1N5P

Solution structure of the cathelin-like domain of protegrins (all amide bonds involving proline residues are in trans conformation)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR Structure of the Cathelin-like domain of the protegrin-3 Precursor

Yang, Y.Sanchez, J.F.Strub, M.P.Brutscher, B.Aumelas, A.

(2003) Biochemistry 42: 4669-4680

  • DOI: 10.1021/bi027133c
  • Primary Citation of Related Structures:  1N5H

  • PubMed Abstract: 
  • In mammals, numerous precursors of antibacterial peptides with unrelated sequences share a similar prosequence of 94-114 residues, termed the cathelin-like domain. The cathelin-like domain of protegrin-3 (ProS) was overexpressed in Escherichia coli a ...

    In mammals, numerous precursors of antibacterial peptides with unrelated sequences share a similar prosequence of 94-114 residues, termed the cathelin-like domain. The cathelin-like domain of protegrin-3 (ProS) was overexpressed in Escherichia coli and uniformly labeled with (15)N or (15)N and (13)C, and its three-dimensional structure was determined by heteronuclear NMR at pH 6.2. Under these conditions and due to the cis-trans isomerization of the R(87)-P(88) and D(118)-P(119) amide bonds, the ProS structure was found to adopt four almost equally populated conformations in slow exchange on the NMR chemical shift time scale. The ProS structure consists of an N-terminal alpha-helix (Y(34)-N(48)) cradled by a four-stranded antiparallel beta-sheet (beta1, N(53)-L(60); beta2, K(74)-P(86); beta3, V(104)-V(111); and beta4, I(122)-C(124)). The solution structure of ProS, which is monomeric, allowed us to determine the structure of the L1 and L2 loops, which are too mobile in the crystal structure. The regions common to the solution and X-ray structures were found to be very similar. Finally, since the overall fold of ProS is very similar to that of cystatins despite a low degree of sequence identity, the ProS solution structure was compared to the solution and X-ray structures of the chicken cystatin. This comparison revealed that the structures of the L1 and L2 loops as well as that of the appending domain are quite different in the two proteins. These differences are mainly due to the high proline residue content (10%) which disorganizes the hydrogen bond network of a part of the ProS beta-sheet in contrast to that of the chicken cystatin structure.


    Organizational Affiliation

    Centre de Biochimie Structurale, UMR 5048 CNRS-UM1/UMR 554 INSERM-UM1, Université Montpellier 1, Faculté de Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protegrins
A
105Sus scrofaGene Names: NPG4
Find proteins for P49933 (Sus scrofa)
Go to UniProtKB:  P49933
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 
  • Olderado: 1N5P Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance