{PDOC51011}
{PS51011; ARID}
{BEGIN}
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* ARID domain profile *
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The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module
found in a large number of eukaryotic transcription factors that regulate cell
proliferation, differentiation  and development [1,2]. The ARID domain appears
as a  single-copy  motif  and  can be found in association with other domains,
such as  JmjC,  JmjN,  Tudor  (see  <PDOC50304>) and PHD-type zinc finger (see
<PDOC50016>) [3].

The basic  structure  of  the ARID domain domain appears to be a series of six
alpha-helices separated  by  beta-strands, loops, or turns, but the structured
region may  extend  to an additional helix at either or both ends of the basic
six. Based  on  primary  sequence homology, they can be partitioned into three
structural classes:

 - Minimal  ARID  proteins  that consist of a core domain formed by six alpha-
   helices;
 - ARID  proteins  that  supplement  the core domain with an N-terminal alpha-
   helix;
 - Extended-ARID proteins, which contain the core domain and additional alpha-
   helices at their N- and C-termini.

Minimal ARIDs  are  distributed  in  all  eukaryotes, while extended ARIDs are
restricted to  metazoans.  The ARID domain binds DNA as a monomer, recognizing
the duplex  through  insertion  of  a  loop  and an alpha-helix into the major
groove, and  by  extensive  non-specific  anchoring  contacts  to the adjacent
sugar-phosphate backbone [1,2,4].

Some proteins known to contain a ARID domain are listed below:

 - Eukaryotic transcription factors of the jumonji family.
 - Mammalian Bright, a B-cell-specific trans-activator of IgH transcription.
 - Mammalian PLU-1, a protein that is upregulated in breast cancer cells.
 - Mammalian RBP1 and RBP2, retinoblastoma binding factors.
 - Mammalian    Mrf-1   and   Mrf-2,   transcriptional   modulators   of   the
   cytomegalovirus major intermediate-early promoter.
 - Drosophila  melanogaster  Dead ringer protein, a transcriptional regulatory
   protein required for early embryonic development.
 - Yeast  SWI1  protein,  from  the  SWI/SNF  complex  involved  in  chromatin
   remodeling and broad aspects of transcription regulation.
 - Drosophila  melanogaster  Osa.  It  is  structurally  related  to  SWI1 and
   associates with  the  brahma complex, which is the Drosophila equivalent of
   the SWI/SNF complex.

The profile we developed covers the ARID core domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: August 2004 / First entry.

[ 1] Iwahara J., Clubb R.T.
     "Solution structure of the DNA binding domain from Dead ringer, a
     sequence-specific AT-rich interaction domain (ARID)."
     EMBO J. 18:6084-6094(1999).
     PubMed=10545119; DOI=10.1093/emboj/18.21.6084
[ 2] Iwahara J., Iwahara M., Daughdrill G.W., Ford J., Clubb R.T.
     "The structure of the Dead ringer-DNA complex reveals how AT-rich
     interaction domains (ARIDs) recognize DNA."
     EMBO J. 21:1197-1209(2002).
     PubMed=11867548; DOI=10.1093/emboj/21.5.1197
[ 3] Wilsker D., Patsialou A., Dallas P.B., Moran E.
     "ARID proteins: a diverse family of DNA binding proteins implicated in
     the control of cell growth, differentiation, and development."
     Cell Growth Differ. 13:95-106(2002).
     PubMed=11959810
[ 4] Kim S., Zhang Z., Upchurch S., Isern N., Chen Y.
     "Structure and DNA-binding sites of the SWI1 AT-rich interaction
     domain (ARID) suggest determinants for sequence-specific DNA
     recognition."
     J. Biol. Chem. 279:16670-16676(2004).
     PubMed=14722072; DOI=10.1074/jbc.M312115200

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