5JLW

AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8

5JLW の概要

• エントリーDOI: 10.2210/pdb5jlw/pdb
• 関連するPDBエントリー: 5JLX
• 分子名称: Homeotic protein antennapedia, DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7R)P*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), ... (6 entities in total)
• 機能のキーワード: homeodomain, dna-binding protein, complex (homeodomain-dna), transcription-dna complex, transcription regulator-dna complex, monothiolated dna, transcription regulator/dna
• 由来する生物種: Drosophila melanogaster (Fruit fly); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 35015.42

構造登録者

White, M.A.,Zandarashvili, L.,Iwahara, J.,Nguyen, D. (登録日: 2016-04-27, 公開日: 2016-06-22, 最終更新日: 2023-09-27)

主引用文献

Nguyen, D.,Zandarashvili, L.,White, M.A.,Iwahara, J.
Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity.
Chembiochem, 17:1636-1642, 2016

PubMed Abstract: Oxygen-to-sulfur substitutions in DNA phosphate often enhance affinity for DNA-binding proteins. Our previous studies have suggested that this effect of sulfur substitution of both OP1 and OP2 atoms is due to an entropic gain associated with enhanced ion pair dynamics. In this work, we studied stereospecific effects of single sulfur substitution of either the OP1 or OP2 atom in DNA phosphate at the Lys57 interaction site of the Antennapedia homeodomain-DNA complex. Using crystallography, we obtained structural information on the RP and SP diastereomers of the phosphoromonothioate and their interaction with Lys57. Using fluorescence-based assays, we found significant affinity enhancement upon sulfur substitution of the OP2 atom. Using NMR spectroscopy, we found significant mobilization of the Lys57 side-chain NH3 (+) group upon sulfur substitution of the OP2 atom. These data provide further mechanistic insights into the affinity enhancement by oxygen-to-sulfur substitution in DNA phosphate.

PubMed: 27271797
DOI: 10.1002/cbic.201600265

実験手法

X-RAY DIFFRACTION (2.088 Å)