title: Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
abstract: The principal determinant of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence was investigated by mutation of both the protein and the DNA base pairs, with analysis by a filter binding assay. Amino acid residue 187 was revealed to interact with the pyrimidine base position, as estimated from our previous complex structure. Unexpectedly, since the pyrimidine preference is retained even in the Gly187 mutant, the principal origin of the base specificity should not occur via the direct-readout mechanism, but by an indirect-readout mechanism, namely in the intrinsic "bendability" of the pyrimidine-purine step of the DNA duplex. A significant but rather small positive base pair roll is detectable in the conformation of DNA in complex with the c-Myb DNA-binding domain. Following the conventional chemical rules of the direct-readout mechanism, amino acid mutagenesis at position 187 yielded several new base preferences for the protein.
authors.affiliation: Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka 565, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Oda
authors.forename: K
authors.initials: K
authors.lastname: Furukawa
authors.forename: K
authors.initials: K
authors.lastname: Ogata
authors.forename: A
authors.initials: A
authors.lastname: Sarai
authors.forename: S
authors.initials: S
authors.lastname: Ishii
authors.forename: Y
authors.initials: Y
authors.lastname: Nishimura
authors.forename: H
authors.initials: H
authors.lastname: Nakamura
mesh_terms: D000595:Amino Acid Sequence; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D002942:Circular Dichroism; D016384:Consensus Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D005998:Glycine; D008961:Models, Structural; D016297:Mutagenesis, Site-Directed; D017354:Point Mutation; D016133:Polymerase Chain Reaction; D017433:Protein Structure, Secondary; D011518:Proto-Oncogene Proteins / Q000737:chemistry* / Q000378:metabolism*; D020598:Proto-Oncogene Proteins c-myb; D011743:Pyrimidines; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D015534:Trans-Activators / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D011518:Proto-Oncogene Proteins; D020598:Proto-Oncogene Proteins c-myb; D011743:Pyrimidines; D011994:Recombinant Proteins; D015534:Trans-Activators; D004247:DNA; D005998:Glycine