The amino acid sequence of bovine blood coagulation Factor IX (Christmas Factor) is presented and compared with the sequences of other vitamin K-dependent plasma proteins and pancreatic trypsinogen. The 416-residue sequence of Factor IX was determined largely by automated Edman degradation of two large segments, containing 181 and 235 residues, isolated after activating Factor IX with a protease from Russell's viper venom. Subfragments of the two segments were produced by enzymatic digestion and by chemical cleavage of methionyl, tryptophyl, and asparaginyl-glycyl bonds.Comparison of the amino acid sequences of Factor IX, Factor X, and Protein C demonstrates that they are homologous throughout. Their homology with prothrombin, however, is restricted to the amino-terminal region, which is rich in y-carboxyglutamic acid, and the carboxyl-terminal region, which represents the catalytic domain of these proteins and corresponds to that of pancreatic serine proteases. Factor IX (Christmas Factor) is the zymogen of a serine protease that participates in the middle phase of the intrinsic pathway of blood coagulation (1). Like several other plasma proteinsi.e., prothrombin, Factor X, Factor VII, Protein C, and Protein S-Factor IX requires vitamin K for its biosynthesis (2-4). Individuals lacking Factor IX (Christmas disease or hemophilia B) show bleeding symptoms essentially identical to those of classic hemophilia or hemophilia A (Factor VIII deficiency) (5, 6). The activity of Factor IX is also depressed in the plasma of patients treated with coumarin analogs, but in such cases the effect can be reversed by the administration of vitamin K (6).Bovine and human Factors IX have been purified and characterized (7)(8)(9)(10)(11)(12) Previous comparison of the partial sequence of bovine Factor IX with the sequences of bovine prothrombin and Factor X revealed homologous regions, indicating that these three proteins may have evolved from a common ancestral protein (16,17). Recently, the light and heavy chains of bovine Protein C, another vitamin K-dependent plasma protein, have been found to be homologous with Factor X (18,19). In the present communication, the complete sequence of Factor IX is presented.Comparison with the sequences of Factor X, Protein C, and prothrombin reveals areas of homology as well as regions lacking obvious similarity. The experimental details of the sequence determination will be published elsewhere. METHODS Factor IX, isolated from bovine plasma (7) and converted to Factor IXaa by a protease from Russell's viper venom (15), was obtained through the courtesy of K. Fujikawa. Factor IXaa was reduced with dithioerythritol and S-alkylated with 4-vinylpyridine. The two peptide chains (segment N and segment C) were separated on a column of SP-Sephadex C-25 by applying a linear gradient of sodium formate buffers in the presence of 7 M urea (20).Segment N (residues 1-181) was divided into two fragments (CB I and CB II), by cleavage with cyanogen bromide under conditions that avoid cleavage at y-carbo...