1ZUF

Solution Structure of DLP-4


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • 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

D-amino acid residue in a defensin-like peptide from platypus venom: effect on structure and chromatographic properties.

Torres, A.M.Tsampazi, C.Geraghty, D.P.Bansal, P.S.Alewood, P.F.Kuchel, P.W.

(2005) Biochem.J. 391: 215-220

  • DOI: 10.1042/BJ20050900
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The recent discovery that the natriuretic peptide OvCNPb (Ornithorhynchus venom C-type natriuretic peptide B) from platypus (Ornithorynchus anatinus) venom contains a D-amino acid residue suggested that other D-amino-acid-containing peptides might be ...

    The recent discovery that the natriuretic peptide OvCNPb (Ornithorhynchus venom C-type natriuretic peptide B) from platypus (Ornithorynchus anatinus) venom contains a D-amino acid residue suggested that other D-amino-acid-containing peptides might be present in the venom. In the present study, we show that DLP-2 (defensin-like peptide-2), a 42-amino-acid residue polypeptide in the platypus venom, also contains a D-amino acid residue, D-methionine, at position 2, while DLP-4, which has an identical amino acid sequence, has all amino acids in the L-form. These findings were supported further by the detection of isomerase activity in the platypus gland venom extract that converts DLP-4 into DLP-2. In the light of this new information, the tertiary structure of DLP-2 was recalculated using a new structural template with D-Met2. The structure of DLP-4 was also determined in order to evaluate the effect of a D-amino acid at position 2 on the structure and possibly to explain the large retention time difference observed for the two molecules in reverse-phase HPLC. The solution structures of the DLP-2 and DLP-4 are very similar to each other and to the earlier reported structure of DLP-2, which assumed that all amino acids were in the L-form. Our results suggest that the incorporation of the D-amino acid at position 2 has minimal effect on the overall fold in solution.


    Related Citations: 
    • Defensin-like peptide-2 from platypus venom: member of a class of peptides with a distinct structural fold
      Torres, A.M.,de Plater, G.M.,Doverskog, M.,Birinyi-Strachan, L.C.,Nicholson, G.M.,Gallagher, C.H.,Kuchel, P.W.
      (2000) Biochem.J. 348: 649


    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Defensin-like peptide 2/4
A
42Ornithorhynchus anatinusMutation(s): 0 
Find proteins for P82140 (Ornithorhynchus anatinus)
Go to UniProtKB:  P82140
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1ZUF Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance