A Common Single Nucleotide Polymorphism in Endoplasmic Reticulum Aminopeptidase 2 Induces a Specificity Switch That Leads to Altered Antigen Processing

Abstract

ER aminopeptidases 1 and 2 (ERAP1 and ERAP2) cooperate to trim antigenic peptide precursors for loading onto MHC class I molecules and help regulate the adaptive immune response. Common coding single nucleotide polymorphisms (SNPs) in ERAP1 and ERAP2 have been linked with predisposition to human diseases ranging from viral and bacterial infections to autoimmunity and cancer. It has been hypothesized that altered antigen processing by these enzymes is a causal link to disease etiology but the molecular mechanisms are obscure. We report here that the common ERAP2 SNP rs2549782 that codes for amino acid variation N392K leads to alterations in both the activity and the specificity of the enzyme. Specifically, the 392N allele excises hydrophobic N-terminal residues from epitope precursors up to 165-fold faster compared to the 392K allele, although both alleles are very similar in excising positively charged N-terminal amino acids. These effects are primarily due to changes in the catalytic turnover rate (kcat) and not in the affinity for the substrate. X-ray crystallographic analysis of the ERAP2 392K allele suggests that the polymorphism interferes with the stabilization of the N-terminus of the peptide both directly and indirectly through interactions with key residues participating in catalysis. This specificity-switch allows the 392N allele of ERAP2 to supplement ERAP1 activity for the removal of hydrophobic N-terminal residues. Our results provide mechanistic insight to the association of this ERAP2 polymorphism with disease and support the idea that polymorphic variation in antigen processing enzymes constitutes a component of immune response variability in humans.

Functionally distinct ERAP1 allotype combinations distinguish individuals with Ankylosing Spondylitis

“…Despite there not being a mouse ortholog of ERAP2, we found little difference in the phenotype of HLA-B27 between murine Erap1 −/− cells and human ERAP1 KO 293T cells, suggesting that any effect ERAP2 has on peptide generation is small, and supporting the idea that ERAP1 is the main component of peptide trimming in cells (30). Nevertheless, it remains to be determined whether ERAP2 molecules in 293T cells are a low activity variant, which can be verified by using the ERAP1 KO 293T cells.…”

“…Finally, the ERAP1 homolog ERAP2 has been linked with AS and a change in trimming function (30,31). Despite there not being a mouse ortholog of ERAP2, we found little difference in the phenotype of HLA-B27 between murine Erap1 −/− cells and human ERAP1 KO 293T cells, suggesting that any effect ERAP2 has on peptide generation is small, and supporting the idea that ERAP1 is the main component of peptide trimming in cells (30).…”

ERAP1–ERAP2 Dimerization Increases Peptide-Trimming Efficiency

“…When probing with single-amino-bond fluorogenic substrates, ERAP1 prefers hydrophobic amino acids (leucine, methionine), whereas ERAP2 displays selectivity for positively charged amino acids (arginine, lysine) (5,(9)(10)(11). However, the activity of both enzymes toward more physiological, longer substrates appears to be less restrictive (5, 9-11) and depends on additional factors such as the C terminus (12) and the internal sequence of peptides (13,14).…”

The interplay between HLA-B27 and ERAP1/ERAP2 aminopeptidases: from anti-viral protection to spondyloarthritis

“…The two haplotypes are almost equally frequent in the different ethnic groups, so that 25% of individuals, being homozygous for the second haplotype, do not express ERAP2. Moreover, a non-synonymous SNP (rs2549782) encoding for the amino acid substitution N392K affects both enzymatic activity and substrate specificity [72]. This functional variant is in strong linkage with SNP rs2248374.…”

“…The trimming activity of ERAP2 is complementary to that of ERAP1 for both Nterminal substrate specificity and peptide length. Indeed, ERAP2 cleaves positively charged residues preferentially and its activity is maximal on octameric substrates and lower on longer peptides [63,[72][73][74]. Therefore, the two aminopeptidases would operate in a concerted manner, ensuring an efficient generation and/or destruction of MHC class I epitopes for a proper functioning and regulation of the adaptive immunity.…”