title: HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG.
abstract: The high mobility group (HMG) protein HMG-D from Drosophila melanogaster is a highly abundant chromosomal protein that is closely related to the vertebrate HMG domain proteins HMG1 and HMG2. In general, chromosomal HMG domain proteins lack sequence specificity. However, using both NMR spectroscopy and standard biochemical techniques we show that binding of HMG-D to a single DNA site is sequence selective. The preferred duplex DNA binding site comprises at least 5 bp and contains the deformable dinucleotide TG embedded in A/T-rich sequences. The TG motif constitutes a common core element in the binding sites of the well-characterized sequence-specific HMG domain proteins. We show that a conserved aromatic residue in helix 1 of the HMG domain may be involved in recognition of this core sequence. In common with other HMG domain proteins HMG-D binds preferentially to DNA sites that are stably bent and underwound, therefore HMG-D can be considered an architecture-specific protein. Finally, we show that HMG-D bends DNA and may confer a superhelical DNA conformation at a natural DNA binding site in the Drosophila fushi tarazu scaffold-associated region.
authors.affiliation: Department of Cell and Structural Biology, University of Illinois, Urbana 61801, USA.
authors.forename: M E
authors.initials: ME
authors.lastname: Churchill
authors.forename: D N
authors.initials: DN
authors.lastname: Jones
authors.forename: T
authors.initials: T
authors.lastname: Glaser
authors.forename: H
authors.initials: H
authors.lastname: Hefner
authors.forename: M A
authors.initials: MA
authors.lastname: Searles
authors.forename: A A
authors.initials: AA
authors.lastname: Travers
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029721:Drosophila Proteins; D004331:Drosophila melanogaster / Q000378:metabolism; D051717:Fushi Tarazu Transcription Factors; D006609:High Mobility Group Proteins / Q000378:metabolism*; D018398:Homeodomain Proteins / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D014443:Tyrosine / Q000378:metabolism
chemical_list: D029721:Drosophila Proteins; D051717:Fushi Tarazu Transcription Factors; D006609:High Mobility Group Proteins; D018398:Homeodomain Proteins; C497169:ftz protein, Drosophila; D014443:Tyrosine; D004247:DNA