1ZMK

Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids.

Xie, C.Prahl, A.Ericksen, B.Wu, Z.Zeng, P.Li, X.Lu, W.Y.Lubkowski, J.Lu, W.

(2005) J Biol Chem 280: 32921-32929

  • DOI: https://doi.org/10.1074/jbc.M503084200
  • Primary Citation of Related Structures:  
    1ZMH, 1ZMI, 1ZMK

  • PubMed Abstract: 

    Defensins are cationic antimicrobial mini-proteins that play important roles in the innate immune defense against microbial infection. Six invariant Cys residues in each defensin form three structurally indispensable intramolecular disulfide bridges. The only other residue invariant in all known mammalian defensins is a Gly. Structural studies indicate that the invariant Gly residue is located in an atypical, classic-type beta-bulge with the backbone torsion angles (Phi, Psi) disallowed for L-amino acids but permissible for D-enantiomers. We replaced the invariant Gly17 residue in human neutrophil alpha-defensin 2 (HNP2) by L-Ala or one of the D-amino acids Ala, Glu, Phe, Arg, Thr, Val, or Tyr. Although L-Ala17-HNP2 could not be folded, resulting in massive aggregation, all of the D-amino acid-substituted analogs folded with high efficiency. The high resolution x-ray crystal structures of dimeric D-Ala17-HNP2 were determined in three different crystal forms, showing a well preserved beta-bulge identical to those found in other defensins. The seven D-analogs of HNP2 exhibited highly variable bactericidal activity against Gram-positive and Gram-negative test strains, consistent with the premise that interplay between charge and hydrophobicity dictates how amphiphilic defensins kill. Further, the bactericidal activity of these d-amino acid analogs of HNP2 correlated well with their ability to induce leakage from large unilamellar vesicles, supporting membrane permeabilization as the lethal event in microbial killing by HNP2. Our findings identify a conformational prerequisite in the beta-bulge of defensins essential for correct folding and native structure, thereby explaining the molecular basis of the Gly-Xaa-Cys motif conserved in all mammalian defensins.


  • Organizational Affiliation

    Institute of Human Virology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil defensin 2
A, B
29Homo sapiensMutation(s): 1 
Gene Names: DEFA3DEF3
UniProt & NIH Common Fund Data Resources
Find proteins for P59666 (Homo sapiens)
Explore P59666 
Go to UniProtKB:  P59666
PHAROS:  P59666
GTEx:  ENSG00000239839 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59666
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.148α = 90
b = 47.148β = 90
c = 50.643γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description