Factor Xa is a serine endopeptidase that forms part of the prothrombinase complex, along with factor Va, in the common pathway in coagulation cascade. The prothrombinase complex increases the conversion rate of prothrombin to thrombin. Subsequently, thrombin catalyzes the conversion of fibrinogen to fibrin monomers which then polymerize for thrombus formation. One molecule of Factor Xa can generate >1000 thrombin molecules. Factor Xa cleaves after the arginine residue in its preferred cleavage site Ile-(Glu or Asp)-Gly-Arg and it will occasionally cleave at other basic residues. However, it will not cleave at a site followed by proline or arginine.
Factor Xa is often used to remove fusion tags from expressed proteins. A factor Xa sensitive site is incorporated between the recombinant protein of interest and peptides or proteins which facilitate purification and/or expression. The target protein is released from the expressed hybrid by cleavage with factor Xa. Factor Xa can then be easily removed by affinity chromatography.