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Amino acid sequence of cyanogen bromide fragment CN-C (residues 24-98) of the mouse histocompatibility antigen H-2Dd. A comparison of the amino-terminal 100 residues of H-2Dd, Dd, Kd, and Kb reveals discrete areas of diversity.

The amino acid sequence of the cyanogen bromide (CNBr) fragment extending from position 24 to position 98 of the H-2Dd murine histocompatibility antigen has been determined by using radiochemical microsequencing techniques. This 75-residue fragment (CN-C) is one of two glycopeptides generated by CNBr cleavage of the extracellular portion of the H-2Dd molecule (H-2Dd papain). Determination of this sequence completes the amino-terminal 100 residues of the H-2Dd molecule. The primary structure of CN-C was established by thrombin digestion of isolated CN-C and sequence determination of the three resulting peptides. The COOH-terminal met and its adjacent residue were determined by sequence analysis of a tryptic peptide which overlaps CNBr fragments C and b4 (residues 99-138). Alignment of the thrombic peptides was accomplished by NH2-terminal sequence analyses of CN-C and peptides generated by Staphylococcus aureus V8 protease digestion of CN-C. The sequence data presented here, together with that already given for H-2Dd [Nairn, R., Nathenson, S. G., & Coligan, J.E. (1980) Eur. J. Immunol. 10,495-503], allow a comparison of the NH2-terminal 100 residues of the Dd, Db, Kd, and Kb molecules. Discrete areas of diversity, in particular, one between residues 62 and 83, are obvious. Comparison over some 180 residues of the Dd and Kb molecules reveals a particularly close similarity between these products of a K and a D gene from widely disparate mouse strains.