title: Nuclear magnetic resonance-based model of a TF1/HmU-DNA complex.
abstract: Transcription factor 1 (TF1), a type II DNA-binding protein encoded by the Bacillus subtilis bacteriophage 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 beta-ribbon and C-terminal alpha-helix are involved in the DNA-binding site of TF1, placing it in the beta-sheet category of DNA-binding proteins proposed to bind by wrapping two beta-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.
authors.affiliation: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093, USA.
authors.forename: M V
authors.initials: MV
authors.lastname: Silva
authors.forename: L B
authors.initials: LB
authors.lastname: Pasternack
authors.forename: D R
authors.initials: DR
authors.lastname: Kearns
mesh_terms: D001412:Bacillus subtilis; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013936:Thymidine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism; D014764:Viral Proteins
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C059361:TF1 DNA-binding protein, Bacteriophage SPO1; D014157:Transcription Factors; D014764:Viral Proteins; C018080:5-hydroxymethyl-2'-deoxyuridine; D004247:DNA; D013936:Thymidine