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Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans.

Sabala I, Jagielska E, Bardelang PT, Czapinska H, Dahms SO, Sharpe JA, James R, Than ME, Thomas NR, Bochtler M - FEBS J. (2014)

Bottom Line: The structure of the mature active enzyme confirms its expected organization into catalytic and cell-wall-targeting domains.It also indicates that the domains are mobile with respect to each other because of the presence of a highly flexible peptide linker.The high-resolution structures of the catalytic domain provide details of Zn(2+) coordination and may serve as a starting point for the engineering of lysostaphin variants with improved biotechnological characteristics. lysostaphin by x-ray crystallography (1, 2).

View Article: PubMed Central - PubMed

Affiliation: International Institute of Molecular and Cell Biology, Warsaw, Poland.

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Catalytic sites of lysostaphin and related enzymes. (A) Active sites in the crystals of mature lysostaphin, the catalytic domain crystals were grown in either the absence (B) or presence (C) of phosphate; (D) active LytM and (E) LasA (previously characterized closely related peptidases). (F) Metal–ligand distances (in Å) for (A–E). The low resolution makes interpretation of the density in (A) very tentative. The distances shown in (E) differ between molecules in the asymmetric unit for all presented structures. The electron-density maps shown in cyan in are composite omit maps contoured at 1.5 rmsd. The maps shown in magenta are Bijvoet-difference Fourier (anomalous scattering density) maps calculated with the phases from the final models depleted of Zn2+ ions, and contoured at 6 rmsd.
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fig05: Catalytic sites of lysostaphin and related enzymes. (A) Active sites in the crystals of mature lysostaphin, the catalytic domain crystals were grown in either the absence (B) or presence (C) of phosphate; (D) active LytM and (E) LasA (previously characterized closely related peptidases). (F) Metal–ligand distances (in Å) for (A–E). The low resolution makes interpretation of the density in (A) very tentative. The distances shown in (E) differ between molecules in the asymmetric unit for all presented structures. The electron-density maps shown in cyan in are composite omit maps contoured at 1.5 rmsd. The maps shown in magenta are Bijvoet-difference Fourier (anomalous scattering density) maps calculated with the phases from the final models depleted of Zn2+ ions, and contoured at 6 rmsd.

Mentions: The lysostaphin catalytic domain shares key features of the M23 family peptidases 27. The core of these structures is an antiparallel β sheet that anchors the catalytic residues, which are grouped around a central Zn2+ cation (Fig. 5). Identification of this metal ion was confirmed crystallographically (by a drop in the anomalous density peak height at the metal ion sites passing from the absorption to the inflection point wavelength). In the high-resolution structures it is additionally supported by typical metal–ligand distances and similar temperature factors for the metal ion and the surrounding ligands. The Zn2+ ion is coordinated by His279 and Asp283 of the characteristic HxxxD motif and His362 of the HxH motif of LAS peptidases, as expected.


Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans.

Sabala I, Jagielska E, Bardelang PT, Czapinska H, Dahms SO, Sharpe JA, James R, Than ME, Thomas NR, Bochtler M - FEBS J. (2014)

Catalytic sites of lysostaphin and related enzymes. (A) Active sites in the crystals of mature lysostaphin, the catalytic domain crystals were grown in either the absence (B) or presence (C) of phosphate; (D) active LytM and (E) LasA (previously characterized closely related peptidases). (F) Metal–ligand distances (in Å) for (A–E). The low resolution makes interpretation of the density in (A) very tentative. The distances shown in (E) differ between molecules in the asymmetric unit for all presented structures. The electron-density maps shown in cyan in are composite omit maps contoured at 1.5 rmsd. The maps shown in magenta are Bijvoet-difference Fourier (anomalous scattering density) maps calculated with the phases from the final models depleted of Zn2+ ions, and contoured at 6 rmsd.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4286107&req=5

fig05: Catalytic sites of lysostaphin and related enzymes. (A) Active sites in the crystals of mature lysostaphin, the catalytic domain crystals were grown in either the absence (B) or presence (C) of phosphate; (D) active LytM and (E) LasA (previously characterized closely related peptidases). (F) Metal–ligand distances (in Å) for (A–E). The low resolution makes interpretation of the density in (A) very tentative. The distances shown in (E) differ between molecules in the asymmetric unit for all presented structures. The electron-density maps shown in cyan in are composite omit maps contoured at 1.5 rmsd. The maps shown in magenta are Bijvoet-difference Fourier (anomalous scattering density) maps calculated with the phases from the final models depleted of Zn2+ ions, and contoured at 6 rmsd.
Mentions: The lysostaphin catalytic domain shares key features of the M23 family peptidases 27. The core of these structures is an antiparallel β sheet that anchors the catalytic residues, which are grouped around a central Zn2+ cation (Fig. 5). Identification of this metal ion was confirmed crystallographically (by a drop in the anomalous density peak height at the metal ion sites passing from the absorption to the inflection point wavelength). In the high-resolution structures it is additionally supported by typical metal–ligand distances and similar temperature factors for the metal ion and the surrounding ligands. The Zn2+ ion is coordinated by His279 and Asp283 of the characteristic HxxxD motif and His362 of the HxH motif of LAS peptidases, as expected.

Bottom Line: The structure of the mature active enzyme confirms its expected organization into catalytic and cell-wall-targeting domains.It also indicates that the domains are mobile with respect to each other because of the presence of a highly flexible peptide linker.The high-resolution structures of the catalytic domain provide details of Zn(2+) coordination and may serve as a starting point for the engineering of lysostaphin variants with improved biotechnological characteristics. lysostaphin by x-ray crystallography (1, 2).

View Article: PubMed Central - PubMed

Affiliation: International Institute of Molecular and Cell Biology, Warsaw, Poland.

Show MeSH
Related in: MedlinePlus