| SMART accession number: | SM00501
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| Description: |
DNA-binding domain containing a helix-turn-helix structure |
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| Interpro abstract (IPR001606): |
Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT 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. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 [(PUBMED:10757798)]. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [(PUBMED:10757798)].
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| GO component: | intracellular (GO:0005622) |
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| GO function: | DNA binding (GO:0003677) |
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| Family alignment: |
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Click on the following links for more information.
- Evolution (species in which this domain is found)
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- Literature (relevant references for this domain)
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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 replication and 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 least sixteen recently identified DNA-binding proteins. The three-dimensional structure of one of these domains, Mrf-2, has been solved using NMR methods. This structure is significantly different from known DNA-binding domain structures. The mechanism of DNA recognition by this motif has been suggested based on conserved residues, surface electrostatic potentials and chemical shift changes. This new DNA-binding motif shares structural homology with T4 RNase H, E. coli endonuclease III and Bacillus subtilis DNA polymerase I. The structural homology suggests a mechanism for substrate recognition by these enzymes.
- Treisman JE, Luk A, Rubin GM, Heberlein U
- eyelid antagonizes wingless signaling during Drosophila development and has homology to the Bright family of DNA-binding proteins.
- Genes Dev. 1997; 11: 1949-62
- Display abstract
In Drosophila, pattern formation at multiple stages of embryonic and imaginal development depends on the same intercellular signaling pathways. We have identified a novel gene, eyelid (eld), which is required for embryonic segmentation, development of the notum and wing margin, and photoreceptor differentiation. In these tissues, eld mutations have effects opposite to those caused by wingless (wg) mutations. eld encodes a widely expressed nuclear protein with a region homologous to a novel family of DNA-binding domains. Based on this homology and on the phenotypic analysis, we suggest that Eld could act as a transcription factor antagonistic to the Wg pathway.
- Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW
- The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein 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) promoter and the intronic enhancer (E mu). The gene encoding a protein that binds a VH promoter proximal site necessary for induced mu-heavy-chain transcription has been cloned. This B-cell specific protein, termed Bright (B cell regulator of IgH transcription), is found in both soluble and matrix insoluble nuclear fractions. Bright binds the minor groove of a restricted ATC sequence that is sufficient for nuclear matrix association. This sequence motif is present in previously described matrix-associating regions (MARs) proximal to the promoter and flanking E mu. Bright can activate E mu-driven transcription by binding these sites, but only when they occur in their natural context and in cell lines permissive for E mu activity. To bind DNA, Bright requires a novel tetramerization domain and a previously undescribed domain that shares identity with several proteins, including SWI1, a component of the SWI/SNF complex.
- Structure (3D structures containing this domain)
3D Structures of BRIGHT 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)
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