1C20

SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN FROM THE DEAD RINGER PROTEIN

Summary for 1C20

• Entry DOI: 10.2210/pdb1c20/pdb
• Descriptor: DEAD RINGER PROTEIN (1 entity in total)
• Functional Keywords: dna-binding domain, arid, at-rich interaction domain, dna-binding protein, dna binding protein
• Biological source: Drosophila melanogaster (fruit fly)
• Total number of polymer chains: 1
• Total formula weight: 14983.27

Authors

Iwahara, J.,Clubb, R.T. (deposition date: 1999-07-22, release date: 1999-11-10, Last modification date: 2024-05-22)

Primary citation

Iwahara, J.,Clubb, R.T.
Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).
EMBO J., 18:6084-6094, 1999

PubMed 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.

PubMed: 10545119
DOI: 10.1093/emboj/18.21.6084

Experimental method

SOLUTION NMR