SNAP output for PDB entry 2c6y [SNAP web server]

PDB-id

2c6y; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription regulation

Method

X-ray (2.4 Å)

Summary

Crystal structure of interleukin enhancer-binding factor 1 bound to DNA

Reference

Tsai K-L, Huang C-Y, Chang C-H, Sun Y-J, Chuang W-J, Hsiao C-D (2006): "Crystal Structure of the Human Foxk1A-DNA Complex and its Implications on the Diverse Binding Specificity of Winged Helix/Forkhead Proteins." J.Biol.Chem., 281, 17400. doi: 10.1074/JBC.M600478200.

Abstract

Interleukin enhancer binding factor (ILF) is a human transcription factor and a new member of the winged helix/forkhead family. ILF can bind to purine-rich regulatory motifs such as the human T-cell leukemia virus-long terminal region and the interleukin-2 promoter. Here we report the 2.4 A crystal structure of two DNA binding domains of ILF (FOXK1a) binding to a 16-bp DNA duplex containing a promoter sequence. Electrophoretic mobility shift assay studies demonstrate that two ILF-DNA binding domain molecules cooperatively bind to DNA. In addition to the recognition helix recognizing the core sequences through the major groove, the structure shows that wing 1 interacts with the minor groove of DNA, and the H2-H3 loop region makes ionic bonds to the phosphate group, which permits the recognition of DNA. The structure also reveals that the presence of the C-terminal alpha-helix in place of a typical wing 2 in a member of this family alters the orientation of the C-terminal basic residues (RKRRPR) when binding to DNA outside the core sequence. These results provide a new insight into how the DNA binding specificities of winged helix/forkhead proteins may be regulated by their less conserved regions.