1F6C

CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE

1F6C の概要

• エントリーDOI: 10.2210/pdb1f6c/pdb
• 関連するPDBエントリー: 1F69 1F6E 1F6I 1F6J
• 分子名称: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3'), SPERMINE (3 entities in total)
• 機能のキーワード: b-dna, e-dna, double helix, dna
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 9455.70

構造登録者

Vargason, J.M.,Eichman, B.F.,Ho, P.S. (登録日: 2000-06-21, 公開日: 2000-08-28, 最終更新日: 2024-02-07)

主引用文献

Vargason, J.M.,Eichman, B.F.,Ho, P.S.
The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.
Nat.Struct.Biol., 7:758-761, 2000

PubMed Abstract: Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3'-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway from B-DNA to A-DNA through the E-DNA intermediate in a single sequence. The E-DNA surface is highly accessible to solvent, with waters in the major groove sitting on exposed faces of the stacked nucleotides. We suggest that the geometry of the waters and the stacked base pairs would promote the spontaneous deamination of 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base pairs.

PubMed: 10966645
DOI: 10.1038/78985

実験手法

X-RAY DIFFRACTION (2.7 Å)