6L4M

Crystal structure of vicilin from Solanum lycopersicum (tomato)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function.

Shikhi, M.Jain, A.Salunke, D.M.

(2020) Biochem Biophys Res Commun 522: 127-132

  • DOI: https://doi.org/10.1016/j.bbrc.2019.11.072
  • Primary Citation of Related Structures:  
    6L4C, 6L4M

  • PubMed Abstract: 

    The plant seed proteins referred to as vicilins belong to a structurally common superfamily. While some of them are reported to exhibit superoxide dismutase activity, vicilins from other sources do not possess this activity. Vicilin from Corylus avellana (HZ.1) and Solanum lycopersicum (SL80.1) were purified and subjected to structure-function analysis. The superoxide dismutase activity assays were performed to understand the functional differences between them. While SL80.1 has the superoxide dismutase activity, HZ.1 was enzymatically inactive. Crystal structure followed by mass spectrometry analysis of both the proteins revealed that while SL80.1 has bound salicylic acid, HZ.1 does not. Comparison of C-terminal binding pocket of both the structures revealed that a point mutation at residue 321 in HZ.1 (Gly→Cys) leads to obstruction in binding of salicylic acid in the pocket. Similarly, copper-binding loop of HZ.1 was reportedly found to be intact and shorter than the loops reported in SL80.1. The copper-binding loop of SL80.1 is rich in polar residues and the absence of these residues in HZ.1 copper-binding loop possibly indicates deficiency in channeling of oxygen radicals to the active center of the enzyme. Difference in the enzymatic activity of vicilin from two evolutionarily distinct sources is due to mutations in its co-factor binding pocket and copper-binding loop.


  • Organizational Affiliation

    Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121 001, India; Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vicilin397Solanum lycopersicumMutation(s): 0 
UniProt
Find proteins for B0JEU3 (Solanum lycopersicum)
Explore B0JEU3 
Go to UniProtKB:  B0JEU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0JEU3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAL
Query on SAL

Download Ideal Coordinates CCD File 
B [auth A]2-HYDROXYBENZOIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.98α = 90
b = 135.98β = 90
c = 135.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description