Colicin E3

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Colicin E3 is a type of Colicin, a 60kDa[1] bacteriocin made by E. coli which acts against other nearby E. coli to kill them with its 16s rRNase activity; it digests the 16s ribosomal subunit, ultimately leading to the death of the cell.


Synthesis and release

The plasmid containing the colicin E3 gene is called ColE3-CA38, which is structurally homologous to that of the Colicin E2 plasmid[2]. The expression of the operon is regulated by the lexA protein, as behind the promotor there are two inverted lexA binding regions[3]. The colicin, alongside its immunity protein, are not produced as a precursor protein requiring modification post-translationally. Instead they leave the colicinergic cell by a non-specific mechanism, whereby the permeability of the cell is increased[4].

When colicin E3 is synthesised, it binds its 10kDa[5] Colicin Immunity Protein, Im3, to its cytotoxic domain in the cytoplasm. This prevents its RNase activity from occurring in the colicinogenic host, so it does not kill it. It is released as this complex into the surrounding area, and Im3 is only released upon binding to a target cell. In the normal state, Im3 is produced at a basal level to protect the cell from the colicin that it is producing, but in the SOS-induced state, initiated by lexA binding, a large amount is produced to protect the cell from externally produced ColE3[6].

Mechanism of uptake

PDB ID 1ujw

Drag the structure with the mouse to rotate
1ujw, resolution 2.75Å ()
Ligands: , , , ,
Related: 1nqe, 1jch
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml

ColE3 initially binds to the BtuB vitamin B12 receptor. Formation of this complex leads to the unfolding of the N terminal receptor binding coiled-coil domain of ColE3[7]. The structure shows the complex formed between BtuB and the ColE3 translocation domain[8]. Cells with a mutation in the gene encoding the BtuB gene show immunity to ColE3 attack, as well as other Colicins that use the same receptor.

After binding to the BtuB receptor, the complex recruits OmpF, and a group of proteins from the Tol group of proteins, TolQRAB. The mechanism by which these proteins aid the translocation of ColE3 is as yet unknown, but the colicin then traverses the outer membrane and reaches the periplasm.

For more information about the uptake of Colicin E3 see the uptake section on Colicin E9, which has a similar mechanism.

Killing Activities

PDB ID 2xfz

Drag the structure with the mouse to rotate
2xfz, resolution 3.20Å ()
Ligands: ,
Non-Standard Residues:
Related: 2xg0, 2xg1, 2xg2, 1ibk, 1ibl, 1jch, 2uuc, 2wdk, 2j02, 1j5e, 2wrq, 2j00, 1hnx, 2b9o, 2x9t, 2wh3, 2uub, 1vov, 1emi, 1pnx, 2v46, 2vqf, 2wh1, 1n32, 2wrn, 2f4v, 2jl5, 1twt, 1e44, 1qzc, 2uxd, 1fka, 1fjg, 2uxc, 1n36, 1hnw, 1l1u, 1hr0, 2v48, 2b64, 1xmq, 2b9m, 1pn8, 2wdg, 1xnr, 1hnz, 1dv4, 1rss, 2wdh, 1jgq, 1i94, 1i96, 2uu9, 1pn7, 1eg0, 1ibm, 1ujw, 2uxb, 2vqe, 1g1x, 2uua, 1i95, 1xnq, 1qd7, 1gix, 1jgo, 1jgp, 2x9r, 1n34, 1n33, 1pns, 2jl7, 1yl4, 2wdm, 1xmo, 1i97

Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml

The C terminal domain of colicin E3 kills the cells that it penetrates with its 16s rRNase activity, by actively degrading the subunit of the cell's 70S ribosome. This prevents the cell from producing any proteins once attacked, which will lead to the death of the cell. This rRNA cleavage is specific in vivo, but random when the rRNA domain is isolated in vitro[9]. The cleavage is unaffected by the presence of cellular ribonucleases[10]. The specific cleavage observed in vivo occurs within the ribosomal decoding A-site, in between A1493 and G1494, resulting in the complete halt of protein biosynthesis, leading to cell death[11].


  1. Chak KF. Expression of the ColE3 operon in maxicells. Proc Natl Sci Counc Repub China B. 1993 Apr;17(2):41-7. PMID:7809274
  2. Hiraga S, Sugiyama T, Itoh T. Comparative analysis of the replicon regions of eleven ColE2-related plasmids. J Bacteriol. 1994 Dec;176(23):7233-43. PMID:7525540
  3. Masaki H, Ohta T. Colicin E3 and its immunity genes. J Mol Biol. 1985 Mar 20;182(2):217-27. PMID:3889348
  4. Jakes KS, Model P. Mechanism of export of colicin E1 and colicin E3. J Bacteriol. 1979 Jun;138(3):770-8. PMID:378936
  5. Chak KF. Expression of the ColE3 operon in maxicells. Proc Natl Sci Counc Repub China B. 1993 Apr;17(2):41-7. PMID:7809274
  6. Masaki H, Ohta T. Colicin E3 and its immunity genes. J Mol Biol. 1985 Mar 20;182(2):217-27. PMID:3889348
  7. Masi M, Vuong P, Humbard M, Malone K, Misra R. Initial steps of colicin E1 import across the outer membrane of Escherichia coli. J Bacteriol. 2007 Apr;189(7):2667-76. Epub 2007 Feb 2. PMID:17277071 doi:10.1128/JB.01448-06
  8. Kurisu G, Zakharov SD, Zhalnina MV, Bano S, Eroukova VY, Rokitskaya TI, Antonenko YN, Wiener MC, Cramer WA. The structure of BtuB with bound colicin E3 R-domain implies a translocon. Nat Struct Biol. 2003 Nov;10(11):948-54. Epub 2003 Oct 5. PMID:14528295 doi:10.1038/nsb997
  9. Ohno S, Imahori K. Colicin E3 is an endonuclease. J Biochem. 1978 Dec;84(6):1637-40. PMID:368047
  10. Meyhack B, Meyhack I, Apirion D. Colicin E3: a unique endoribonuclease. Proc Natl Acad Sci U S A. 1973 Jan;70(1):156-60. PMID:4567332
  11. Zarivach R, Ben-Zeev E, Wu N, Auerbach T, Bashan A, Jakes K, Dickman K, Kosmidis A, Schluenzen F, Yonath A, Eisenstein M, Shoham M. On the interaction of colicin E3 with the ribosome. Biochimie. 2002 May-Jun;84(5-6):447-54. PMID:12423788

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