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11  structures 75  species 0  interactions 138  sequences 3  architectures

Family: Bacteriocin_II (PF01721)

Summary: Class II bacteriocin

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Class II bacteriocin Edit Wikipedia article

Class II bacteriocin
PDB 2leu EBI.jpg
Three-dimensional structure of leucocin A, a type IIa bacteriocin.[1]
Identifiers
Symbol Bacteriocin_II
Pfam PF01721
InterPro IPR002633
PROSITE PDOC60030
SCOP 3leu
SUPERFAMILY 3leu
TCDB 1.C.24
OPM superfamily 150
OPM protein 1ohm

Class II bacteriocins are a class of small peptides that inhibit the growth of various bacteria.

Many Gram-positive bacteria produce ribosomally synthesized antimicrobial peptides, termed bacteriocins.

Bacteriocins for which disulfide bonds are the only modification to the peptide are Class II bacteriocins.

Class IIa

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.[2][3][4]

Class IIa bacteriocins contain between 37 and 48 residues.[5] 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. 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 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.[3][4]

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

Class IIb

Class IIb bacteriocin
Identifiers
Pfam PF08129
Pfam clan CL0400
InterPro IPR012950
TCDB 1.C.25
OPM superfamily 316
OPM protein 2jpj

The class IIb bacteriocins (two-peptide bacteriocins) require two different peptides for activity. It includes the alpha enterocins and lactococcin G peptides. These peptides have some antimicrobial properties; they inhibit the growth of Enterococcus spp. and a few other Gram-positive bacteria. These peptides act as pore-forming toxins that create cell membrane channels through a barrel-stave mechanism and thus produce an ionic imbalance in the cell[6]

Class IIc

Bacteriocin_IIc
PDB 1o82 EBI.jpg
x-ray structure of bacteriocin as-48 at ph 4.5. sulphate bound form
Identifiers
Symbol Bacteriocin_IIc
Pfam PF09221
InterPro IPR009086
SCOP 1o82
SUPERFAMILY 1o82
TCDB 1.C.28
OPM superfamily 84
OPM protein 1o82

Other class II bacteriocins can be grouped together as Class IIc (circular bacteriocins). These have a wide range of effects on membrane permeability, cell wall formation and pheromone actions of target cells. In particular, Bacteriocin AS-48 is a cyclic peptide antibiotic produced by the eubacteria Enterococcus faecalis (Streptococcus faecalis) that shows a broad antimicrobial spectrum against both Gram-positive and Gram-negative bacteria. Bacteriocin AS-48 is encoded by the pheromone-responsive plasmid pMB2, and acts on the plasma membrane in which it opens pores leading to ion leakage and cell death.[7] The globular structure of bacteriocin AS-48 consists of five alpha helices enclosing a hydrophobic core. The mammalian NK-lysin effector protein of T and natural killer cells has a similar structure, though it lacks sequence homology with bacteriocins AS-48.

