Abstract
Interleukin enhancer binding factor (ILF) is a transcription factor that binds to purine-rich regulatory motifs in both the human T-cell leukemia virus long terminal region (HILV-1 LTR) and the interleukin-2 (IL-2) promoter. The DNA-binding domain of ILF (ILF-DBD) belongs to a member of winged helix/forkhead family. Here we report a 2.4 Å crystal structure of two copies of the DBD of ILF bound to 16-bp DNA. Extensive contacts are formed between the recognition helix (H3) and the major groove of DNA through direct and water-mediated hydrogen bonds. ILF-DBD is a new member of the winged helix/forkhead proteins because the presence of a C-terminal α-helix (H4) in place of a typical wing 2 changes the orientation of the C-terminal basic residues (RKRRPR) of H4 to recognize DNA. The structure also shows that wing 1 interacts with minor groove of DNA, and the residues (Lys45) from the H2-H3 loop region make interactions with DNA. Comparison of the ILF-DBD/DNA complex with HNF-3□/DNA complex revealed some differences in DNA recognition at both the “TAAACA” core and the flanking regions of the DNA site. Taken together, these results offer new insights into the modulation of DNA binding specificity within a conserved DNA-binding domain, and provide how highly homologous winged helix/forkhead proteins exhibit differential DNA-binding properties.