2HSK

NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)

2HSK の概要

• エントリーDOI: 10.2210/pdb2hsk/pdb
• 関連するPDBエントリー: 2HOU 2HPX 2HSL 2HSR 2HSS
• 分子名称: 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)-3', 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' (2 entities in total)
• 機能のキーワード: abasic site, dna lesion, base excision repair, ape1, dna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7836.09

構造登録者

Chen, J.,Dupradeau, F.Y.,Case, D.A.,Turner, C.J.,Stubbe, J. (登録日: 2006-07-21, 公開日: 2007-05-29, 最終更新日: 2024-05-01)

主引用文献

Chen, J.,Dupradeau, F.Y.,Case, D.A.,Turner, C.J.,Stubbe, J.
Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.
Biochemistry, 46:3096-3107, 2007

PubMed Abstract: A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.

PubMed: 17323932
DOI: 10.1021/bi6024269

実験手法

SOLUTION NMR