Structurally, it is a member of the large PA clan of proteases. Prothrombin is composed of four domains; an N-terminal Gla domain, two kringle domains and a C-terminal trypsin-like serine protease domain. Factor Xa with factor V as a cofactor leads to cleavage of the Gla and two Kringle domains (forming together a fragment called fragment 1.2) and leave thrombin, consisting solely of the serine protease domain.As is the case for all serine proteases, prothrombin is converted to active thrombin by proteolysis of an internal peptide bond, exposing a new N-terminal Ile-NH3. The historic model of activation of serine proteases involves insertion of this newly formed N-terminus of the heavy chain into the β-barrel promoting the correct conformation of the catalytic residues. Contrary to crystal structures of active thrombin, hydrogen-deuterium exchange mass spectrometry studies indicate that this N-terminal Ile-NH3 does not become inserted into the β-barrel in the apo form of thrombin. However, binding of the active fragment of thrombomodulin appears to allosterically promote the active conformation of thrombin by inserting this N-terminal region. Gene
The thrombin (prothrombin) gene is located on the eleventh chromosome (11p11-q12).There are an estimated 30 people in the world that have been diagnosed with the congenital form of Factor II deficiency, which should not be confused with the prothrombin G20210A mutation, which is also called the factor II mutation. Prothrombin G20210A is congenital.Prothrombin G20210A is not usually accompanied by other factor mutations (i.e., the most common is factor V Leiden).
Anti-coagulation & proteases on YouTube by The Proteolysis Map-animation
[1] PMAP: The Proteolysis Map/Thrombin
Thrombin: RCSB PDB Molecule of the Month Archived 2013-10-05 at the Wayback Machine
Prothrombin Structure
PDBe-KB provides an overview of all the structure information available in the PDB for Human Thrombin. PDBe-KB provides an overview of all the structure information available in the PDB for Mouse Thrombin.