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PMID:15640446

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Citation

Patsialou, A, Wilsker, D and Moran, E (2005) DNA-binding properties of ARID family proteins. Nucleic Acids Res. 33:66-80

Abstract

The ARID (A-T Rich Interaction Domain) is a helix-turn-helix motif-based DNA-binding domain, conserved in all eukaryotes and diagnostic of a family that includes 15 distinct human proteins with important roles in development, tissue-specific gene expression and proliferation control. The 15 human ARID family proteins can be divided into seven subfamilies based on the degree of sequence identity between individual members. Most ARID family members have not been characterized with respect to their DNA-binding behavior, but it is already apparent that not all ARIDs conform to the pattern of binding AT-rich sequences. To understand better the divergent characteristics of the ARID proteins, we undertook a survey of DNA-binding properties across the entire ARID family. The results indicate that the majority of ARID subfamilies (i.e. five out of seven) bind DNA without obvious sequence preference. DNA-binding affinity also varies somewhat between subfamilies. Site-specific mutagenesis does not support suggestions made from structure analysis that specific amino acids in Loop 2 or Helix 5 are the main determinants of sequence specificity. Most probably, this is determined by multiple interacting differences across the entire ARID structure.

Links

PubMed PMC546134 Online version:10.1093/nar/gki145

Keywords

Amino Acid Sequence; Amino Acids, Aromatic/genetics; Binding Sites; DNA/chemistry; DNA/metabolism; DNA-Binding Proteins/chemistry; DNA-Binding Proteins/classification; DNA-Binding Proteins/metabolism; Drosophila Proteins/chemistry; Drosophila Proteins/genetics; Helix-Turn-Helix Motifs; Homeodomain Proteins/chemistry; Homeodomain Proteins/genetics; Humans; Molecular Sequence Data; Mutation; Nuclear Proteins/chemistry; Nuclear Proteins/genetics; Nucleic Acid Conformation; Protein Structure, Tertiary; Sequence Alignment; Transcription Factors/chemistry; Transcription Factors/genetics

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

HUMAN:ARI1A

enables

GO:0003677: DNA binding

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

HUMAN:ARI4A

enables

GO:0003677: DNA binding

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

HUMAN:KDM5A

enables

GO:0003677: DNA binding

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

HUMAN:ARI5A

enables

GO:0043565: sequence-specific DNA binding

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

HUMAN:ARI5A

enables

GO:0003677: DNA binding

ECO:0000304: author statement supported by traceable reference used in manual assertion

F

Seeded From UniProt

complete

HUMAN:ARI5A

involved_in

GO:0045892: negative regulation of transcription, DNA-templated

ECO:0000304: author statement supported by traceable reference used in manual assertion

P

Seeded From UniProt

complete

HUMAN:ARI5B

involved_in

GO:0045892: negative regulation of transcription, DNA-templated

ECO:0000304: author statement supported by traceable reference used in manual assertion

P

Seeded From UniProt

complete

HUMAN:KDM5B

enables

GO:0003677: DNA binding

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

HUMAN:ARID2

enables

GO:0003677: DNA binding

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete


See also

References

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