3S8K

Crystal structure of a papaya latex serine protease inhibitor (PPI) at 1.7A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The plasticity of the beta-Trefoil fold constitutes an evolutionary platform for protease inhibition

Azarkan, M.Martinez-Rodriguez, S.Buts, L.Baeyens-Volant, D.Garcia-Pino, A.

(2011) J.Biol.Chem. 286: 43726-43734

  • DOI: 10.1074/jbc.M111.291310
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteases carry out a number of crucial functions inside and outside the cell. To protect the cells against the potentially lethal activities of these enzymes, specific inhibitors are produced to tightly regulate the protease activity. Independent re ...

    Proteases carry out a number of crucial functions inside and outside the cell. To protect the cells against the potentially lethal activities of these enzymes, specific inhibitors are produced to tightly regulate the protease activity. Independent reports suggest that the Kunitz-soybean trypsin inhibitor (STI) family has the potential to inhibit proteases with different specificities. In this study, we use a combination of biophysical methods to define the structural basis of the interaction of papaya protease inhibitor (PPI) with serine proteases. We show that PPI is a multiple-headed inhibitor; a single PPI molecule can bind two trypsin units at the same time. Based on sequence and structural analysis, we hypothesize that the inherent plasticity of the β-trefoil fold is paramount in the functional evolution of this family toward multiple protease inhibition.


    Organizational Affiliation

    Protein Chemistry Unit, Faculty of Medicine, Université Libre de Bruxelles, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Latex serine proteinase inhibitor
A, B
184Carica papayaMutation(s): 0 
Find proteins for P80691 (Carica papaya)
Go to UniProtKB:  P80691
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NH4
Query on NH4

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Download CCD File 
A, B
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CO
Query on CO

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Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.262α = 90.00
b = 81.992β = 90.00
c = 140.891γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
MAR345data collection
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-05-29 
  • Released Date: 2011-11-02 
  • Deposition Author(s): Garcia-Pino, A.

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description