ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of transcription factors, found in a broad array of organisms from fungi to mammals, is characterized by a highly conserved, helix-turn-helix DNA binding domain that binds to the major groove of DNA. The ARID domain, also called BRIGHT, was first identified in the mouse B-cell-specific transcription factor Bright and in the product of the dead ringer (dri) gene of Drosophila melanogaster. ARID family members are implicated in normal development, differentiation, cell cycle regulation, transcriptional activation and chromatin remodeling. Different family members exhibit different DNA-binding properties. Drosophila Dri, mammalian ARID3A/3B/3C and ARID5A/5B, selectively bind AT-rich sites. However, ARID1A/1B, Drosophila Osa, yeast SWI1, ARID2, ARID4A/4B, JARID1A/1B/1C/1D, and JARID2, bind DNA without sequence specificity.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFEEYCRS 80
Cdd:cd16883    13 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYRKYLYGFEEYCTS 92

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1, or RBBP1L1), is a tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating cell cycle. ARID4B contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFEEYCRS 80
Cdd:cd16883    13 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYRKYLYGFEEYCTS 92

chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; Retinoblastoma-binding protein 1 (RBP1), also termed AT-rich interaction domain 4A, is a ubiquitously expressed nuclear protein. RBP1 is a tumor and leukemia suppressor that binds both methylated histone tails and DNA, and is involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. The chromo barrel domain of RBP1 has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. RBP1 binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation; pRB represses transcription by recruiting RBP1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain.

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                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720376127 254 MKVQVRYGRGKNQKMYEASIKDSDVEGGEALYLVHYCGWNVRYDEWIKADKIVRPADK 311
Cdd:cd18641     1 TKVKVKYGRGKTQKIYEASIKSTEIDDGEVLYLVHYYGWNVRYDEWVKADRIIWPLDK 58

RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilization of Ht2 is essential for RNA binding.

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                  ....*....|....*....|....*....|....*....|....*.
gi 1720376127 260 YGRGKNQKMYEASIKDSDVEGGEALYLVHYCGWNVRYDEWIKADKI 305
Cdd:pfam11717   8 LVRKRDGEWRLAEILSIRPKKGKYEYYVHYVGFNKRLDEWVPEDRI 53

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1, or RBBP1L1), is a tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating cell cycle. ARID4B contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFEEYCRS 80
Cdd:cd16883    13 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYRKYLYGFEEYCTS 92

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1, or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B (also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities. It is also involved in the pocket domain of pRb-mediated repression of E2F-dependent transcription and cellular proliferation. Moreover, it acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFE 75
Cdd:cd16882    13 MEDRGTPINKPPVLGYKDLNLFKLFRLVYQQGGCDNIESGSVWKQIYMDLGIPILNSAASYNVKTAYRKYLYGFE 87

BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720376127    1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFEEYCR 79
Cdd:smart00501  14 MEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPYERFLR 92

chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; Retinoblastoma-binding protein 1 (RBP1), also termed AT-rich interaction domain 4A, is a ubiquitously expressed nuclear protein. RBP1 is a tumor and leukemia suppressor that binds both methylated histone tails and DNA, and is involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. The chromo barrel domain of RBP1 has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. RBP1 binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation; pRB represses transcription by recruiting RBP1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain.

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                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720376127 254 MKVQVRYGRGKNQKMYEASIKDSDVEGGEALYLVHYCGWNVRYDEWIKADKIVRPADK 311
Cdd:cd18641     1 TKVKVKYGRGKTQKIYEASIKSTEIDDGEVLYLVHYYGWNVRYDEWVKADRIIWPLDK 58

malignant brain tumor (MBT) repeat found in PHD finger protein 20-like protein 1 (PHF20L1) and similar domains; PHF20L1 associates with SOX2, antagonizes SOX2 ubiquitination and the sequential degradation induced by MLL1/WDR5 complexes. It binds both monomethylated Lys-42 and Lys-117 in SOX2 and thereby prevents SOX2 proteolysis. PHF20L1 also reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 degradation. PHF20L1 contains one MBT (malignant brain tumor) repeat. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the MBT repeat of PHF20L1 and similar domains that contains the semi-aromatic cage that may bind methylated lysine residues.

