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PROSITE documentation PDOC51011 [for PROSITE entry PS51011]

ARID domain profile





Description

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 α-helices separated by β-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 α- helices;
  • ARID proteins that supplement the core domain with an N-terminal α- helix;
  • Extended-ARID proteins, which contain the core domain and additional α- 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 α-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.

Last update:

August 2004 / First entry.

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Technical section

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

ARID, PS51011; ARID domain profile  (MATRIX)


References

1AuthorsIwahara J. Clubb R.T.
TitleSolution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).
SourceEMBO J. 18:6084-6094(1999).
PubMed ID10545119
DOI10.1093/emboj/18.21.6084

2AuthorsIwahara J. Iwahara M. Daughdrill G.W. Ford J. Clubb R.T.
TitleThe structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA.
SourceEMBO J. 21:1197-1209(2002).
PubMed ID11867548
DOI10.1093/emboj/21.5.1197

3AuthorsWilsker D. Patsialou A. Dallas P.B. Moran E.
TitleARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development.
SourceCell Growth Differ. 13:95-106(2002).
PubMed ID11959810

4AuthorsKim S. Zhang Z. Upchurch S. Isern N. Chen Y.
TitleStructure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition.
SourceJ. Biol. Chem. 279:16670-16676(2004).
PubMed ID14722072
DOI10.1074/jbc.M312115200



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