1JKZ

NMR Solution Structure of Pisum sativum defensin 1 (Psd1)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of Pisum sativum defensin 1 by high resolution NMR: plant defensins, identical backbone with different mechanisms of action.

Almeida, M.S.Cabral, K.M.Kurtenbach, E.Almeida, F.C.Valente, A.P.

(2002) J.Mol.Biol. 315: 749-757

  • DOI: 10.1006/jmbi.2001.5252

  • PubMed Abstract: 
  • Pisum sativum defensin 1 (Psd1) is a 46 amino acid residue plant defensin isolated from seeds of pea. The three-dimensional structure in solution of Psd1 was determined by two-dimensional NMR data recorded at 600 MHz. Experimental restraints were use ...

    Pisum sativum defensin 1 (Psd1) is a 46 amino acid residue plant defensin isolated from seeds of pea. The three-dimensional structure in solution of Psd1 was determined by two-dimensional NMR data recorded at 600 MHz. Experimental restraints were used for structure calculation using CNS and torsion-angle molecular dynamics. The 20 lowest energy structures were selected and further subjected to minimization, giving a root-mean-square deviation of 0.78(+/- 0.22) A in the backbone and 1.91(+/-0.60) A for over all atoms of the molecule. The protein has a globular fold with a triple-stranded antiparalell beta-sheet and an alpha-helix (from residue Asn17 to Leu27). Psd1 presents the so called "cysteine stabilized alpha/beta motif" and presents identical three-dimensional topology in the backbone with other defensins and neurotoxins. Comparison of the electrostatic surface potential among proteins with high three-dimensional (selected using the softwares TOP and DALI) topology gave insights into the mode of action of Psd1. The surface topologies between proteins that present antifungal activity or sodium channel inhibiting activity are different. On the other hand the surface topology presents several common features with potassium channel inhibitors, suggesting that Psd1 presents this activity. Other common features with potassium channel inhibitors were found including the presence of a lysine residue essential for inhibitory activity. The identity of Psd1 in primary sequence is not enough to infer a mechanism of action, in contrast with the strategy proposed here.


    Related Citations: 
    • Characterization of two novel defense peptides from pea (Pisum sativum) seeds
      ALMEIDA, M.S.,CABRAL, K.M.,ZINGALI, R.B.,KURTENBACH, E.
      (2000) Arch.Biochem.Biophys. 378: 278
    • cDNA CLONING AND HETEROLOGOUS EXPRESSION OF FUNCTIONAL CYS-RICH ANTIFUNGAL PROTEIN PSD1 IN THE YEAST PICHIA PASTORIS
      ALMEIDA, M.S.,CABRAL, K.M.S.,MEDEIROS, L.N.,VALENTE, A.P.,ALMEIDA, F.C.L.,KURTENBACH, E.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Departamento de Bioquímica Médica, ICB/CCS/UFRJ. CEP., Rio de Janeiro, 21941-590, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEFENSE-RELATED PEPTIDE 1
A
46Pisum sativumMutation(s): 0 
Find proteins for P81929 (Pisum sativum)
Go to UniProtKB:  P81929
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1JKZ Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance