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44  structures 762  species 0  interactions 4291  sequences 164  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 , plants [2] 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.[3] 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.[4] 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.[4]

References

  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. ^ Zheng B, He H, Zheng Y, Wu W, McCormick S (2014) An ARID Domain-Containing Protein within Nuclear Bodies Is Required for Sperm Cell Formation in Arabidopsis thaliana. PLoS Genet 10(7): e1004421. doi: 10.1371/journal.pgen.1004421
  3. ^ 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. 
  4. ^ 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 85608Freely accessible. 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

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 [PUBMED:10545119, PUBMED:11867548]. The ARID domain appears as a single-copy motif and can be found in association with other domains, such as JmjC, JmjN, Tudor and PHD-type zinc finger [PUBMED:11959810].

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 [PUBMED:10545119, PUBMED:11867548, PUBMED:14722072].

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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HTH (CL0123), which has the following description:

This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

The clan contains the following 256 members:

AbiEi_3_N AbiEi_4 ANAPC2 AphA_like Arg_repressor ARID B-block_TFIIIC Bac_DnaA_C BetR Bot1p BrkDBD C_LFY_FLO Cdc6_C CENP-B_N Cro Crp CSN8_PSD8_EIF3K Cullin_Nedd8 CUT DDRGK DEP Dimerisation Dimerisation2 DsrD DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF2582 DUF3116 DUF3253 DUF3853 DUF3860 DUF3908 DUF433 DUF4364 DUF4447 DUF480 DUF722 DUF739 DUF742 DUF977 E2F_TDP EAP30 ELL ESCRT-II Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC FokI_C FokI_N Forkhead Ftsk_gamma FUR GcrA GerE GntR HARE-HTH HemN_C HNF-1_N Homeobox Homeobox_KN Homez HPD HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_46 HTH_47 HTH_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_micro HTH_OrfB_IS605 HTH_psq HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IBD IF2_N IRF KicB KORA KorB La LacI LexA_DNA_bind Linker_histone LZ_Tnp_IS481 MADF_DNA_bdg MarR MarR_2 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 Mor MotA_activ MqsA_antitoxin MRP-L20 Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-bind_7 Myb_DNA-binding Neugrin NUMOD1 OST-HTH P22_Cro PaaX PadR PAX PCI Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S19e Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP RuvB_C SAC3_GANP SANT_DAMP1_like SatD SelB-wing_1 SelB-wing_2 SelB-wing_3 SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_ner Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SLIDE SMC_ScpB SpoIIID STN1_2 Sulfolobus_pRN SWIRM TBPIP Terminase_5 TetR_N TFIIE_alpha TFIIE_beta TFIIF_alpha TFIIF_beta Tn7_Tnp_TnsA_C Tn916-Xis TraI_2_C Trans_reg_C TrfA TrmB Trp_repressor UPF0122 Vir_act_alpha_C YdaS_antitoxin YjcQ YokU z-alpha

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(453)
Full
(4291)
Representative proteomes UniProt
(6628)
NCBI
(12161)
Meta
(7)
RP15
(906)
RP35
(2041)
RP55
(3213)
RP75
(4021)
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  Seed
(453)
Full
(4291)
Representative proteomes UniProt
(6628)
NCBI
(12161)
Meta
(7)
RP15
(906)
RP35
(2041)
RP55
(3213)
RP75
(4021)
Alignment:
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  Seed
(453)
Full
(4291)
Representative proteomes UniProt
(6628)
NCBI
(12161)
Meta
(7)
RP15
(906)
RP35
(2041)
RP55
(3213)
RP75
(4021)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: [2]
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 453
Number in full: 4291
Average length of the domain: 87.30 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 8.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.5
Model length: 89
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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 44 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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