Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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ARID ARID/BRIGHT DNA binding domain

SMART accession number:	SM01014
Description:	Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure (PUBMED:10838570). 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; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 987 ARID domains in 985 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a ARID domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with ARID domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Cellular role (predicted cellular role)

• Cellular role: chromatin
  Binding / catalysis: DNA binding

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y
  • A novel DNA-binding motif shares structural homology to DNA replicationand repair nucleases and polymerases.
  • Nat Struct Biol. 1998; 5: 959-64
  • Display abstract

  • A novel class of DNA-binding domains has been established from at leastsixteen recently identified DNA-binding proteins. The three-dimensionalstructure of one of these domains, Mrf-2, has been solved using NMRmethods. This structure is significantly different from known DNA-bindingdomain structures. The mechanism of DNA recognition by this motif has beensuggested based on conserved residues, surface electrostatic potentialsand chemical shift changes. This new DNA-binding motif shares structuralhomology with T4 RNase H, E. coli endonuclease III and Bacillus subtilisDNA polymerase I. The structural homology suggests a mechanism forsubstrate recognition by these enzymes.

  • Gregory SL, Kortschak RD, Kalionis B, Saint R
  • Characterization of the dead ringer gene identifies a novel, highlyconserved family of sequence-specific DNA-binding proteins.
  • Mol Cell Biol. 1996; 16: 792-9
  • Display abstract

  • We reported the identification of a new family of DNA-binding proteinsfrom our characterization of the dead ringer (dri) gene of Drosophilamelanogaster. We show that dri encodes a nuclear protein that contains asequence-specific DNA-binding domain that bears no similarity to knownDNA-binding domains. A number of proteins were found to contain sequenceshomologous to this domain. Other proteins containing the conserved motifinclude yeast SWI1, two human retinoblastoma binding proteins, and othermammalian regulatory proteins. A mouse B-cell-specific regulator exhibits75% identity with DRI over the 137-amino-acid DNA-binding domains of theseproteins, indicating a high degree of conservation of this domain. Gelretardation and optimal binding site screens revealed that the in vitrosequence specificity of DRI is strikingly similar to that of manyhomeodomain proteins, although the sequence and predicted secondarystructure do not resemble a homeodomain. The early general expression ofdri and the similarity of DRI and homeodomain in vitro DNA-bindingspecificity compound the problem of understanding the in vivo specificityof action of these proteins. Maternally derived dri product is foundthroughout the embryo until germ band extension, when dri is expressed ina developmentally regulated set of tissues, including salivary glandducts, parts of the gut, and a subset of neural cells. The discovery ofthis new, conserved DNA-binding domain offers an explanation for theregulatory activity of several important members of this class andpredicts significant regulatory roles for the others.

  • Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW
  • The immunoglobulin heavy-chain matrix-associating regions are bound byBright: a B cell-specific trans-activator that describes a new DNA-bindingprotein family.
  • Genes Dev. 1995; 9: 3067-82
  • Display abstract

  • B lymphocyte-restricted transcription of immunoglobulin heavy-chain (IgH)genes is specified by elements within the variable region (VH) promoterand the intronic enhancer (E mu). The gene encoding a protein that binds aVH promoter proximal site necessary for induced mu-heavy-chaintranscription has been cloned. This B-cell specific protein, termed Bright(B cell regulator of IgH transcription), is found in both soluble andmatrix insoluble nuclear fractions. Bright binds the minor groove of arestricted ATC sequence that is sufficient for nuclear matrix association.This sequence motif is present in previously described matrix-associatingregions (MARs) proximal to the promoter and flanking E mu. Bright canactivate E mu-driven transcription by binding these sites, but only whenthey occur in their natural context and in cell lines permissive for E muactivity. To bind DNA, Bright requires a novel tetramerization domain anda previously undescribed domain that shares identity with severalproteins, including SWI1, a component of the SWI/SNF complex.

• Structure (3D structures containing this domain)

• 3D Structures of ARID domains in PDB

  PDB code	Main view	Title
  1c20		Solution structure of the dna-binding domain from the dead ringer protein
  1ig6		Human mrf-2 domain, nmr, 11 structures
  1kkx		Solution structure of the dna-binding domain of adr6
  1kn5		Solution structure of arid domain of adr6 from saccharomyces cerevisiae
  1kqq		Solution structure of the dead ringer arid-dna complex
  1ryu		Solution structure of the swi1 arid
  2cxy		Crystal structure of the hbaf250b at-rich interaction domain (arid)
  2eh9		Crystal structure of the hbaf250b at-rich interaction domain (arid)
  2eqy		Solution structure of the arid domain of jarid1b protein
  2jrz		Solution structure of the bright/arid domain from the human jarid1c protein.
  2jxj		Nmr structure of the arid domain from the histone h3k4 demethylase rbp2
  2kk0		Solution structure of dead ringer-like protein 1 (at-rich interactive domain-containing protein 3a) from homo sapiens, northeast structural genomics consortium (nesg) target hr4394c
  2oeh		Determination of the three-dimensional structure of the mrf2-dna complex using paramagnetic spin labeling
  2rq5		Solution structure of the at-rich interaction domain (arid) of jumonji/jarid2
  2yqe		Solution structure of the arid domain of jarid1d protein

• Links (links to other resources describing this domain)

• PFAM	ARID

Send comments to Ivica Letunic