Prothrombin is synthesized in the liver and secreted as a single-chain 579 residue protein (UniProtKB – P00734 (THRB_HUMAN)).
It is composed of four domains: the Gla domain (residues 1-65); the first Kringle domain (K1; residues 66-144; the second Kringle domain (K2; residues 170-248); and the catalytic domain (Pro; residues 272-579).
The Gla and K1 domains are in intimate contact, as are the K2 and catalytic domains. A flexible stretch of 26 residues links K1 to K2, and can be cleaved by thrombin at R155 to form Fragment 1 (F1) and Prethrombin-1 (Pre-1).
The protease responsible for cleavage of prothrombin is factor Xa (fXa). On its own it cleaves R271 to form Fragment 1.2 (F1.2) and Prethrombin-2 (Pre-2), and then at R320 to form the active protease thrombin.
The physiological activator of prothrombin is the prothrombinase complex, formed of fXa and fVa on a negatively-charged phospholipid membrane. It cleaves R320 first to form the active intermediate Meizothrombin, then it cleaves R155 to release F1.2 and thrombin.