6V64

Crystal structure of human thrombin bound to ppack with tryptophans replaced by 5-F-tryptophan

Summary for 6V64

• Entry DOI: 10.2210/pdb6v64/pdb
• Related: 1ppb
• Descriptor: Thrombin light chain, Thrombin heavy chain, SODIUM ION, ... (5 entities in total)
• Functional Keywords: hydrolase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 33960.07

Authors

Ruben, E.A.,Chen, Z.,Di Cera, E. (deposition date: 2019-12-04, release date: 2020-05-13, Last modification date: 2023-10-11)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.29 Å)