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Volume 272, Number 29, Issue of July 18, 1997 pp. 17966-17971
©1997 by The American Society for Biochemistry and Molecular Biology, Inc.

Investigation of the Pyrimidine Preference by the c-Myb DNA-binding Domain at the Initial Base of the Consensus Sequence

(Received for publication, January 31, 1997, and in revised form, April 17, 1997)

Masayuki Oda , Koji Furukawa , Kazuhiro Ogata ^§¶ , Akinori Sarai , Shunsuke Ishii , Yoshifumi Nishimura ^** and Haruki Nakamura

From the  Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka 565, ^§ Kanagawa Academy of Science and Technology (KAST), Kanazawa-ku, Yokohama 236, ^¶ Department of Structural Biology, School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236,  Tsukuba Life Science Center, Institute of Physical and Chemical Research (RIKEN), Tsukuba, Ibaraki 305, and ^** Graduate School of Integrated Science, Yokohama City University, Kanazawa-ku, Yokohama 236, Japan

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.

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