3M7Q

Crystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Caribbean sea anemone stichodactyla helianthus in complex with bovine pancreatic trypsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into serine protease inhibition by a marine invertebrate BPTI Kunitz-type inhibitor.

Garcia-Fernandez, R.Pons, T.Perbandt, M.Valiente, P.A.Talavera, A.Gonzalez-Gonzalez, Y.Rehders, D.Chavez, M.A.Betzel, C.Redecke, L.

(2012) J Struct Biol 180: 271-279

  • DOI: 10.1016/j.jsb.2012.08.009
  • Primary Citation of Related Structures:  
    3M7Q

  • PubMed Abstract: 
  • Proteins isolated from marine invertebrates are frequently characterized by exceptional structural and functional properties. ShPI-1, a BPTI Kunitz-type inhibitor from the Caribbean Sea anemone Stichodactyla helianthus, displays activity not only aga ...

    Proteins isolated from marine invertebrates are frequently characterized by exceptional structural and functional properties. ShPI-1, a BPTI Kunitz-type inhibitor from the Caribbean Sea anemone Stichodactyla helianthus, displays activity not only against serine-, but also against cysteine-, and aspartate proteases. As an initial step to evaluate the molecular basis of its activities, we describe the crystallographic structure of ShPI-1 in complex with the serine protease bovine pancreatic trypsin at 1.7Å resolution. The overall structure and the important enzyme-inhibitor interactions of this first invertebrate BPTI-like Kunitz-type inhibitor:trypsin complex remained largely conserved compared to mammalian BPTI-Kunitz inhibitor complexes. However, a prominent stabilizing role within the interface was attributed to arginine at position P3. Binding free-energy calculations indicated a 10-fold decrease for the inhibitor affinity against trypsin, if the P3 residue of ShPI-1 is mutated to alanine. Together with the increased role of Arg(11) at P3 position, slightly reduced interactions at the prime side (Pn') of the primary binding loop and at the secondary binding loop of ShPI-1 were detected. In addition, the structure provides important information for site directed mutagenesis to further optimize the activity of rShPI-1A for biotechnological applications.


    Organizational Affiliation

    Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, Calle 25 No 411, Havana, Cuba.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cationic trypsinA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Kunitz-type proteinase inhibitor SHPI-1B61Stichodactyla helianthusMutation(s): 0 
Find proteins for P31713 (Stichodactyla helianthus)
Explore P31713 
Go to UniProtKB:  P31713
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.279α = 90
b = 66.551β = 90
c = 70.937γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-03
    Changes: Database references
  • Version 1.3: 2012-11-14
    Changes: Database references