6QBL

NMR Structure of Big-defensin 1 from oyster Crassostrea gigas


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 10 
  • Selection Criteria: total energies and restraint violation statistics 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Ancestral N-Terminal Domain of Big Defensins Drives Bacterially Triggered Assembly into Antimicrobial Nanonets.

Loth, K.Vergnes, A.Barreto, C.Voisin, S.N.Meudal, H.Da Silva, J.Bressan, A.Belmadi, N.Bachere, E.Aucagne, V.Cazevielle, C.Marchandin, H.Rosa, R.D.Bulet, P.Touqui, L.Delmas, A.F.Destoumieux-Garzon, D.

(2019) Mbio 10: --

  • DOI: 10.1128/mBio.01821-19
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Big defensins, ancestors of β-defensins, are composed of a β-defensin-like C-terminal domain and a globular hydrophobic ancestral N-terminal domain. This unique structure is found in a limited number of phylogenetically distant species, including mol ...

    Big defensins, ancestors of β-defensins, are composed of a β-defensin-like C-terminal domain and a globular hydrophobic ancestral N-terminal domain. This unique structure is found in a limited number of phylogenetically distant species, including mollusks, ancestral chelicerates, and early-branching cephalochordates, mostly living in marine environments. One puzzling evolutionary issue concerns the advantage for these species of having maintained a hydrophobic domain lost during evolution toward β-defensins. Using native ligation chemistry, we produced the oyster Crassostrea gigas BigDef1 ( Cg- BigDef1) and its separate domains. Cg- BigDef1 showed salt-stable and broad-range bactericidal activity, including against multidrug-resistant human clinical isolates of Staphylococcus aureus We found that the ancestral N-terminal domain confers salt-stable antimicrobial activity to the β-defensin-like domain, which is otherwise inactive. Moreover, upon contact with bacteria, the N-terminal domain drives Cg- BigDef1 assembly into nanonets that entrap and kill bacteria. We speculate that the hydrophobic N-terminal domain of big defensins has been retained in marine phyla to confer salt-stable interactions with bacterial membranes in environments where electrostatic interactions are impaired. Those remarkable properties open the way to future drug developments when physiological salt concentrations inhibit the antimicrobial activity of vertebrate β-defensins. IMPORTANCE β-Defensins are host defense peptides controlling infections in species ranging from humans to invertebrates. However, the antimicrobial activity of most human β-defensins is impaired at physiological salt concentrations. We explored the properties of big defensins, the β-defensin ancestors, which have been conserved in a number of marine organisms, mainly mollusks. By focusing on a big defensin from oyster ( Cg- BigDef1), we showed that the N-terminal domain lost during evolution toward β-defensins confers bactericidal activity to Cg- BigDef1, even at high salt concentrations. Cg- BigDef1 killed multidrug-resistant human clinical isolates of Staphylococcus aureus Moreover, the ancestral N-terminal domain drove the assembly of the big defensin into nanonets in which bacteria are entrapped and killed. This discovery may explain why the ancestral N-terminal domain has been maintained in diverse marine phyla and creates a new path of discovery to design β-defensin derivatives active at physiological and high salt concentrations.


    Organizational Affiliation

    HydroSciences Montpellier, Département de Microbiologie, CHU Nîmes, CNRS, IRD, Université de Montpellier, Nîmes, France.,Centre de Biophysique Moléculaire UPR4301 CNRS, Orléans, France.,Plateforme BioPark d'Archamps, Archamps Technopole, Archamps, France.,COMET, Plateau de microscopie électronique, Plateforme Montpellier RIO Imaging, Montpellier, France.,Equipe mixte Institut Pasteur/Paris V Mucoviscidose et Bronchopathies Chroniques, Institut Pasteur, Paris, France.,IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France.,UFR CoST, Université d'Orléans, Orléans, France.,Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.,Institute for Advanced Biosciences, CR Université Grenoble Alpes, CNRS UMR5309, La Tronche, France.,IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France ddestoum@ifremer.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Big defensin 1
A
93Crassostrea gigasMutation(s): 0 
Gene Names: bigdef1
Find proteins for F6M2J2 (Crassostrea gigas)
Go to UniProtKB:  F6M2J2
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
AAR
Query on AAR
A
L-PEPTIDE LINKINGC6 H16 N5 OARG
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 10 
  • Selection Criteria: total energies and restraint violation statistics 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release