PDBsum entry 1zmh

Antimicrobial protein

PDB id: 1zmh

Contents

Protein chains

29 a.a.

Ligands

SO4 ×3

P6G

GOL ×2

Waters ×111

PDB id:

1zmh

Name:

Antimicrobial protein

Title:

Crystal structure of human neutrophil peptide 2, hnp-2 (variant gly16- > d-ala)

Structure:

Neutrophil defensin 2. Chain: a, b, c, d. Synonym: hnp-2. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: defa3, def3. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Not given

Resolution:

1.50Å R-factor: 0.179 R-free: 0.213

Authors:

J.Lubkowski,A.Prahl,W.Lu

Key ref:

C.Xie et al. (2005). Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids. J Biol Chem, 280, 32921-32929. PubMed id: 15894545 DOI: 10.1074/jbc.M503084200

Date:

10-May-05 Release date: 16-Aug-05

Protein chains

P59666  (DEF3_HUMAN) -  Neutrophil defensin 3 from Homo sapiens

Seq: 94 a.a.

Struc: 29 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M503084200

J Biol Chem 280:32921-32929 (2005)

PubMed id: 15894545

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

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

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.

Selected figure(s)

Figure 1.
FIGURE 1. Amino acid sequence alignment of mammalian -defensins from human, mouse, rhesus macaque, rabbit, guinea pig, and rat (us.expasy.org/sprot). The invariant residues, including six Cys and Gly17 (HNP1 numbering), are shaded in black. The boxed residues, Arg5 and Glu13, form a salt bridge in the structure and are highly conserved.

Figure 7.
FIGURE 7. The hydrogen-bonding pattern of the -bulge in a representative dimer of D-Ala^17-HNP2.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 32921-32929) copyright 2005.

Figures were selected by an automated process.