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17  structures 289  species 0  interactions 1730  sequences 96  architectures

Family: ARID (PF01388)

Summary: ARID/BRIGHT DNA binding domain

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This is the Wikipedia entry entitled "ARID domain". More...

ARID domain Edit Wikipedia article

ARID
PDB 1ig6 EBI.jpg
human mrf-2 domain, nmr, 11 structures
Identifiers
Symbol ARID
Pfam PF01388
InterPro IPR001606
SCOP 1ig6
SUPERFAMILY 1ig6

In molecular biology, the ARID domain (AT-rich interaction domain; also known as BRIGHT domain))[1] is a protein domain that binds to DNA. ARID domain-containing 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.[2] The basic structure of the ARID 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.[3] 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 with 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.[3]

References[edit]

  1. ^ Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW (1995). "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 9 (24): 3067–82. doi:10.1101/gad.9.24.3067. PMID 8543152. 
  2. ^ Kortschak RD, Tucker PW, Saint R (June 2000). "ARID proteins come in from the desert". Trends Biochem. Sci. 25 (6): 294–9. doi:10.1016/S0968-0004(00)01597-8. PMID 10838570. 
  3. ^ a b Dallas PB, Pacchione S, Wilsker D, Bowrin V, Kobayashi R, Moran E (May 2000). "The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity". Mol. Cell. Biol. 20 (9): 3137–46. doi:10.1128/MCB.20.9.3137-3146.2000. PMC 85608. PMID 10757798. 

This article incorporates text from the public domain Pfam and InterPro IPR001606

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

ARID/BRIGHT DNA binding domain Provide feedback

This domain is know as ARID for AT-Rich Interaction Domain [1] and also known as the BRIGHT domain [3].

Literature references

  1. Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW; , Genes Dev 1995;9:3067-3082.: 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. PUBMED:8543152 EPMC:8543152

  2. Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y; , Nat Struct Biol 1998;5:959-964.: A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases. PUBMED:9808040 EPMC:9808040

  3. Gregory SL, Kortschak RD, Kalionis B, Saint R; , Mol Cell Biol 1996;16:792-799.: Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins. PUBMED:8622680 EPMC:8622680


External database links

This tab holds annotation information from the InterPro database.

InterPro entry 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].

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(53)
Full
(1730)
Representative proteomes NCBI
(1669)
Meta
(7)
RP15
(277)
RP35
(474)
RP55
(782)
RP75
(1077)
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  Seed
(53)
Full
(1730)
Representative proteomes NCBI
(1669)
Meta
(7)
RP15
(277)
RP35
(474)
RP55
(782)
RP75
(1077)
Alignment:
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Sequence:
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  Seed
(53)
Full
(1730)
Representative proteomes NCBI
(1669)
Meta
(7)
RP15
(277)
RP35
(474)
RP55
(782)
RP75
(1077)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Curation and family details

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Curation View help on the curation process

Seed source: [2]
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 53
Number in full: 1730
Average length of the domain: 89.90 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 8.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.3
Noise cut-off 20.8 20.9
Model length: 92
Family (HMM) version: 16
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Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ARID domain has been found. There are 17 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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