6V5T
Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan
Summary for 6V5T
| Entry DOI | 10.2210/pdb6v5t/pdb |
| Related | 3sqh |
| Descriptor | Prothrombin, GLYCEROL, SULFATE ION, ... (4 entities in total) |
| Functional Keywords | hydrolase |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 1 |
| Total formula weight | 33759.35 |
| 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 Cited by 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: 32358061DOI: 10.1074/jbc.RA120.013419 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
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