1D41

STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)

1D41 の概要

• エントリーDOI: 10.2210/pdb1d41/pdb
• 分子名称: DNA (5'-D(*(5CM)P*GP*UP*AP*(5CM)P*G)-3'), MAGNESIUM ION (3 entities in total)
• 機能のキーワード: z-dna, double helix, modified, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3695.10

構造登録者

Zhou, G.,Ho, P.S. (登録日: 1991-05-07, 公開日: 1992-04-15, 最終更新日: 2024-04-03)

主引用文献

Zhou, G.W.,Ho, P.S.
Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG).
Biochemistry, 29:7229-7236, 1990

PubMed Abstract: Methylation of cytosine bases at the C5 position has been known to stabilize Z-DNA. We had previously predicted from calculations of solvent-accessible surfaces that the methyl group at the same position of thymine has a destabilizing effect on Z-DNA. In the current studies, the sequence d(m5CGUAm5CG) has been crystallized and its structure solved as Z-DNA to 1.3-A resolution. A well-defined octahedral hexaaquomagnesium complex was observed to bridge the O4 oxygens of the adjacent uridine bases at the major groove surface, and four well-structured water molecules were found in the minor groove crevice at the d(UA) dinucleotide. These solvent interactions were not observed in the previously published Z-DNA structure of the analogous d(m5CGTAm5CG) sequence. A comparison of the thymine and uridine structures supports our prediction that demethylation of thymine bases helps to stabilize Z-DNA. A comparison of this d(UA)-containing Z-DNA structure with the analogous d(TA) structure shows that access of the O4 position is hindered by the C5 methyl of thymine due to steric and hydrophobic inhibition. In the absence of the methyl group, a magnesium-water complex binds to and slightly affects the structure of the Z-DNA major groove surface. This perturbation of the solvent structure at the major groove surface is translated into a much larger 1.41-A widening of the minor groove crevice, thereby allowing the specific binding of two water molecules at well-defined sites of each internal d(UA) base pair. Possible mechanisms by which modifications at the major groove surface of Z-DNA can affect the solvent properties of the minor groove crevice are discussed.

PubMed: 2207101
DOI: 10.1021/bi00483a010

実験手法

X-RAY DIFFRACTION (1.3 Å)