6PXJ

Crystal structure of human thrombin mutant I16T

6PXJ の概要

• エントリーDOI: 10.2210/pdb6pxj/pdb
• 関連するPDBエントリー: 1PPB
• 分子名称: Thrombin light chain, Thrombin heavy chain, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: hydrolase, trypsin -like proteases, ionic interaction
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 67937.90

構造登録者

Stojanovski, B.,Chen, Z.,Koester, S.K.,Pelc, L.A.,Di Cera, E. (登録日: 2019-07-26, 公開日: 2019-12-18, 最終更新日: 2024-11-20)

主引用文献

Stojanovski, B.M.,Chen, Z.,Koester, S.K.,Pelc, L.A.,Di Cera, E.
Role of the I16-D194 ionic interaction in the trypsin fold.
Sci Rep, 9:18035-18035, 2019

PubMed Abstract: Activity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na binding, reduces stability of the transition state, collapses the 215-217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na binding and the E*-E equilibrium.

PubMed: 31792294
DOI: 10.1038/s41598-019-54564-6

実験手法

X-RAY DIFFRACTION (1.7 Å)