5DSA

Crystal structure of Holliday junctions stabilized by 5-methylcytosine in GCC junction core

5DSA の概要

• エントリーDOI: 10.2210/pdb5dsa/pdb
• 分子名称: 5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3', CALCIUM ION (3 entities in total)
• 機能のキーワード: holliday junction, 5-methylcytosine, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6202.17

構造登録者

Vander Zanden, C.M.,Ho, P.S. (登録日: 2015-09-17, 公開日: 2016-09-28, 最終更新日: 2023-09-27)

主引用文献

Vander Zanden, C.M.,Rowe, R.K.,Broad, A.J.,Robertson, A.B.,Ho, P.S.
Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions.
Biochemistry, 55:5781-5789, 2016

PubMed Abstract: 5-Hydroxymethylcytosine (C) is an epigenetic marker that has recently been shown to promote homologous recombination (HR). In this study, we determine the effects of C on the structure, thermodynamics, and conformational dynamics of the Holliday junction (the four-stranded DNA intermediate associated with HR) in its native stacked-X form. The hydroxymethyl and the control methyl substituents are placed in the context of an amphimorphic GCC trinucleotide core sequence (where C is C, C, or the methylated C), which is part of a sequence also recognized by endonuclease G to promote HR. The hydroxymethyl group of the C junction adopts two distinct rotational conformations, with an in-base-plane form being dominant over the competing out-of-plane rotamer that has typically been seen in duplex structures. The in-plane rotamer is seen to be stabilized by a more stable intramolecular hydrogen bond to the junction backbone. Stabilizing hydrogen bonds (H-bonds) formed by the hydroxyl substituent in C or from a bridging water in the C structure provide approximately 1.5-2 kcal/mol per interaction of stability to the junction, which is mostly offset by entropy compensation, thereby leaving the overall stability of the GCC and GCC constructs similar to that of the GCC core. Thus, both methyl and hydroxymethyl modifications are accommodated without disrupting the structure or stability of the Holliday junction. Both C and C are shown to open the structure to make the junction core more accessible. The overall consequences of incorporating C into a DNA junction are thus discussed in the context of the specificity in protein recognition of the hydroxymethyl substituent through direct and indirect readout mechanisms.

PubMed: 27653243
DOI: 10.1021/acs.biochem.6b00801

実験手法

X-RAY DIFFRACTION (1.6896 Å)