3GNY: Crystal structure of human alpha-defensin 1 (HNP1)

Despite the small size and conserved tertiary structure of defensins, little is known at a molecular level about the basis of their functional versatility. For insight into the mechanism(s) of defensin function, we prepared enantiomeric pairs of four human defensins, HNP1, HNP4, HD5, and HBD2, and studied their killing of bacteria, inhibition of anthrax lethal factor, and binding to HIV-1 gp120. Unstructured HNP1, HD5, and HBD3 and several other human alpha- and beta-defensins were also examined. Crystallographic analysis showed a plane of symmetry that related (L)HNP1 and (D)HNP1 to each other. Either d-enantiomerization or linearization significantly impaired the ability of HNP1 and HD5 to kill Staphylococcus aureus but not Escherichia coli. In contrast, (L)HNP4 and (D)HNP4 were equally bactericidal against both bacteria. d-Enantiomers were generally weaker inhibitors or binders of lethal factor and gp120 than their respective native, all-l forms, although activity differences were modest, particularly for HNP4. A strong correlation existed among these different functions. Our data indicate: (a) that HNP1 and HD5 kill E. coli by a process that is mechanistically distinct from their actions that kill S. aureus and (b) that chiral molecular recognition is not a stringent prerequisite for other functions of these defensins, including their ability to inhibit lethal factor and bind gp120 of HIV-1.
PDB ID: 3GNYDownload
MMDB ID: 75638
PDB Deposition Date: 2009/3/18
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 1.56  Å
Similar Structures:
Biological Unit for 3GNY: tetrameric; determined by author and by software (PISA)
Molecular Components in 3GNY
Label Count Molecule
Proteins (4 molecules)
Neutrophil Defensin 1(Gene symbol: DEFA1)
Molecule annotation
Chemicals (5 molecules)
Molecule information is not avaliable.
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Citing MMDB