Nonclassical binding of formylated peptide in crystal structure of the MHC class lb molecule H2-M3

Abstract

H2-M3 is a class Ib MHC molecule of the mouse with a 10(4)-fold preference for binding N-formylated peptides. To elucidate the basis of this unusual specificity, we expressed and crystallized a soluble form of M3 with a formylated nonamer peptide, fMYFINILTL, and determined the structure by X-ray crystallography. M3, refined at 2.1 A resolution, resembles class la MHC molecules in its overall structure, but differs in the peptide-binding groove. The A pocket, which usually accommodates the free N-terminus of a bound peptide, is closed, and the peptide is shifted one residue, such that the P1 side chain is lodged in the B pocket. The formyl group is coordinated by His-9 and a bound water on the floor of the groove.

Human mitochondria-derivedN-formylated peptides are novel agonists equally active on FPR and FPRL1, whileListeria monocytogenes-derived peptides preferentially activate FPR

“…They were thus postulated to use N-formyl peptide receptors. A nonamer of the rat form of ND1 (N-formyl-MYFINILTL), which binds to MHC class Ib molecule H2-M3 [33], has been shown to stimulate neutrophil chemotaxis and to compete for binding of [ 3 H]lipoxin A4 (LXA4) to LXA4R/FPRL1 expressed in HEK293 cells [34]. However, in our hands, the hexapeptide that derived from the human form of ND1 was inactive on the human members of the FPR family.…”

MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape

“…In addition, there have been isolated reports of peptides with residues overhanging the C-terminal pocket of HLA-A*02:01 12,40 and H2-M3 41 . It was not clear, however, whether such overhangs could occur beyond the more buried N-terminal pocket.…”

Promiscuity of MHC Class Ib-Restricted T Cell Responses

“…Taking this into consideration, the requirements that are essential for binding to H2-M3, namely hydrophobic amino acid composition and interactions with essentially only four N-terminal residues, the number of N-terminal sequence permutations for H2-M3 ligands is limited. Of those hydrophobic peptides that do bind to H2-M3, the amino acid side chains are buried within the H2-M3-binding groove and therefore inaccessible to TCR (9,41). Hence, similar surface characteristics that are formed by the H2-M3 molecule with different ligands might result in cross-reactive recognition by a given TCR.…”

“…This can be explained in part by the distinct structural features of MHC class Ib molecules. For example, the binding groove of H2-M3 and other MHC class I-like molecules such as CD1 is narrower and more hydrophobic than that of most MHC class Ia molecules (9,35). Only a few of the 13 mitochondrial proteins, the only source for endogenous H2-M3 ligands, and some bacterially derived N-terminal sequences fulfill the requirements for this molecular pattern (21,36).…”

“…Mitochondrial protein synthesis initiates with N-formyl methionine, and H2-M3 selectively binds peptides containing this modified amino acid (6 -8). The crystal structure of H2-M3 revealed a hydrophobic peptide-binding groove that specifically accommodates N-formyl methionine as an essential anchor residue (9). The specificity for N-formylated peptides positions H2-M3 especially well for presentation of bacterial ligands, because prokaryotic protein synthesis initiates with N-formyl methionine.…”