PROSITE documentation PDOC51979
YebF/Cmi domain profile


Bacteriocins are proteins secreted by many bacterial cells to kill related bacteria of the same niche. To avoid their own suicide through reuptake of secreted bacteriocins, these bacteria protect themselves by co-expression of immunity proteins in the compartment of colicin destination. Colicin M (ColM) is an enzyme (phosphodiesterase) catalyzing the hydrolysis of the peptidoglycan lipid II precursor undecaprenyl-pyrophospho-MurNAc (-pentapeptide)-GlcNAc (where MurNAc and GlcNAc represent N-acetylmuramic acid and N-acetylglucosamine, respectively), thereby inhibiting peptidoglycan polymerization steps and provoking cell lysis. ColM-producing strains are protected from the toxin that they produce by coexpression of a specific immunity protein, named Cmi. Cmi is anchored in the cytoplasmic membrane with an α-helix and contains a periplasmic domain that shows sequence similarity to YebF-like proteins which are known to be secreted into the external medium by some Gram-negative bacteria. The YebF/Cmi domain is typified by two cysteine residues, required for Cmi folding and structure stabilization [1,2,3,4].

The monomeric YebF/Cmi domain shows a mixed αβ-fold stabilized by a single disulfide bond. The core YebF/Cmi domain comprises a long N-terminal α-helix followed by a four-stranded C-terminal β-sheet (see <PDB:2XGL>) [2,4]. Dimerization of the domain has been shown to occur in monomer-dimer equilibrium and is mediated by an extended interface of hydrogen bond interactions between the α-helix and the four-stranded β-sheet of the symmetry related molecule. Two intermolecular disulfide bridges covalently connect this dimer to further lock this complex (see <PDB:4AEQ>) [3].

The profile we developed covers the entire YebF/Cmi domain.

Last update:

July 2021 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

YEBF_CMI, PS51979; YebF/Cmi domain profile  (MATRIX)


1AuthorsGhequire M.G.K. Buchanan S.K. De Mot R.
TitleThe ColM Family, Polymorphic Toxins Breaching the Bacterial Cell Wall.
SourcemBio 9:0-0(2018).
PubMed ID29440573

2AuthorsGerard F. Brooks M.A. Barreteau H. Touze T. Graille M. Bouhss A. Blanot D. van Tilbeurgh H. Mengin-Lecreulx D.
TitleX-ray structure and site-directed mutagenesis analysis of the Escherichia coli colicin M immunity protein.
SourceJ. Bacteriol. 193:205-214(2011).
PubMed ID21037007

3AuthorsUson I. Patzer S.I. Rodriguez D.D. Braun V. Zeth K.
TitleThe crystal structure of the dimeric colicin M immunity protein displays a 3D domain swap.
SourceJ. Struct. Biol. 178:45-53(2012).
PubMed ID22366279

4AuthorsPrehna G. Zhang G. Gong X. Duszyk M. Okon M. McIntosh L.P. Weiner J.H. Strynadka N.C.J.
TitleA protein export pathway involving Escherichia coli porins.
SourceStructure 20:1154-1166(2012).
PubMed ID22658749

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