6V5T

Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan

6V5T の概要

• エントリーDOI: 10.2210/pdb6v5t/pdb
• 関連するPDBエントリー: 3sqh
• 分子名称: Prothrombin, GLYCEROL, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: hydrolase
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 33759.35

構造登録者

Ruben, E.A.,Chen, Z.,Di Cera, E. (登録日: 2019-12-04, 公開日: 2020-05-13, 最終更新日: 2023-10-11)

主引用文献

Ruben, E.A.,Gandhi, P.S.,Chen, Z.,Koester, S.K.,DeKoster, G.T.,Frieden, C.,Di Cera, E.
19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2.
J.Biol.Chem., 295:8227-8235, 2020

PubMed Abstract: The conformational properties of trypsin-like proteases and their zymogen forms remain controversial because of a lack of sufficient information on their free forms. Specifically, it is unclear whether the free protease is zymogen-like and shifts to its mature form upon a ligand-induced fit or exists in multiple conformations in equilibrium from which the ligand selects the optimal fit via conformational selection. Here we report the results of F NMR measurements that reveal the conformational properties of a protease and its zymogen precursor in the free form. Using the trypsin-like, clotting protease thrombin as a relevant model system, we show that its conformation is quite different from that of its direct zymogen precursor prethrombin-2 and more similar to that of its fully active Na-bound form. The results cast doubts on recent hypotheses that free thrombin is zymogen-like and transitions to protease-like forms upon ligand binding. Rather, they validate the scenario emerged from previous findings of X-ray crystallography and rapid kinetics supporting a pre-existing equilibrium between open (E) and closed (E*) forms of the active site. In this scenario, prethrombin-2 is more dynamic and exists predominantly in the E* form, whereas thrombin is more rigid and exists predominantly in the E form. Ligand binding to thrombin takes place exclusively in the E form without significant changes in the overall conformation. In summary, these results disclose the structural architecture of the free forms of thrombin and prethrombin-2, consistent with an E*-E equilibrium and providing no evidence that free thrombin is zymogen-like.

PubMed: 32358061
DOI: 10.1074/jbc.RA120.013419

実験手法

X-RAY DIFFRACTION (2.1 Å)