Mutational and Structural Analysis of KIR3DL1 Reveals a Lineage-Defining Allotypic Dimorphism That Impacts Both HLA and Peptide Sensitivity

Abstract

Killer Ig-like receptors (KIRs) control the activation of human NK cells via interactions with peptide-laden HLAs. KIR3DL1 is a highly polymorphic inhibitory receptor that recognizes a diverse array of HLA molecules expressing the Bw4 epitope, a group with multiple polymorphisms incorporating variants within the Bw4 motif. Genetic studies suggest that KIR3DL1 variation has functional significance in several disease states, including HIV infection. However, owing to differences across KIR3DL1 allotypes, HLA-Bw4, and associated peptides, the mechanistic link with biological outcome remains unclear. In this study, we elucidated the impact of KIR3DL1 polymorphism on peptide-laden HLA recognition. Mutational analysis revealed that KIR residues involved in water-mediated contacts with the HLA-presented peptide influence peptide binding specificity. In particular, residue 282 (glutamate) in the D2 domain underpins the lack of tolerance of negatively charged C-terminal peptide residues. Allotypic KIR3DL1 variants, defined by neighboring residue 283, displayed differential sensitivities to HLA-bound peptide, including the variable HLA-B*57:01–restricted HIV-1 Gag-derived epitope TW10. Residue 283, which has undergone positive selection during the evolution of human KIRs, also played a central role in Bw4 subtype recognition by KIR3DL1. Collectively, our findings uncover a common molecular regulator that controls HLA and peptide discrimination without participating directly in peptide-laden HLA interactions. Furthermore, they provide insight into the mechanics of interaction and generate simple, easily assessed criteria for the definition of KIR3DL1 functional groupings that will be relevant in many clinical applications, including bone marrow transplantation.

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

“…Notably, the degree to which binding was reduced was observed in a KIR3DL1-allotype dependent manner. There are also well-described C-terminal escape mutations within the TW10 epitope, of which G9D has similarly been shown to abrogate KIR3DL1 recognition in a KIR3DL1-allotype dependent manner 59 . This is in-line with recent reports on KIR3DL1 allomorph specificity 60 and suggests that KIR3DL1 polymorphism may be an important determinant shaping viral fitness.…”

KIR and HLA Genotypes Predictive of Low-Affinity Interactions Are Associated with Lower Relapse in Autologous Hematopoietic Cell Transplantation for Acute Myeloid Leukemia

“…Differences between KIR3DL1*002 and KIR3DL1*007 alter ligand-binding strength and inhibition of lysis of the NK-sensitive, HLA class I-deficient 721.221 cell line that is transfected with HLA-Bw4 alleles in a model system using NK leukemia cell lines transduced with distinct KIR3DL1 alleles (33). In HLA class I tetramer-binding studies, certain KIR3DL1 alleles show preferential binding of HLA-Bw4-80Ile over HLA-Bw4-80Thr, whereas other KIR3DL1 alleles interact equally well with both HLA-Bw4 molecules (19). HLA-B*13 and HLA-A*25 fail to engage KIR3DL1 and inhibit NK cell cytotoxicity despite the presence of an HLA-Bw4 sequence motif (47,48,62).…”

“…Beyond HLA polymorphism within the Bw4 binding motif, other factors influence NK cell phenotype and function and may similarly influence AHCT outcomes (18,19,33,61). KIR3DL1 allelic variants can influence NK cell responses in unexpected ways.…”

“…During this period, innate immunity provides an immediate response to foreign pathogens and may provide early protection from leukemia relapse, as suggested in HLA-identical alloHCT, in which NK cells contribute to graft-versus-leukemia (GVL) effects (12)(13)(14)(15)(16)(17). Although NK cells are ready to kill as soon as they are formed, NK cell immunity is variable and regulated by genetic polymorphisms among receptors and ligands (18)(19)(20). Because the immunogenetic factors that influence NK cell function may similarly influence antileukemia reactivity in the posttransplant period, variation in NK cell receptor and ligand combinations among AML patients may affect AHCT outcomes.…”

Deciphering the killer‐cell immunoglobulin‐like receptor system at super‐resolution for natural killer and T‐cell biology

“…A synergy of population genetics, phylogenetic analysis and comparison of nucleotide substitution rates among codons showed that this diversity is focused towards the parts of the KIR molecule that bind the HLA class I and peptide 61. The prediction that these major lineages of KIR3DL1/S1 have distinct ligand HLA/peptide‐binding properties has been borne out with crystallographic and functional studies 35, 39, 41, 42, 62, 63, 64, 65. Expansion of the phylogenetic analyses to include other KIR molecules revealed natural selection has consistently been focused towards residues that affect interaction with the HLA class I ligand,66 as well as those that affect the signalling properties of the receptor 67…”