1HXE

SERINE PROTEASE

1HXE の概要

• エントリーDOI: 10.2210/pdb1hxe/pdb
• 分子名称: THROMBIN, HIRUDIN VARIANT-1, RUBIDIUM ION, ... (5 entities in total)
• 機能のキーワード: serine protease in blood coagulation, hydrolase, serine protease, hydrolase-hydrolase inhibitor complex, hydrolasee-hydrolase inhibitor complex, hydrolasee/hydrolase inhibitor
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Secreted, extracellular space: P00734 P00734; Secreted: P01050
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 35258.96

構造登録者

Tulinsky, A.,Zhang, E. (登録日: 1995-12-07, 公開日: 1996-11-08, 最終更新日: 2024-10-09)

主引用文献

Zhang, E.,Tulinsky, A.
The molecular environment of the Na+ binding site of thrombin.
Biophys.Chem., 63:185-200, 1997

PubMed Abstract: When Na+ binds to thrombin, a conformational change is induced that renders the enzyme kinetically faster and more specific in the activation of fibrinogen. Two Na+ binding sites have here been identified crystallographically by exchanging Na+ with Rb+. One is intermolecular, found on the surface between two symmetry-related thrombin molecules. Since it is not present in thrombin crystal structures having different crystal systems, the other Na+ site is the functionally relevant one. The second site has octahedral coordination with the carbonyl oxygen atoms of Arg221A and Lys224 and four conserved water molecules. It is located near Asp189 of the S1 specificity site in an elongated solvent channel (8 x 18 A) formed by four antiparallel beta-strands between Cys182-Cys191 and Val213-Tyr228. This channel, extending from the active site to the opposite surface of the enzyme, was first noted in the hirudin-thrombin structure and contains about 20 conserved water molecules linked together by a hydrogen bonding network that connects to the main chain of thrombin. Although the antiparallel beta-strand interactions of the functional Na+ binding site are the same in prethrombin2, the loops between the strands are very different, so that Asp189 and Arg221A are not positioned properly for either substrate or Na+ binding in prethrombin2. A water molecule with octahedral coordination has also been identified in factor Xa at the topologically equivalent Na+ site position of thrombin. Since activated protein C shows enhanced activity with monovalant cation binding, the same position is probably utilized by Na+. Since thrombin crystals could not be grown in the absence of Na+, the cation was leached from Na(+)-bound thrombin crystals by diffusion/exchange. Although both Na+ and their coordinating water molecules were removed from the Na+ binding sites, the remainder of the thrombin structure was, unexpectedly, the same. The lack of an allosteric change is most likely attributable to crystal packing effects. Thus, the structure of the slow form remains to be established crystallographically.

PubMed: 9108691
DOI: 10.1016/S0301-4622(96)02227-2

実験手法

X-RAY DIFFRACTION (2.1 Å)