{PDOC52015}
{PS52015; TONB_CTD}
{BEGIN}
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* TonB C-terminal domain profile *
**********************************

The cell  wall  of  Gram-negative bacteria consists of two lipid bilayers, the
outer membrane  (OM)  and the cytoplasmic membrane (CM) with the peptidoglycan
layer in  between.  The  OM protects Gram-negative bacteria from environmental
hazards such  as  antibiotics  and detergents. At the same time, Gram-negative
bacteria require  rare  essential  nutrients  such  as iron, vitamins that are
present in  the  extracellular  environment  at very low concentrations. Gram-
negative bacteria   have  evolved  active  acquisition  systems  to  pass  the
essential nutrients  through  OM  and  CM.  Since  there is no electrochemical
gradient to power the active transport at the OM and no ATP in the periplasmic
space, these  transporters must extract energy from the CM. These transporters
in the  OM  are  termed  TonB-dependent transporters (TBDTs) (see <PDOC00354>)
because they  presumably extract the energy from the proton-motive force (pmf)
of the CM via the trans-periplasmic protein, TonB protein. Whereas generally a
single TonB protein allows the acquisition of several nutrients through their
cognate receptor,  in  some  species  one  particular  TonB  is dedicated to a
specific system.  TonB  is  generally  found in complex with the ExbB and ExbD
proteins, located  in  the  cytoplasmic  membrane. ExbB and ExbD are accessory
proteins anchored  in  the  CM that convey the pmf across the CM to TonB. TonB
protein mediates  the energy transduction from the CM to TBDTs. TonB has an N-
terminal transmembrane  (TM)  domain  anchored  in  the  CM.  The TM domain is
followed by  the  central  region  mostly  consisting  of  Pro-Glu and Pro-Lys
repeats. Extended  conformation  of  the  central region allows the protein to
span the  periplasmic  space between OM and CM. The C-terminal domain (CTD) of
TonB protein  has  a  globular structure of ~100 residues and interacts with a
conserved TonB  box  motif  located  at  the N-terminus of TBDTs, which likely
induces structural changes in the OM transporters (see <PDOC00354>) [1,2,3,4].

The TonB  C-terminal  domain  is composed of a mixed alpha/beta structure that
contains three beta-strands and one alpha-helix (see <PDB:1XX3>) [1,2,3,4].

The profile we developed covers the entire TonB C-terminal domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: January 2023 / First entry.

[ 1] Oeemig J.S., Ollila O.H.S., Iwai H.
     "NMR structure of the C-terminal domain of TonB protein from
     Pseudomonas  aeruginosa."
     PeerJ 6:E5412-E5412(2018).
     PubMed=30186676; DOI=10.7717/peerj.5412
[ 2] Koedding J., Killig F., Polzer P., Howard S.P., Diederichs K.,
     Welte W.
     "Crystal structure of a 92-residue C-terminal fragment of TonB from
     Escherichia  coli reveals significant conformational changes compared
     to structures of smaller  TonB fragments."
     J. Biol. Chem. 280:3022-3028(2005).
     PubMed=15522863; DOI=10.1074/jbc.M411155200
[ 3] Peacock R.S., Weljie A.M., Howard S.P., Price F.D., Vogel H.J.
     "The solution structure of the C-terminal domain of TonB and
     interaction studies  with TonB box peptides."
     J. Mol. Biol. 345:1185-1197(2005).
     PubMed=15644214; DOI=10.1016/j.jmb.2004.11.026
[ 4] de Amorim G.C., Prochnicka-Chalufour A., Delepelaire P., Lefevre J.,
     Simenel C., Wandersman C., Delepierre M., Izadi-Pruneyre N.
     "The structure of HasB reveals a new class of TonB protein fold."
     PLoS One. 8:E58964-E58964(2013).
     PubMed=23527057; DOI=10.1371/journal.pone.0058964

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