5YCZ

Crystal structure of Alocasin, protease inhibitor from Giant Taro (Arum macrorrhizon)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a novel Kunitz type inhibitor, alocasin with anti-Aedes aegypti activity targeting midgut proteases.

Vajravijayan, S.Pletnev, S.Pletnev, V.Z.Nandhagopal, N.Gunasekaran, K.

(2018) Pest Manag Sci 74: 2761-2772

  • DOI: https://doi.org/10.1002/ps.5063
  • Primary Citation of Related Structures:  
    5YCZ

  • PubMed Abstract: 

    The pesticidal properties of many Kunitz-type inhibitors have been reported previously; however, the mechanism of action is not well established. In this study, the activity of alocasin against Aedes aegypti is demonstrated and the structure-activity relationship of this Kunitz-type inhibitor is explained through X-ray structure analyses. Alocasin was purified from mature rhizomes of Alocasia as a single polypeptide chain of ∼ 20 kDa. The structure at 2.5 Å resolution revealed a Kunitz-type fold, but variation in the loop regions makes this structure unique; one loop with a single disulfide bridge is replaced by a long loop with two bridges. Alignment of homologous sequences revealed that this long loop contains a conserved Arg residue and modeling studies showed interaction with the catalytic Ser residue of trypsin-like enzymes. The anti-Aedes aegypti activity of alocasin is examined and discussed in detail. The in vitro activity of alocasin against midgut proteases of Aedes aegypti showed profound inhibition. Further, morphological changes in larvae upon treatment with alocasin revealed its activity against Ae. aegypti. Docking studies of alocasin with trypsin (5G1), a midgut protease involved in the development cycle and blood meal digestion, illustrated its insecticidal activity. The three-dimensional structure of alocasin was determined and its structure-function relationship established for its anti Ae. aegypti activity. © 2018 Society of Chemical Industry.


  • Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trypsin/chymotrypsin inhibitor
A, B
184Alocasia macrorrhizosMutation(s): 0 
UniProt
Find proteins for P35812 (Alocasia macrorrhizos)
Explore P35812 
Go to UniProtKB:  P35812
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35812
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.446α = 90
b = 51.446β = 90
c = 298.184γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references