A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution

Abstract

Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained from methanol solutions of purified bergofungin mixed with water. Although there are differences in the intramolecular hydrogen-bonding scheme of samarosporin I, the overall folding is very similar for both peptaibols, namely 3₁₀-helical at the termini and α-helical in the middle of the molecules. Bergofungin A and samarosporin I molecules are arranged in a similar way in both lattices. However, the packing of bergofungin A exhibits a second solvent channel along the twofold axis. This latter channel occurs in the vicinity of the N-terminus, where the natural substitution resides.

Keywords: 310-helix; Emericellopsis donezkii; crystal structure; hydrogen bond; peptaibols; peptide antibiotics; α-helix.

Figure 1

Electron density of the 2F _o − F _c map contoured at 3σ around Iva12.

Figure 2

Stereoview of bergofungin A. Hydrogen bonds of type 1←4 are shown in blue and of type 1←5 are shown in green.

Figure 3

Arrangement of the molecules in the crystal viewed along the short b axis. Molecules translated along the unit-cell edges are coloured uniformly, whereas the four molecules of different colour are related by space-group symmetry. A single molecular layer is shown in the ac plane.

Figure 4

Solvent-accessible spaces in the crystals of bergofungin A (a) and samarosporin (b) calculated and plotted with PLATON (Spek, 2009 ▸). The parts of the channels corresponding to one unit cell are shown, viewed approximately along the b axis.