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PROSITE documentation PDOC51512

DFDF domain and FFD and TFG boxes profiles





Description

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 α 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.

PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html --------------------------------------------------------------------------------.

Last update:

May 2011 / First entry.

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Technical section

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

DFDF, PS51512; DFDF domain profile  (MATRIX)

FFD, PS51513; FFD box profile  (MATRIX)

TFG, PS51536; TFG box profile  (MATRIX)


References

1AuthorsAlbrecht M. Lengauer T.
TitleNovel Sm-like proteins with long C-terminal tails and associated methyltransferases.
SourceFEBS Lett. 569:18-26(2004).
PubMed ID15225602
DOI10.1016/j.febslet.2004.03.126

2AuthorsTritschler F. Braun J.E. Eulalio A. Truffault V. Izaurralde E. Weichenrieder O.
TitleStructural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B.
SourceMol. Cell 33:661-668(2009).
PubMed ID19285948
DOI10.1016/j.molcel.2009.02.014



PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.

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