if you have the Fatt.Xa site, probably your plasmid contain also a tag (e.g His, Trx, GST? FLAG) and the protease site is introduced in the sequence to give you the possibility after protein purification to cut your protein, remove the tag and obtain the un-tagged protein.
Tags are usefull for improve expression, solubility and purification but for several application (e.g immunization, structural characterization), tag removal step has to be performed.