Primary structure of murine major histocompatibility complex alloantigens. Amino acid sequence of the NH2-terminal ninety-eight residues of the H-2Db glycoprotein.

The NH2-terminal 98 amino acid residues of the murine histocompatibility antigen H-2Db have been assigned using radiochemical methodology. This represents the first extensive, continuous sequence information for a histocompatibility antigen encoded by the H-2D locus and allows comparison with the recently determined amino acid sequence of the H-2Kb molecule. The amino acid sequence was obtained from the sequences of three CNBr peptides, CN-E, CN-D, and CN-B, which comprise residues 1-5, 6-52, and 53-98, respectively. The amino acid sequence of CN-E was determined directly while the sequences of CN-D and CN-B were determined by NH2-terminal sequence analyses and sequence determinations of peptides produced by thrombin, staphylococcal V8 protease, and trypsin cleavage. Alignment of the CNBr peptides was accomplished by NH2-terminal sequence analysis of the H-2Db papain fragment (CN-E to CN-D) and by analyzing peptides from a tryptic digest of the intact H-2Db molecule. Positive identification was possible for all amino acids except Asp and Asn-86 which were indirectly assigned (in italics). The sequence obtained was Gly-Pro-His-Ser-Met-Arg-Tyr-Phe-Glu-Thr-Ala-Val-Ser-Arg-Pro-Gly-Leu-Glu-Glu-Pro -Arg-Tyr-Ile-Ser-Val-Gly-Tyr-Val-Asp-Asn-Lys-Glu-Phe-Val-Arg-Phe-Asp-Ser-Asp-Ala-Glu-Asn-Pro-Arg-Tyr-Glu-Pro-Arg-Ala-Pro-Trp-Met-Glu-Gln-Glu-Gly-Pro-Glu-Tyr-T rp-Glu-Arg-Glu-Thr-Gln-Lys-Ala-Lys-Gly-Gln-Glu-Gln-Trp-Phe-Arg-Val-Ser-Leu-Arg-Asn-Leu-Leu-Gly-Tyr-Tyr-Asn-Gln-Ser-Ala-Gly-Gly-Ser-His-Thr-Leu-Gln-Gln-Met.