Thrombin
Created by Philip Eby
Thrombin (pbd id=1sgi) is a trypsin-like serine protease and participates in multiple processes of the body(2). Arguably, the most important of these functionsis its role in the clotting cascade(4). Thrombin participates in the clotting cascade by cleaving fibrinogen into fibrin(2), as well as, activation of blood platelets which go on to form a clot. For this to occur, thrombin must obtain is physiological form as a dimer(9).
The formation of a dimer gets its two anion-binding exosites into the proper orientation(3). These sites are known as anion-binding exosite I and anion-binding exosite II. These anion-binding exosites are on the surface of thrombin and mediate its interactions with cofactors and substrates(3). They are on the opposite ends of the molecule(9) and when two thrombin form a dimer, the exosite I of one thrombin is adjacent to the exosite II of the other thrombin (9). Thrombin's ability to specifically recognize awide range of substrates is due to these exosites(3).
When thrombin is in standard position, anion-binding exosite I can be seen on the eastern face(3). This site is particularly positive patch and extends across the convex of thrombin, just to the right of the active site cleft, mainly on the 70-80 residue loop(10). This electro statically positive site is capable of cleaving fibrinogen(8). This site is also used to bind fibrinogen in conjunction with the active site to ensure the specific cleavage(3).
Anion-binding exosite II is on the northwestern face of thrombin when viewed from standard position(3). It extends from the intermediate helix towards the C-terminus end of thrombin(10). This site is particularly susceptible toinhibition by heparin and is also known as "heparin-binding site"(10). This is also the site of binding for anithrombin III, another inhibitor of thrombin(5). Exosite II's binding to its ligand, n-acetyl-d-glucosamine, switches off its ability to participate in the coagulation cascade by mediating its irreversible inhibition by seripins and ultimate binding to endothelialcell surface receptor thrombomodulin(3).
In contrast to the positively charged exosites, the catalytic site is negatively charged. This site gives thrombin all of its serine protease abilities(5). This site is located on the B-chain of thrombin and is composed of 2 adjacent beta-barrels(10). The active site residues Ser-195(yellow), His-57 (purple), and Asp-102 (green)(2) are at the junction of these two barrels(10).
The active site cleft projects perpendicular to this junction and extends the length of the barrels(10). Insertion loops 60 and 149 borderand shape this active site cleft, making it very deep and narrow, with thereactive Ser-195 at the bottom(10). These loops block access to the active sitewhich is the reason for thrombin's specificity.
This particular image of thrombin is in the slow form. When compaired to the fast form, the most notible difference is in shift of the catalytic Ser-195(7). The difference in location of Ser-195 explains the slow form's catalytic abilities and coagulation functions(7).
When comparing bovine and human thrombin, it is easy to see the similarities(11). Both of their catalytic sites contain the catalytic residues Ser-195, His-57, and Asp-102 which are characteristic of a serine protease. This similarity in structure accounts for their similar functions. They are both indispensible parts of the coagulation pathway in their respective animals.
In conclusion, thrombin is an important protein in all animals with a cardiovascular system(1). It is able to perform all of its functions because of its unique structure. Even though relatively simple, with an A-chain consisting of 36 residues and 259 in its B-chain linked covalently by a disulfide bridge(10), it was shaped by evolution to perform its vital role in life.