{PDOC60030}
{PS60030; BACTERIOCIN_IIA}
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* Bacteriocin class IIa family signature *
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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 [1-3].

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 beta-sheet supported by the conserved
disulfide bridge  (see <PDB:1OG7>). This cationic N-terminal beta-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.

-Conserved pattern: Y-G-N-G-[VL]-x-C-x(4)-C
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Expert(s) to contact by email:
           Ramakumar S.; ramak@physics.iisc.ernet.in

-Last update: March 2006 / First entry.

[ 1] Ennahar S., Sonomoto K., Ishizaki A.
     "Class IIa bacteriocins from lactic acid bacteria: antibacterial
     activity and food preservation."
     J. Biosci. Bioeng. 87:705-716(1999).
     PubMed=16232543
[ 2] Johnsen L., Fimland G., Nissen-Meyer J.
     "The C-terminal domain of pediocin-like antimicrobial peptides (class
     IIa bacteriocins) is involved in specific recognition of the
     C-terminal part of cognate immunity proteins and in determining the
     antimicrobial spectrum."
     J. Biol. Chem. 280:9243-9250(2005).
     PubMed=15611086; DOI=10.1074/jbc.M412712200
[ 3] Fimland G., Johnsen L., Dalhus B., Nissen-Meyer J.
     "Pediocin-like antimicrobial peptides (class IIa bacteriocins) and
     their immunity proteins: biosynthesis, structure, and mode of
     action."
     J. Pept. Sci. 11:688-696(2005).
     PubMed=16059970; DOI=10.1002/psc.699

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