PROSITE documentation PDOC51676
FF domain domain profile


The FF domain is a 60 amino acid residue phosphopeptide-binding module containing two conserved phenylalanine (FF) residues that give name to the domain. While protein-interaction modules are commonly found in functionally unrelated proteins, FF domains are primarily present in only three eukaryotic protein families:

  • the splicing factors FBP11 and Prp40,
  • the transcription factor CA150,
  • p190 RhoGTPase-related proteins.

FF domains are found singly or in multiple copies but the number of FF domains in protein sequences ranges, in general, between two and six [1,2,3,4,5,6].

The FF domain is composed of three α-helices arranged in an orthogonal bundle with a 3(10) helix in the loop between the second and third α helices (see <PDB:1H40>). The two highly conserved phenylalanine residues are in the middle of the first and third α helices, and form part of the hydrophobic core of the protein [3,4,5,6.].

The profile we developed covers the entire FF domain.

Last update:

June 2013 / First entry.


Technical section

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

FF, PS51676; FF domain profile  (MATRIX)


1AuthorsBedford M.T. Leder P.
TitleThe FF domain: a novel motif that often accompanies WW domains.
SourceTrends Biochem. Sci. 24:264-265(1999).
PubMed ID10390614

2AuthorsMorris D.P. Greenleaf A.L.
TitleThe splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II.
SourceJ. Biol. Chem. 275:39935-39943(2000).
PubMed ID10978320

3AuthorsAllen M. Friedler A. Schon O. Bycroft M.
TitleThe structure of an FF domain from human HYPA/FBP11.
SourceJ. Mol. Biol. 323:411-416(2002).
PubMed ID12381297

4AuthorsGasch A. Wiesner S. Martin-Malpartida P. Ramirez-Espain X. Ruiz L. Macias M.J.
TitleThe structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains.
SourceJ. Biol. Chem. 281:356-364(2006).
PubMed ID16253993

5AuthorsBonet R. Ramirez-Espain X. Macias M.J.
TitleSolution structure of the yeast URN1 splicing factor FF domain: comparative analysis of charge distributions in FF domain structures-FFs and SURPs, two domains with a similar fold.
SourceProteins 73:1001-1009(2008).
PubMed ID18536009

6AuthorsBonet R. Ruiz L. Morales B. Macias M.J.
TitleSolution structure of the fourth FF domain of yeast Prp40 splicing factor.
SourceProteins 77:1000-1003(2009).
PubMed ID19722265

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