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EMBO J. 1999 Nov 1;18(21):6084-94.

Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).

Author information

1
Department of Chemistry and Biochemistry, Molecular Biology Institute and the UCLA-DOE Laboratory of Structural Biology and Genetics, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1570, USA.

Abstract

The Dead ringer protein from Drosophila melanogaster is a transcriptional regulatory protein required for early embryonic development. It is the founding member of a large family of DNA binding proteins that interact with DNA through a highly conserved domain called the AT-rich interaction domain (ARID). The solution structure of the Dead ringer ARID (residues Gly262-Gly398) was determined using NMR spectroscopy. The ARID forms a unique globular structure consisting of eight alpha-helices and a short two-stranded anti-parallel beta-sheet. Amino acid sequence homology indicates that ARID DNA binding proteins are partitioned into three structural classes: (i) minimal ARID proteins that consist of a core domain formed by six alpha-helices; (ii) ARID proteins that supplement the core domain with an N-terminal alpha-helix; and (iii) extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. Studies of the Dead ringer-DNA complex suggest that the major groove of DNA is recognized by a helix-turn-helix (HTH) motif and the adjacent minor grooves are contacted by a beta-hairpin and C-terminal alpha-helix. Primary homology suggests that all ARID-containing proteins contact DNA through the HTH and hairpin structures, but only extended-ARID proteins supplement this binding surface with a terminal helix.

PMID:
10545119
PMCID:
PMC1171673
DOI:
10.1093/emboj/18.21.6084
[Indexed for MEDLINE]
Free PMC Article

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