Peptide selection by an MHC H-2Kb class I molecule devoid of the central anchor ("C") pocket

The peptide-binding site of the murine MHC class I molecule H-2K(b) contains a deep C pocket, that is critical for peptide binding, as it accepts the anchor phenylalanine or tyrosine residue located in the middle (position 5, P5F/Y) of H-2K(b) binding peptides, H-2K(b) predominantly binds octameric peptides, By both criteria, H-2K(b) is unique among the known murine and human class I molecules, none of which have a deep C pocket or preferentially select octamers, We investigated the relative importance of the C pocket in peptide selection and binding by the MHC, An MHC class I H-2K(b) variant, K-bW9, predicted to contain no C pocket, was engineered by replacing valine at MHC9 with tryptophan. This mutation drastically altered the selection of peptides bound to K-bW9. The K-bW9 molecule predominantly, if not exclusively, bound nonamers, New peptide anchor residues substituted for the loss of the P5F/Y:C pocket interaction, P3P/Y, which plays an auxiliary role in binding to K-b, assumed the role of a primary anchor, and P5R was selected as a new primary anchor, most likely contacting the E pocket, These experiments demonstrate that the presence of a deep C pocket is responsible for the selection of octameric peptides as the preferred ligands for K-b and provide insight into the adaptation of peptides to a rearranged MHC groove.