Nase-specific T cell recognize the 86-100 peptide in association with B10.A APC. Clone N40 recognizes the 86-100 peptide in association with B10.A (Ek alpha Ek beta) and B10.A (5R) (Ek alpha Eb beta) APCs. We demonstrate here that a single amino acid substitution in the staphylococcal nuclease protein alters the structure of the processed peptide such that the T cell epitope recognized by clone N40 was only available for recognition in conjunction with B10.A (5R) but not the B10.A APCs. Other Nase-specific T cells recognize the mutant nuclease, and a synthetic peptide corresponding to the immunodominant region of the mutant protein was stimulatory for all the Nase-specific T cells. These results suggest that the mutation either affects the processing of the protein into antigenic peptides or affects the conformation of the processed fragment differently from that of the peptide.