title: Structure and dynamics of KH domains from FBP bound to single-stranded DNA.
abstract: Gene regulation can be tightly controlled by recognition of DNA deformations that are induced by stress generated during transcription. The KH domains of the FUSE-binding protein (FBP), a regulator of c-myc expression, bind in vivo and in vitro to the single-stranded far-upstream element (FUSE), 1,500 base pairs upstream from the c-myc promoter. FBP bound to FUSE acts through TFIIH at the promoter. Here we report the solution structure of a complex between the KH3 and KH4 domains of FBP and a 29-base single-stranded DNA from FUSE. The KH domains recognize two sites, 9-10 bases in length, separated by 5 bases, with KH4 bound to the 5' site and KH3 to the 3' site. The central portion of each site comprises a tetrad of sequence 5'd-ATTC for KH4 and 5'd-TTTT for KH3. Dynamics measurements show that the two KH domains bind as articulated modules to single-stranded DNA, providing a flexible framework with which to recognize transient, moving targets.
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Demetrios T
authors.initials: DT
authors.lastname: Braddock
authors.forename: John M
authors.initials: JM
authors.lastname: Louis
authors.forename: James L
authors.initials: JL
authors.lastname: Baber
authors.forename: David
authors.initials: D
authors.lastname: Levens
authors.forename: G Marius
authors.initials: GM
authors.lastname: Clore
mesh_terms: D000595:Amino Acid Sequence; D004265:DNA Helicases; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D005786:Gene Expression Regulation; D016259:Genes, myc; D006801:Humans; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins
chemical_list: D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; C492258:FUBP1 protein, human; D046911:Macromolecular Substances; D016601:RNA-Binding Proteins; D004265:DNA Helicases