Molecular Architecture of the Major Histocompatibility Complex Class I-binding Site of Ly49 Natural Killer Cell Receptors

Abstract

The cytolytic activity of NK cells is regulated by a delicate balance of activating and inhibitory signals mediated through distinct classes of receptors found on their surface. The dominant signal received by an NK cell through its interaction with normal levels of major histocompatibility complex class I (MHC-I) molecules on target cells is inhibitory. If the level of MHC-I is reduced through tumorigenic or infectious processes, this inhibitory signal is attenuated, and the NK cell is activated (1-3). In this way, cells with abnormal MHC-I expression become targets of NK lytic activity.Several receptor families have been identified on primate and rodent NK cells that monitor MHC-I expression on surrounding cells (3-5). These include the killer immunoglobulin-like receptors, members of the Ly49 family (Ly49s), and the CD94-NKG2 family of receptors. Additionally, the activating receptor NKG2D recognizes MHC-like molecules, such as MICA, that are up-regulated in stressed tissues (6). The mouse Ly49 family includes at least 23 expressed or potential members (Ly49A-W), along with about 15 allelic variants (2, 7). These highly polymorphic receptors constitute the main MHC-monitoring molecules on rodent NK cells. Although most Ly49s inhibit NK cell-mediated cytolysis after binding to MHC-I ligands, some are activating. Ly49s recognize one or more H-2D or H-2K alleles, independently of the MHC-bound peptide (2, 3). Their binding properties range from the broad recognition of MHC-I molecules by Ly49C to the allelic specificity of Ly49A. Recently, crucial roles for Ly49 receptors in antiviral immunity have been discovered. In one case, the m157 gene product of mouse cytomegalovirus (MCMV) was shown to interact directly with an inhibitory Ly49 (Ly49I) in a susceptible mouse strain and with an activating Ly49 (Ly49H) in a resistant one (8, 9). In another case, the activating receptor Ly49P was found to confer resistance to MCMV by interacting with H-2D molecules on MCMV-infected cells (10).Ly49 receptors belong to the C-type lectin-like family of proteins, which also includes CD94-NKG2 and NKG2D (4, 5). Ly49s are homodimeric type II glycoproteins, with each chain composed of a C-type lectin-like domain, termed the natural killer receptor domain (NKD), connected by a stalk of ϳ70 residues to the transmembrane and cytoplasmic domains. Crystal structures have been reported for Ly49A bound to H-2D d (11) and for Ly49C bound to H-2K b (12). These structures showed that both Ly49s engage MHC-I at a broad cavity beneath the * This work was supported, in whole or in part, by National Institutes of Health Grant AI047990. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. The atomic coordinates and structure factors (codes 3C8J, 3CAD, and 3C8K)

Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity

“…Only in the case of rNKR-P1A was an alternative technique tried. The neighboring sequence from the Neighbor-Joining phylogenetic tree (1000× bootstrapped) was used, i.e., structure 3CAD (lectin-related NK cell receptor LY49G1 [36]). Alignment of template and modeled sequences used ClustalX.…”

Peptide Modulation of Class I Major Histocompatibility Complex Protein Molecular Flexibility and the Implications for Immune Recognition*

“…The six positions on the ␣-helices encompass regions contacted by TCRs and were within the fragments studied by HDX-MS. The positions on the ␤-sheet were also in a fragment identified by HDX-MS and are in proximity to the binding sites for the ␤ 2 -microglobulin subunit, the CD8 coreceptor, and, for murine class I MHC proteins, the Ly49 class of inhibitory receptors (28,29). The positions chosen for labeling have side chains in the wild-type protein that are polar or charged and, in the structures of the various pMHC complexes, point away from the protein and make no contacts to peptide ( Fig.…”

Recognition of Class I MHC by a Rat Ly49 NK Cell Receptor Is Dependent on the Identity of the P2 Anchor Amino Acid of Bound Peptide

“…In mouse Ly49C, part of this L3 loop forms an a-helix, which is not seen in mouse Ly49A or Ly49G. Exchange of the Ly49C L3/a3 loop into Ly49A led to a gain in recognition of H-2K b (41). Notably, the L3 loop interacts with MHC-I on the platform below the peptide binding groove in an area proximal to the A-, B-, and D-pockets.…”

“…A recent report has indicated that residues 211-231 encompassing the L3 loop on mouse Ly49 determines the allele specificity for H-2K b (41). In mouse Ly49C, part of this L3 loop forms an a-helix, which is not seen in mouse Ly49A or Ly49G.…”