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12  structures 43  species 3  interactions 84  sequences 10  architectures

Family: Cloacin (PF03515)

Summary: Colicin-like bacteriocin tRNase domain

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This is the Wikipedia entry entitled "Colicin". More...

Colicin Edit Wikipedia article

Colicin
PDB 2ivz EBI.jpg
structure of tolb in complex with a peptide of the colicin e9 t-domain
Identifiers
Symbol Colicin
Pfam PF03515
Pfam clan CL0446
InterPro IPR003058
SCOP 1jch
SUPERFAMILY 1jch

A colicin is a type of bacteriocin produced by and toxic to some strains of Escherichia coli.[1] Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis.

Structure[edit]

Channel-forming colicins (colicins A, B, E1, Ia, Ib, and N) are transmembrane proteins that depolarize the cytoplasmic membrane, leading to dissipation of cellular energy.[2] These colicins contain at least three domains: an N-terminal translocation domain responsible for movement across the outer membrane and periplasmic space; a central domain responsible for receptor recognition; and a C-terminal cytotoxic domain responsible for channel formation in the cytoplasmic membrane.[3][4] One domain regulates the target and binds to the receptor on the sensitive cell. The second is involved with translocation, co-opting the machinery of the target cell. The third is the 'killing' domain and may produce a pore in the target cell membrane, or act as a nuclease to chop up the DNA or RNA of the target cell.

Translocation[edit]

Most colicins are able to translocate the outer membrane by a two-receptor system, where one receptor is used for the initial binding and the second for translocation. The initial binding is to cell surface receptors such as the porins OmpF, FepA, BtuB, Cir and FhuA; colicins have been classified according which receptors they bind to. The presence of specific periplasmic proteins, such as TolA, TolB, TolC, or TonB, are required for translocation across the membrane.[5] Cloacin DF13 is a bacteriocin that inactivates ribosomes by hydrolysing 16S RNA in 30S ribosomes at a specific site.[6]

Resistance[edit]

Because they target specific receptors and use specific translocation machinery, cells can make themselves resistant to the colicin by repressing or deleting the genes for these proteins. Such resistant cells may suffer the lack of a key nutrient (such as iron or vitamin B) but benefit by not being killed. Colicins exhibit a '1-hit killing kinetic' which doesn't necessarily mean a single molecule is sufficient to kill, but certainly that it only takes a small number. In his Nobel Laureate speech, Salvador E. Luria, 1969, speculated that colicins could only be this toxic by causing a domino effect that destabilized the cell membrane.[7] He was not entirely correct, but pore-forming colicins do de-polarize the membrane and thus eliminate the energy source for the cell. The colicins are highly effective toxins.

Genetic organisation[edit]

Virtually all colicins are carried on plasmids. There are two general classes of colicinogenic plasmids, large, low-copy number plasmids, and small high copy number plasmids. The larger plasmids carry other genes as well as the colicin operon. The colicin operons are generally organized with several major genes. These include an immunity gene, a colicin structural gene, and a BRP (bacteriocin release protein), or lysis, gene. The immunity gene is often produced constitutively, while the BRP is generally produced only as a read-through of the stop codon on the colicin structural gene. The colicin itself is repressed by the SOS response and may be regulated in other ways as well.

Research indicates that retaining the colicin plasmid is very important for cells that live with their relatives, because if a cell loses the immunity gene, it quickly becomes subject to destruction by circulating colicin. At the same time, colicin is only released from a producing cell by the use of the lysis protein, which results in that cell's death. This suicidal production mechanism would appear to be very costly, except for the fact that it is regulated by the SOS response, which responds to significant DNA damage. In short, colicin production may only occur in terminally-ill cells. Still these matters require further research. The Professor Kleanthous Research Group at the University of York study colicins extensively as a model system for characterising and investigating protein-protein interactions and recognition.[8]

BACTIBASE[9][10] database is an open-access database for bacteriocins including colicins (view complete list).

