{PDOC51526}
{PS51526; RFX_DBD}
{BEGIN}
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* RFX-type winged-helix DNA-binding domain profile *
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The RFX  family  of  transcription  factors  is characterized by a unique ~75-
residue DNA-binding  domain.  RFX genes have been isolated in yeasts, nematode
and vertebrates.  The  characteristic RFX-type HTH DNA binding domain has been
recruited into  otherwise  very  divergent regulatory factors functioning in a
diverse spectrum  of  unrelated  systems,  including regulation of the mitotic
cell cycle  in  fission  yeast, the control of the immune response in mammals,
and infection by human hepatitis B virus [1,2].

The RFX-type  DNA-binding  domain  is  an  unusual  member of the winged-helix
subfamily of helix-turn-helix domains because it uses a beta-hairpin (or wing)
to recognize  DNA  instead of the recognition helix typical of helix-tun-helix
domains. It  consists  of  three alpha-helices (H), three beta-strands (S) and
three connecting  loops (L), arranged in the order H1-S1-H2-L1-H3-L2-S2-W1-S3.
The third  loop,  connecting  beta-strands  S2  and  S3,  forms wing W1 of the
winged-helix motif  (see  <PDB:1DP7>).  In  contrast  to  previously described
winged-helix DBDs (typically 110 residues long with two wings, W1 and W2), the
shorter RFX-type winged-helix DNA-binding domain has only one wing [3].

Some proteins  known to contain a RFX-type winged-helix DNA-binding domain are
listed below:

 - Human RFX1, a cellular transactivator that is used by the highly pathogenic
   hepatitis B virus.
 - Human RFX2.
 - Human RFX3, a transcription factor required for ciliogenesis and islet cell
   differentiation during endocrine pancreas development.
 - Human RFX5, a regulator of MHC class II gene transcription.
 - Human  ARID2,  a  component  of  the  SWI/SNF-B (PBAF) chromatin remodeling
   complex [4].
 - Yeast  Crt1,  an  effector  of  the  DNA damage and replication checkpoint.
 - Schizosaccharomyces pombe sak1, an essential regulatory protein in the life
   cycle. It  allows  cells  to  exit  the  mitotic cycle and enter either the
   stationary phase or the pathway leading to sexual differentiation.

The profile  we  developed covers the entire RFX-type winged-helix DNA-binding
domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: March 2011 / First entry.

[ 1] Emery P., Durand B., Mach B., Reith W.
     "RFX proteins, a novel family of DNA binding proteins conserved in the
     eukaryotic kingdom."
     Nucleic Acids Res. 24:803-807(1996).
     PubMed=8600444
[ 2] Durand B., Vandaele C., Spencer D., Pantalacci S., Couble P.
     "Cloning and characterization of dRFX, the Drosophila member of the
     RFX family of transcription factors."
     Gene 246:285-293(2000).
     PubMed=10767550
[ 3] Gajiwala K.S., Chen H., Cornille F., Roques B.P., Reith W., Mach B.,
     Burley S.K.
     "Structure of the winged-helix protein hRFX1 reveals a new mode of DNA
     binding."
     Nature 403:916-921(2000).
     PubMed=10706293; DOI=10.1038/35002634
[ 4] Patsialou A., Wilsker D., Moran E.
     "DNA-binding properties of ARID family proteins."
     Nucleic Acids Res. 33:66-80(2005).
     PubMed=15640446; DOI=10.1093/nar/gki145

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