{PDOC51512}
{PS51512; DFDF}
{PS51513; FFD}
{PS51536; TFG}
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* DFDF domain and FFD and TFG boxes profiles *
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Sm and  Sm-like  proteins  of  the RNA-binding Lsm (like Sm) domain family are
found in  all  domains  of  life  and are generally involved in important RNA-
processing tasks.  Lsm13-16 homologs share a domain organization consisting of
a divergent  N-terminal Lsm domain and a central or C-terminal consensus motif
DFDF-x(7)-F closely  preceded  and  followed  by  further  phenylalanines  and
charged aspartates/glutamates  and  arginines/lysines/histidines. The variable
seven-residue tract  of this consensus motif usually contains an asparagine at
the third  or  fourth  position except of one sequence where the asparagine is
replaced by  a  glycine. In few other sequences, the DFDF box is replaced by a
DYDF or  EFDF  box  [1]. The DFDF domain is a heterodimerization domain, which
adopts a helical conformation upon binding (see <PDB:2WAX>). It folds into two
consecutive alpha  helices  that  are  preceded and connected by the FDF and a
related FDK sequence [2].

Two other  strongly  conserved FFD box and TFG box sequence motifs Y-x-K-x(3)-
FFD-x-[IL]-S and   [RKH]-x(2,5)-E-x(0-2)-[RK]-x(3,4)-[DE]-TFG   contained   in
Lsm13-15, but  not  Lsm16, homologs succeed the DFDF-x(7)-F motif and are also
predicted to be of helical nature [1].

The profiles we developed cover the entire DFDF domain and FFD and TFG boxes.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: May 2011 / First entry.

[ 1] Albrecht M., Lengauer T.
     "Novel Sm-like proteins with long C-terminal tails and associated
     methyltransferases."
     FEBS Lett. 569:18-26(2004).
     PubMed=15225602; DOI=10.1016/j.febslet.2004.03.126
[ 2] Tritschler F., Braun J.E., Eulalio A., Truffault V., Izaurralde E.,
     Weichenrieder O.
     "Structural basis for the mutually exclusive anchoring of P body
     components EDC3 and Tral to the DEAD box protein DDX6/Me31B."
     Mol. Cell 33:661-668(2009).
     PubMed=19285948; DOI=10.1016/j.molcel.2009.02.014

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