Nuclear Magnetic Resonance-Based Model of a TF1/HmU-DNA Complex

Transcription factor 1 (TF1), a type II DNA-binding protein encoded by theBacillus subtilisbacteriophage SPO1, has the capacity for sequence-selective DNA binding and a preference for 5-hydroxymethyl-2′-deoxyuridine (HmU)-containing DNA. In NMR studies of the TF1/HmU-DNA complex, intermolecular NOEs indicate that the flexible β-ribbon and C-terminal α-helix are involved in the DNA-binding site of TF1, placing it in the β-sheet category of DNA-binding proteins proposed to bind by wrapping two β-ribbon “arms” around the DNA. Intermolecular and intramolecular NOEs were used to generate an energy-minimized model of the protein–DNA complex in which both DNA bending and protein structure changes are evident.