218D

THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS

218D の概要

• エントリーDOI: 10.2210/pdb218d/pdb
• 分子名称: DNA (5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3') (2 entities in total)
• 機能のキーワード: b-dna, double helix, modified, mismatched, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7384.86

構造登録者

Vojtechovsky, J.,Eaton, M.D.,Gaffney, B.,Jones, R.,Berman, H.M. (登録日: 1995-07-18, 公開日: 1995-10-15, 最終更新日: 2024-02-14)

主引用文献

Vojtechovsky, J.,Eaton, M.D.,Gaffney, B.,Jones, R.,Berman, H.M.
Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs.
Biochemistry, 34:16632-16640, 1995

PubMed Abstract: The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been determined to a resolution of 2.25 A and refined to a final R factor of 16.7%. The volume of the unit cell is significantly smaller by 16% than the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is in a different position in the unit cell, rotated by -85.9 degrees, and translated by 9.9 A around the helical axis with respect to the parent structure. The intermolecular arrangement of helices, characterized by double hydrogen bonded guanine-guanine minor groove interactions, remains conserved. The molecular geometry exhibits several significant changes that are related to the changed position of the helix and the presence of two mismatched base pairs with O6-methylguanine. Both mispairs are found in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups are in proximal orientation. The hydration pattern of the structure is different and can be related to changes in the minor groove geometry. An incorrect model that was isomorphous to the parent dodecamer could be refined to a low R factor. Characteristics of the refinement and of the geometry that are indicative of incorrect structures have been analyzed.

PubMed: 8527436
DOI: 10.1021/bi00051a011

実験手法

X-RAY DIFFRACTION (2.25 Å)