4DIH

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions

4DIH の概要

• エントリーDOI: 10.2210/pdb4dih/pdb
• 関連するPDBエントリー: 4DII
• 関連するBIRD辞書のPRD_ID: PRD_000020
• 分子名称: Prothrombin, Thrombin binding aptamer, ZINC ION, ... (9 entities in total)
• 機能のキーワード: protein-dna complex, serine protease, blood coagulation, aptamer, hydrolase-hydrolase inhibitor-dna complex, serine protease fold, dna aptamer, blood, g-quadruplex, hydrolase/hydrolase inhibitor/dna
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 39608.11

構造登録者

Russo Krauss, I.,Merlino, A.,Mazzarella, L.,Sica, F. (登録日: 2012-01-31, 公開日: 2012-07-18, 最終更新日: 2024-11-06)

主引用文献

Russo Krauss, I.,Merlino, A.,Randazzo, A.,Novellino, E.,Mazzarella, L.,Sica, F.
High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.
Nucleic Acids Res., 40:8119-8128, 2012

PubMed Abstract: The G-quadruplex architecture is a peculiar structure adopted by guanine-rich oligonucleotidic sequences, and, in particular, by several aptamers, including the thrombin-binding aptamer (TBA) that has the highest inhibitory activity against human α-thrombin. A crucial role in determining structure, stability and biological properties of G-quadruplexes is played by ions. In the case of TBA, K(+) ions cause an enhancement of the aptamer clotting inhibitory activity. A detailed picture of the interactions of TBA with the protein and with the ions is still lacking, despite the importance of this aptamer in biomedical field for detection and inhibition of α-thrombin. Here, we fill this gap by presenting a high-resolution crystallographic structural characterization of the thrombin-TBA complex formed in the presence of Na(+) or K(+) and a circular dichroism study of the structural stability of the aptamer both free and complexed with α-thrombin, in the presence of the two ionic species. The results indicate that the different effects exerted by Na(+) and K(+) on the inhibitory activity of TBA are related to a subtle perturbation of a few key interactions at the protein-aptamer interface. The present data, in combination with those previously obtained on the complex between α-thrombin and a modified aptamer, may allow the design of new TBA variants with a pharmacological performance enhancement.

PubMed: 22669903
DOI: 10.1093/nar/gks512

実験手法

X-RAY DIFFRACTION (1.8 Å)