Many Gram-positive bacteria produce ribosomally synthesized antimicrobial peptides, often termed bacteriocins. One important and well studied class of bacteriocins is the class IIa or pediocin-like bacteriocins produced by lactic acid bacteria. All class IIa bacteriocins are produced by food-associated strains, isolated from a variety of food products of industrial and natural origins, including meat products, dairy products and vegetables. Class IIa bacteriocins are all cationic, display anti-Listeria activity, and kill target cells by permeabilizing the cell membrane [1,2,3].

Class IIa bacteriocins contain between 37 and 48 residues. Based on their primary structures, the peptide chains of class IIa bacteriocins may be divided roughly into two regions: a hydrophilic, cationic and highly conserved N-terminal region, and a less conserved hydrophobic/amphiphilic C-terminal region. The N-terminal region contains the conserved Y-G-N-G-V/L 'pediocin box' motif and two conserved cysteine residues joined by a disulfide bridge. It forms a three-stranded antiparallel β-sheet supported by the conserved disulfide bridge (see <PDB:1OG7>). This cationic N-terminal β-sheet domain mediates binding of the class IIa bacteriocin to the target cell membrane. The C-terminal region forms a hairpin-like domain (see <PDB:1OG7>) that penetrates into the hydrophobic part of the target cell membrane, thereby mediating leakage through the membrane. The two domains are joined by a hinge, which enables movement of the domains relative to each other [2,3].

Some proteins known to belong to the class IIa bacteriocin family are listed below:

• Pediococcus acidilactici pediocin PA-1.
• Leuconostoc mesenteroides mesentericin Y105.
• Carnobacterium piscicola carnobacteriocin B2.
• Lactobacillus sake sakacin P.
• Enterococcus faecium enterocin A.
• Enterococcus faecium enterocin P.
• Leuconostoc gelidum leucocin A.
• Lactobacillus curvatus curvacin A.
• Listeria innocua listeriocin 743A.

The pattern we developed for the class IIa bacteriocin family covers the 'pediocin box' motif.