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720376127 250 YPPGMKVQVRYGRGKnqkMYEASIKDSDVEGGEalYLVHYCGWNVRYDEWIKAD 303
Cdd:cd20104     1 FKVGDRVDALDGEGK---WYEAKIVEVDEEENK--VLVHYDGWSSRYDEWIDRD 49

chromo barrel domain of MOF acetyltransferase, and similar proteins; This group includes the chromo barrel domains found in human Tat-interactive protein 60 (TIP60, (also known as KAT5 or HTATIP), Drosophila melanogaster males-absent on the first (MOF) protein, human male-specific lethal (MSL) complex subunit 3 (MSL3), and retinoblastoma binding protein 1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. The chromobarrel domains include a MOF-like subgroup which may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720376127 255 KVQVRYGRGKNQKMYEASIKDSDV---EGGEALYLVHYCGWNVRYDEWIKADKIVRPADK 311
Cdd:cd18643     2 KVLVFEPDPKARVLYDAKILSVITgkdGRAPPEYLVHYVGWNRRLDEWVAEDRVLPDLDE 61

ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins; This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVlNSAAGYNVKCAYKKYLYGFEeyCR 79
Cdd:cd16865    14 MEERGSPITNCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIGA-SSSAAFTLRKNYIKYLLAYE--CR 89

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ARID3B, ARID3C, dead ringer (Dri) from Drosophila melanogaster, and similar proteins; The ARID3 subfamily includes AT-rich interactive domain (ARID, also known as BRIGHT)-containing proteins ARID3A, ARID3B and ARID3C, which are the most direct mammalian counterparts of the Drosophila "dead ringer" protein Dri. They consist of an acidic N-terminal region of unknown function, the central ARID matrix association (or attachment) region (MAR)-DNA binding domain, a SUMO-I conjugation (SUMO) motif, and a multifunctional homomerization/nuclear export REKLES domain in the C-terminal third of the molecule. The ARID domain in this subfamily has been described as the "extended" or e-ARID due to additional conserved sequences at both the N and C termini of the core ARID region. The REKLES domain is found only in the ARID3 subfamily. It has co-evolved with and regulates functional properties of the ARID DNA-binding domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFE 75
Cdd:cd16867    24 MQKRGTPVNRIPIMAKQVLDLYELYRLVVEKGGLVEVINKKIWREITKGLNLPSSITSAAFTLRTQYMKYLYPYE 98

ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar proteins; Dri, also termed retained (retn), is a nuclear protein with a sequence-specific DNA-binding domain termed AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is a founding member of the ARID family. Sequence comparison shows that DRI belongs to the "extended" or e-ARID subfamily, which exhibits an extended region of similarity either side of the ARID. Dri plays an important role in embryogenesis. It functions as an essential transcription factor involved in aspects of dorsal/ventral and anterior/posterior axis patterning, as well as myogenesis and hindgut development.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFE 75
Cdd:cd16881    31 MQKRGTPVNRIPIMAKQVLDLYELYNLVVARGGLVEVINKKLWREITKGLHLPSSITSAAFTLRTQYMKYLYPYE 105

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins; ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720376127   4 RGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFE 75
Cdd:cd16866    16 RGTPFKKIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFALKQIYLRYLEAYE 87

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins; ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex, which is a signal-sensing modulator of histone methylation and gene transcription. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Its polymorphism has been associated with risk for pediatric acute lymphoblastic leukemia (ALL). ARID5B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which can bind both the major and minor grooves of its target sequences.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYKKYLYGFEEYCR 79
Cdd:cd16885    13 MKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERLILPYERFIK 91

chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; This subgroup includes human male-specific lethal (MSL) complex subunit 3 (MSL3, also known as MSL3L1). The MSL3 chromodomain specifically recognizes the H4K20 monomethyl mark, in a DNA-dependent manner, and may be involved in chromosomal targeting of the MSL complex. Also included is MORF-related gene on chromosome 15 (MRG15, also known as MORF4L1) which specifically binds to Lys36-methylated histone H3 and plays a role in transcriptional regulation and in DNA repair. This subgroup also includes Arabidopsis thaliana Morf Related Gene 2 (MRG2) which acts as a H3K4me3/H3K36me3 reader involved in the regulation of Arabidopsis flowering. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

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                  ....*....|....*....|....*....|....*....|....*.
gi 1720376127 268 MYEASIKDSDVEGGEALYLVHYCGWNVRYDEWIKADKIVRPADKNV 313
Cdd:cd18983    11 LYEAKILDVIPDKKEWKYFIHYNGWNKSWDEWVPEDRVLKYTDENL 56

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins; ARID1A, also called B120, BRG1-associated factor 250a (BAF250A), Osa homolog 1(OSA1), SWI-like protein, SWI/SNF complex protein p270, or SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 (SWI1), has been identified as a novel tumor suppressor in various tumor types. It interacts with BRG1 adenosine triphosphatase to form a SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complex, which plays a critical role in transcriptional control and gene expression. ARID1A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and Eld/Osa homology domains (EHD) 1 and 2 within the C-terminus. The ARID in ARID1A binds nonspecific DNA in general and plays an important role in targeting SWI/SNF to chromatin. The EHD1 may be capable of mediating an intramolecular association with EHD2, and/or an intermolecular association resulting in homo- or hetero-dimerization. The EHD2 binds Swi2/Brahma homologue Brahma-related gene 1 (BRG1, also known as Snf2b), a human homologue of yeast Swi2.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720376127   1 MEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGyNVKCAYKKYLYGFE 75
Cdd:cd16876    14 TEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTSSSAAS-SLKKQYIQCLYAFE 87