affinity over native BPTI. Using this engineered inhibitor, we demonstrate the efficacy of pharmacological inhibition of mesotrypsin in assays of breast cancer cell malignant growth and pancreatic cancer cell invasion. Although further improvements in inhibitor selectivity will be important before clinical potential can be realized, the results of the present study support the feasibility of engineering protein protease inhibitors of mesotrypsin and highlight their therapeutic potential.


  • Organizational Affiliation

    Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRSS3 protein224Homo sapiensMutation(s): 1 
Gene Names: PRSS3
EC: 3.4.21.4
UniProt & NIH Common Fund Data Resources
Find proteins for P35030 (Homo sapiens)
Explore P35030 
Go to UniProtKB:  P35030
PHAROS:  P35030
GTEx:  ENSG00000010438 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35030
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pancreatic trypsin inhibitorB [auth E]58Bos taurusMutation(s): 2 
UniProt
Find proteins for P00974 (Bos taurus)
Explore P00974 
Go to UniProtKB:  P00974
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00974
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.115 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.282α = 90
b = 39.222β = 100.28
c = 68.807γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-11-09
    Changes: Database references
  • Version 1.2: 2014-10-08
    Changes: Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary