Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3.
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.
Wang
C R
CR
Department of Biochemistry, University of Texas Southwestern Medical Center Dallas 75235-9050, USA.
Castaño
A R
AR
Peterson
P A
PA
Slaughter
C
C
Lindahl
K F
KF
Deisenhofer
J
J
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D018076:DNA, Complementary / Q000235:genetics; D004563:Electrochemistry; D015395:Histocompatibility Antigens Class I / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D066298:In Vitro Techniques; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009239:N-Formylmethionine / Q000378:metabolism; D009842:Oligopeptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation
D018076:DNA, Complementary; D015395:Histocompatibility Antigens Class I; D009842:Oligopeptides; D009239:N-Formylmethionine