References

  1. ^ Fregeau Gallagher NL, Sailer M, Niemczura WP, Nakashima TT, Stiles ME, Vederas JC (December 1997). "Three-dimensional structure of leucocin A in trifluoroethanol and dodecylphosphocholine micelles: spatial location of residues critical for biological activity in type IIa bacteriocins from lactic acid bacteria". Biochemistry 36 (49): 15062–72. doi:10.1021/bi971263h. PMID 9398233. 
  2. ^ Ennahar S, Sonomoto K, Ishizaki A (1999). "Class IIa bacteriocins from lactic acid bacteria: antibacterial activity and food preservation". J. Biosci. Bioeng. 87 (6): –. doi:10.1016/S1389-1723(99)80142-X. PMID 16232543. 
  3. ^ a b Fimland G, Nissen-Meyer J, Johnsen L (2005). "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 (10): –. doi:10.1074/jbc.M412712200. PMID 15611086. 
  4. ^ a b Dalhus B, Fimland G, Nissen-Meyer J, Johnsen L (2005). "Pediocin-like antimicrobial peptides (class IIa bacteriocins) and their immunity proteins: biosynthesis, structure, and mode of action". J. Pept. Sci. 11 (11): –. doi:10.1002/psc.699. PMID 16059970. 
  5. ^ Simon L, Fremaux C, Cenatiempo Y, Berjeaud JM (2002). "Sakacin g, a new type of antilisterial bacteriocin". Appl. Environ. Microbiol. 68 (12): 6416–20. doi:10.1128/AEM.68.12.6416-6420.2002. PMC 134399. PMID 12450870. 
  6. ^ Balla E, Dicks LM, Du Toit M, Van Der Merwe MJ, Holzapfel WH (April 2000). "Characterization and cloning of the genes encoding enterocin 1071A and enterocin 1071B, two antimicrobial peptides produced by Enterococcus faecalis BFE 1071". Appl. Environ. Microbiol. 66 (4): 1298–304. doi:10.1128/aem.66.4.1298-1304.2000. PMC 91984. PMID 10742203. 
  7. ^ González C, Langdon GM, Bruix M, Gálvez A, Valdivia E, Maqueda M, Rico M (October 2000). "Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin". Proc. Natl. Acad. Sci. U.S.A. 97 (21): 11221–6. doi:10.1073/pnas.210301097. PMC 17181. PMID 11005847. 

Further reading

  1. Papathanasopoulos, M. A.; Dykes, G. A.; Revol-Junelles, A. M.; Delfour, A.; Von Holy, A.; Hastings, J. W. (1998). "Sequence and structural relationships of leucocins A-, B- and C-TA33a from Leuconostoc mesenteroides TA33a". Microbiology (Reading, England). 144 ( Pt 5): 1343–1348. PMID 9611809. 
  2. Fregeau Gallagher, N. L.; Sailer, M.; Niemczura, W. P.; Nakashima, T. T.; Stiles, M. E.; Vederas, J. C. (1997). "Three-Dimensional Structure of Leucocin a in Trifluoroethanol and Dodecylphosphocholine Micelles:  Spatial Location of Residues Critical for Biological Activity in Type IIa Bacteriocins from Lactic Acid Bacteria†,‡". Biochemistry 36 (49): 15062–15072. doi:10.1021/bi971263h. PMID 9398233. 

This article incorporates text from the public domain Pfam and InterPro IPR002633

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Class II bacteriocin Provide feedback

The bacteriocins are small peptides that inhibit the growth of various bacteria. Bacteriocins of lactic acid bacteria may inhibit their target cells by permeabilising the cell membrane [1].

Literature references

  1. Papathanasopoulos MA, Dykes GA, Revol-Junelles AM, Delfour A, von Holy A, Hastings JW; , Microbiology 1998;144:1343-1348.: Sequence and structural relationships of leucocins A-, B- and C-TA33a from Leuconostoc mesenteroides TA33a. PUBMED:9611809 EPMC:9611809

  2. Fregeau Gallagher NL, Sailer M, Niemczura WP, Nakashima TT, Stiles ME, Vederas JC; , Biochemistry 1997;36:15062-15072.: Three-dimensional structure of leucocin A in trifluoroethanol and dodecylphosphocholine micelles: spatial location of residues critical for biological activity in type IIa bacteriocins from lactic acid bacteria. PUBMED:9398233 EPMC:9398233


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002633

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 [PUBMED:16232543, PUBMED:15611086, PUBMED:16059970].

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 disulphide bridge. It forms a three-stranded antiparallel beta-sheet supported by the conserved disulphide bridge. 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 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 [PUBMED:15611086, PUBMED:16059970].

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

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Seed source: Pfam-B_1954 (release 4.1)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 19
Number in full: 138
Average length of the domain: 35.30 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 58.83 %

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Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 22.2 25.3
Noise cut-off 21.0 21.0
Model length: 36
Family (HMM) version: 13
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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Bacteriocin_II domain has been found. There are 11 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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