References[edit]

  1. ^ * Feldgarden, M., & Riley, M. A. (August 1999). The phenotypic and fitness effects of colicin resistance in Escherichia coli K-12" Evolution 53(4), 1019-27. [1]
  2. ^ Kang C, Postle K, Chen G, Park H, Youn B, Hilsenbeck JL (2004). "Crystal structure of the cytotoxic bacterial protein colicin B at 2.5 A resolution". Mol. Microbiol. 51 (3): –. doi:10.1111/j.1365-2958.2003.03884.x. PMID 14731273. 
  3. ^ Cramer WA, Zakharov SD, Antonenko YN, Kotova EA (2004). "On the role of lipid in colicin pore formation". Biochim. Biophys. Acta 1666 (1): –. doi:10.1016/j.bbamem.2004.07.001. PMID 15519318. 
  4. ^ Cascales et al. (2007). Colicin Biology. Microbio. and Mol. Bio. Rev. 71(1), 158-229. Abstractpdf
  5. ^ Cao Z, Klebba PE (2002). "Mechanisms of colicin binding and transport through outer membrane porins". Biochimie 84 (5-6): 399–412. doi:10.1016/S0300-9084(02)01455-4. PMID 12423783. 
  6. ^ van den Elzen PJ, Veltkamp E, Nijkamp HJ, Walters HH (1983). "Molecular structure and function of the bacteriocin gene and bacteriocin protein of plasmid Clo DF13". Nucleic Acids Res. 11 (8): 2465–2477. doi:10.1093/nar/11.8.2465. PMC 325896. PMID 6344017. 
  7. ^ Luria, S. E. (1969) Nobel Lecture
  8. ^ "Kleanthous Research Group". University of York. Retrieved 11 April 2011. 
  9. ^ Hammami R, Zouhir A, Ben Hamida J, Fliss I (2007). "BACTIBASE: a new web-accessible database for bacteriocin characterization". BMC Microbiology 7: 89. doi:10.1186/1471-2180-7-89. PMC 2211298. PMID 17941971. 
  10. ^ Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I (2010). "BACTIBASE second release: a database and tool platform for bacteriocin characterization.". BMC Microbiology 10: 22. doi:10.1186/1471-2180-10-22. PMC 2824694. PMID 20105292. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR000290

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

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Colicin-like bacteriocin tRNase domain Provide feedback

The C-terminal region of colicin-like bacteriocins is either a pore-forming or an endonuclease-like domain. Cloacin and Pyocins have similar structures and activities to the colicins from E coli and the klebicins from Klebsiella spp. Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro [1]. The full-length molecule has an N-terminal translocation domain and a middle, double alpha-helical region which is receptor-binding [2].

Literature references

  1. Masaki H, Ogawa T;, Biochimie. 2002;84:433-438.: The modes of action of colicins E5 and D, and related cytotoxic tRNases. PUBMED:12423786 EPMC:12423786

  2. Soelaiman S, Jakes K, Wu N, Li C, Shoham M;, Mol Cell. 2001;8:1053-1062.: Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. PUBMED:11741540 EPMC:11741540


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016128

This entry represents a structural domain with a complex fold made of several coiled beta-sheets. This domain is found at the N-terminal of both colicin E3 and colicin B, and acts as a translocation domain. It also occurs in S-type pyocin. Both pyocin and cloacin are bacteriocins, protein antibiotics that kill bacteria closely related to the producing species. Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism [PUBMED:12409205].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Bacteriocin_TLN (CL0446), which has the following description:

A number of different bacterial species produce bacteriocins to kill competitor species, and the colicin class is a group of complex three-domain structures. The receptor-binding domain recognises and binds to specific cell surface receptors on the target cells; the N-terminal translocation domain interacts with cell membrane proteins to gain access to the cell interior; the C-terminal domain specifies a killing activity, such as pore formation or nuclease activity. This superfamily is a collection of the translocating domains.

The clan contains the following 2 members:

Cloacin Pyocin_S

Alignments

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(97)
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RP35
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RP55
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RP75
(4)
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Full
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Representative proteomes NCBI
(97)
Meta
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RP15
(2)
RP35
(2)
RP55
(4)
RP75
(4)
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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: PRINTS
Previous IDs: none
Type: Family
Author: Griffiths-Jones SR
Number in seed: 8
Number in full: 84
Average length of the domain: 272.40 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 49.83 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 37.0 31.6
Noise cut-off 20.9 20.4
Model length: 297
Family (HMM) version: 9
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Species distribution

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Interactions

There are 3 interactions for this family. More...

Colicin E2R135 Cloacin_immun

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 Cloacin domain has been found. There are 12 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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