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ARID-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
Superfamily:   ARID-like [ 46774]
Families:   ARID domain [ 46775] (4)


Superfamily statistics
Genomes (471) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,267 8,016 5
Proteins 3,264 7,986 5


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 0.000000000004533 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000006529 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000008325 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0001273 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000197 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0008426 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.827 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.09315 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1083 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5848 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.6113 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.7209 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.00000000006501 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000000004052 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000000113 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0000000163 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0000002109 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000005468 Moderately Informative Direct
Biological Process (BP) reproduction 0.000004387 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00001484 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0002162 Moderately Informative Direct
Biological Process (BP) tissue development 0.002439 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.8072 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.02671 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3307 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.6196 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.9629 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2927 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.002288 Moderately Informative Inherited
Biological Process (BP) immune system process 0.0465 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) reproductive system development 0.000002461 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.000002518 Informative Direct
Biological Process (BP) single organism reproductive process 0.00000382 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.000009463 Informative Direct
Biological Process (BP) regulation of organelle organization 0.00001212 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.0003239 Informative Direct
Biological Process (BP) regulation of protein modification process 0.0004717 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.01304 Informative Inherited
Biological Process (BP) cell development 0.3432 Informative Inherited
Biological Process (BP) epithelium development 0.6305 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.1804 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.8092 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) hemopoiesis 0.7396 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.08478 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) demethylation 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00000000005838 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.000000001011 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.00000001696 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.000004638 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000009072 Highly Informative Direct
Biological Process (BP) protein alkylation 0.00001002 Highly Informative Direct
Biological Process (BP) sex differentiation 0.00001078 Highly Informative Direct
Biological Process (BP) myeloid cell differentiation 0.0001654 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0007779 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.0009926 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.001349 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.1005 Highly Informative Inherited
Molecular Function (MF) binding 0.00004609 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.000000000004017 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.03791 Moderately Informative Inherited
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.00000000007109 Informative Direct
Molecular Function (MF) DNA binding 0.000003481 Informative Direct
Molecular Function (MF) zinc ion binding 0.00008488 Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 0.00000000002785 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000001969 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.00001189 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.0002335 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000008411 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000000459 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000000004135 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000001352 Moderately Informative Direct
Cellular Component (CC) transferase complex 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.00002732 Informative Direct
Cellular Component (CC) nucleoplasm part 0.7143 Informative Inherited
Cellular Component (CC) chromatin 0.0000006564 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.06453 Highly Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processBiological rhythms0.000000000000004272InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainRepeat0.00001096Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0.000000004864Least InformativeDirect
Molecular functionIron0.00000001645Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationActivator0.000000000000001753Moderately InformativeDirect
Post-translational modificationRepressor0.000000000000005641Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00000000000004282Moderately InformativeDirect
Post-translational modificationOxidoreductase0.00008396Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000000000000003323Moderately InformativeDirect
Post-translational modificationMethylation0.0006408Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001606 SSF46774 Protein matches
Abstract

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 [PubMed10838570]. 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 [PubMed10757798]. 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 [PubMed10757798].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 4 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a ARID-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 4 hidden Markov models representing the ARID-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]