Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1

Abstract

ERAP1 trims antigen precursors to fit into MHC class I proteins. To perform this function, ERAP1 has unique substrate preferences, trimming long peptides while sparing shorter ones. To identify the structural basis for ERAP1's unusual properties, we determined the X-ray crystal structure of human ERAP1 bound to bestatin. The structure reveals an open conformation with a large interior compartment. An extended groove originating from the enzyme's catalytic center can accommodate long peptides and has features that explain ERAP1's broad specificity for antigenic peptide precursors. Structural and biochemical analysis suggest a mechanism for ERAP1's length-dependent trimming activity, whereby binding of long but not short substrates induces a conformational change with reorientation of a key catalytic residue towards the active site. ERAP1's unique structural elements suggest how a generic aminopeptidase structure has been adapted for the specialized function of trimming antigenic precursors.

ERAP1–ERAP2 Dimerization Increases Peptide-Trimming Efficiency

“…The latter feature refers to the low ERAP1-trimming activity toward most peptides shorter than eight residues (12,16). Absence of ERAP activity has been shown to drastically change the profile of MHC class I-associated peptides (17) and/or alter Ag presentation in vitro and in vivo in numerous experimental systems (18)(19)(20).…”

“…ERAP1 crystallizes as a trimer and ERAP2 as a dimer. Interestingly, the interaction sites in these multimers correspond to residues conserved between the two enzymes (16,21). However, the functional significance of dimer formation for ERAP-trimming activity remains unknown.…”

“…ERAP1 has been shown to possess regulatory sites different from the active site that modulates its activity (16). Dimerization might represent an additional level of allosteric regulation.…”

MHC Class I Quality Control

“…The crystal structure of ERAP1 (bound to bestatin) reveals a large cavity that would explain the preference for longer substrates compared to most other aminopeptidases (Nguyen, Chang et al 2011). In this large cavity a catalytic site is found to which the Nterminal part of the peptide binds.…”

“…It has been proposed that in close proximity to this catalytic site a regulatory site is found to which the C-terminal part of the peptide is bound, this "double binding" ensures a closed conformation of the ERAP1 molecule resulting in effective cleaving of the peptide. However, if the peptide is too short the C-terminal will not reach the regulatory site and the "double binding" will not be achieved resulting in an ineffective cleaving of the peptide (Nguyen, Chang et al 2011). …”