PDBsum entry 1c20

DNA binding protein

PDB id: 1c20

Contents

Protein chain

128 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Solution structure of the DNA binding domain from dead ringer, A sequence-Specific at-Rich interaction domain (arid).

Authors

J.Iwahara, R.T.Clubb.

Ref.

EMBO J, 1999, 18, 6084-6094. [DOI no: 10.1093/emboj/18.21.6084]

PubMed id

10545119

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.

Figure 1.
Figure 1 Schematic of the VRR from the zen gene. Dorsal protein binding sites are shown as hatched rectangles (dl1 -dl3). Sites AT1 -AT3 contain semi-conserved AT-rich sequences that have been shown to interact with proteins (dark squares). The Dead ringer and Cut proteins bind to sites AT2 and AT3. The cognate protein for site AT1 has not been identified. Binding sites for the Dorsal switch protein 1 (NRE) and the NTF-1/Elf-1 protein (DRE) are represented by open and closed diamonds, respectively. Circles correspond to GC-rich sequences that interact with an as yet unidentified protein. The displayed region is located -1.17 to -1.35 kb from the start of transcription.

Figure 5.
Figure 5 Comparison of the DRI-DBD with three homologous HTH-containing DNA binding proteins. The structures of the DRI-DBD, histone H5 (1hst-A) (Ramakrishnan et al., 1993), the Mu transposase I DBD (2ezk) (Schumacher et al., 1997) and the first repeat of the Myb proto-oncogene DBD (1mbe) (Ogata et al., 1995) are displayed. Color code: red, helices of the HTH; gold, the third stabilizing helix; cyan, the turn in the HTH.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 6084-6094) copyright 1999.