3S8J

Crystal structure of a papaya latex serine protease inhibitor (PPI) at 2.6A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1074/jbc.M111.291310
  • Primary Citation of Related Structures:  
    3S8J, 3S8K

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Latex serine proteinase inhibitor
A, B
184Carica papayaMutation(s): 0 
UniProt
Find proteins for P80691 (Carica papaya)
Explore P80691 
Go to UniProtKB:  P80691
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80691
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.699α = 90
b = 74.699β = 90
c = 78.97γ = 120
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary