{PDOC51979}
{PS51979; YEBF_CMI}
{BEGIN}
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* YebF/Cmi domain profile *
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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 alpha-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 AlphaBeta-fold stabilized by a
single disulfide  bond.  The  core YebF/Cmi domain comprises a long N-terminal
alpha-helix followed by a four-stranded C-terminal beta-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  alpha-helix and the four-stranded beta-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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: July 2021 / First entry.

[ 1] Ghequire M.G.K., Buchanan S.K., De Mot R.
     "The ColM Family, Polymorphic Toxins Breaching the Bacterial Cell
     Wall."
     mBio 9:0-0(2018).
     PubMed=29440573; DOI=10.1128/mBio.02267-17
[ 2] Gerard F., Brooks M.A., Barreteau H., Touze T., Graille M., Bouhss A.,
     Blanot D., van Tilbeurgh H., Mengin-Lecreulx D.
     "X-ray structure and site-directed mutagenesis analysis of the
     Escherichia coli colicin M immunity protein."
     J. Bacteriol. 193:205-214(2011).
     PubMed=21037007; DOI=10.1128/JB.01119-10
[ 3] Uson I., Patzer S.I., Rodriguez D.D., Braun V., Zeth K.
     "The crystal structure of the dimeric colicin M immunity protein
     displays a 3D domain swap."
     J. Struct. Biol. 178:45-53(2012).
     PubMed=22366279; DOI=10.1016/j.jsb.2012.02.004
[ 4] Prehna G., Zhang G., Gong X., Duszyk M., Okon M., McIntosh L.P.,
     Weiner J.H., Strynadka N.C.J.
     "A protein export pathway involving Escherichia coli porins."
     Structure 20:1154-1166(2012).
     PubMed=22658749; DOI=10.1016/j.str.2012.04.014

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{END}