7YAQ

Phloem lectin (PP2)C34S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus.

Bobbili, K.B.Sivaji, N.Priya, B.Suguna, K.Surolia, A.

(2023) Structure 31: 464

  • DOI: https://doi.org/10.1016/j.str.2023.02.008
  • Primary Citation of Related Structures:  
    7YAQ

  • PubMed Abstract: 

    Phloem protein 2 (PP2) contributes crucially to phloem-based defense in plants by binding to carbohydrates displayed by pathogens. However, its three-dimensional structure and the sugar binding site remained unexplored. Here, we report the crystal structure of the dimeric PP2 Cus17 from Cucumis sativus in its apo form and complexed with nitrobenzene, N-acetyllactosamine, and chitotriose. Each protomer of Cus17 consists of two antiparallel four-stranded twisted β sheets, a β hairpin, and three short helices forming a β sandwich architectural fold. This structural fold has not been previously observed in other plant lectin families. Structure analysis of the lectin-carbohydrate complexes reveals an extended carbohydrate binding site in Cus17, composed mostly of aromatic amino acids. Our studies suggest a highly conserved tertiary structure and a versatile binding site capable of recognizing motifs common to diverse glycans on plant pathogens/pests, which makes the PP2 family suited for phloem-based plant defense.


  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
17 kDa phloem lectin154Cucumis sativusMutation(s): 1 
Gene Names: Lec17-7
UniProt
Find proteins for Q8LK69 (Cucumis sativus)
Explore Q8LK69 
Go to UniProtKB:  Q8LK69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LK69
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.264 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.97α = 90
b = 51.97β = 90
c = 261.521γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)India--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references