3RFI | pdb_00003rfi

Crystal structure of the saposin-like domain of plant aspartic protease from Solanum tuberosum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.250 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure and Mechanism of the Saposin-like Domain of a Plant Aspartic Protease.

Bryksa, B.C.Bhaumik, P.Magracheva, E.De Moura, D.C.Kurylowicz, M.Zdanov, A.Dutcher, J.R.Wlodawer, A.Yada, R.Y.

(2011) J Biological Chem 286: 28265-28275

  • DOI: https://doi.org/10.1074/jbc.M111.252619
  • Primary Citation Related Structures: 
    3RFI

  • PubMed Abstract: 

    Many plant aspartic proteases contain an additional sequence of ~100 amino acids termed the plant-specific insert, which is involved in host defense and vacuolar targeting. Similar to all saposin-like proteins, the plant-specific insert functions via protein-membrane interactions; however, the structural basis for such interactions has not been studied, and the nature of plant-specific insert-mediated membrane disruption has not been characterized. In the present study, the crystal structure of the saposin-like domain of potato aspartic protease was resolved at a resolution of 1.9 Å, revealing an open V-shaped configuration similar to the open structure of human saposin C. Notably, vesicle disruption activity followed Michaelis-Menten-like kinetics, a finding not previously reported for saposin-like proteins including plant-specific inserts. Circular dichroism data suggested that secondary structure was pH-dependent in a fashion similar to influenza A hemagglutinin fusion peptide. Membrane effects characterized by atomic force microscopy and light scattering indicated bilayer solubilization as well as fusogenic activity. Taken together, the present study is the first report to elucidate the membrane interaction mechanism of plant saposin-like domains whereby pH-dependent membrane interactions resulted in bilayer fusogenic activity that probably arose from a viral type pH-dependent helix-kink-helix motif at the plant-specific insert N terminus.


  • Organizational Affiliation
    • Department of Food Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada.

Macromolecule Content 

  • Total Structure Weight: 11.78 kDa 
  • Atom Count: 696 
  • Modeled Residue Count: 80 
  • Deposited Residue Count: 108 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Asp108Solanum tuberosumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6B9W9 (Solanum tuberosum)
Explore Q6B9W9 
Go to UniProtKB:  Q6B9W9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B9W9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.250 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.47α = 90
b = 56.47β = 90
c = 55.34γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2011-08-24
    Changes: Database references
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Structure summary