ERAP2

Last updated
ERAP2
Crystal structure ERAP2 - PDB 3SE6.jpg
Available structures
PDB Human UniProt search: PDBe RCSB
Identifiers
Aliases ERAP2 , L-RAP, LRAP, endoplasmic reticulum aminopeptidase 2
External IDs OMIM: 609497; HomoloGene: 75183; GeneCards: ERAP2; OMA:ERAP2 - orthologs
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001130140
NM_022350
NM_001329229
NM_001329233

n/a

RefSeq (protein)

NP_001123612
NP_001316158
NP_001316162
NP_071745

n/a

Location (UCSC) Chr 5: 96.88 – 96.92 Mb n/a
PubMed search [2] n/a
Wikidata
View/Edit Human

Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a protein that in humans is encoded by the ERAP2 gene. ERAP2 is part of the M1 aminopeptidase family. It is expressed along with ERAP1 in the endoplasmic reticulum (ER). In the ER, both enzymes help process and present antigens by trimming the ends of precursor peptides. This creates the optimal pieces for display by Major Histocompatibility Complex (MHC) class I molecules.

Contents

Biology / Functions

Expression

ERAP2 expression is regulated by interferon gamma signalling. While ERAP2 and homologous enzyme ERAP1 are both expressed in immune cells, the expression of the enzymes is independently regulated in other tissues without significant correlation of expression levels. However, coordinated expression patterns have also been observed, in which ERAP2 downregulation is counterbalanced by an increase in ERAP1 expression. [3] Overexpression of ERAP2 in various cancer types, including melanomas and different adenocarcinomas, has been suggested to modulate the presentation of cancer antigens on MHC-I, which may affect cancer invasion by immune cells. [4] ERAP2 is not expressed in mice making it more difficult to study.

Antigen presentation

Unlike ERAP1, ERAP2 can trim efficiently peptides that already have optimal length for MHC class I presentation. Thus ERAP2 has been shown to shorten peptides of 9 or fewer amino acids, thereby destroying antigenic peptides in some cases. [5] [6] ERAP2 displays a preference for peptide substrates that carry N-terminal basic residues (arginine, lysine). [7] A fraction of ERAP2 is reported to form complexes with ERAP1, as seen in co-precipitation experiments. [7] Heterodimer formation improves peptide-trimming efficiency, resulting in an expanded antigenic repertoire and a more diverse immune response. [8] The ERAP1-ERAP2 complex can trim free peptides in the ER and may also be able to trim MHC I-bound precursor peptides, according to some authors. [9] Individuals homozygous for ERAP2 haplotype B lack ERAP2 protein expression and have significantly lower MHC class I levels on the surface of B cells. This may result in an altered presentation of antigens and resulting immune responses. [10]

Other functions

ERAP2 can modulate the renin-angiotensin system (RAS) in blood pressure homeostasis through angiotensin cleavage. In concert with ERAP1, ERAP2 counteracts angiotensin II activity, inducing vasodilation and hypertension reduction. [11] Blood pressure modulation by ERAP2 is supported by the association of ERAP2 with blood pressure progression and hypertension incidence. [12] Its link to pre-eclampsia in multiple populations shows further support for the role of ERAP2 in blood pressure homeostasis. [13] [14]

Genetics / clinical significance

Gene / location

ERAP2 gene is located on human chromosome 5 in between the ERAP1 and LNPEP genes encoding the other two family members of the M1 aminopeptidases. It has 41,438 base pair length and consists of 19 exons. [15]

SNPs and disease association

The ERAP2 gene is highly polymorphic and contains many common single nucleotide variants (SNVs) that are in strong linkage disequilibrium and are maintained at intermediate frequencies through balancing selection. [16] There are two common SNVs in ERAP2 that facilitate the alternative splicing of three haplotypes by altering splice motifs. [16] [17] The A allele of splice variant rs2248374 tags haplotype A, which results in the full-length 960 amino acid long ERAP2 protein being produced. [16] However, the G allele of rs2248374 (i.e., haplotype B) disrupts splicing at exon 10, introducing downstream premature stop codons. [16] Under steady state conditions, the truncated mRNA is destroyed by nonsense mediated decay (NMD), but during influenza infections it is translated to two truncated isoforms. [18] Accordingly, 25% of the general population (haplotype B homozygotes) are deficient in full-length ERAP2 protein. The G allele of SNV rs17486481 activates a cryptic splice site upstream of exon 12 that also introduces premature stop codons and makes the transcript likely vulnerable to NMD (haplotype C). Different ERAP2 protein haplotypes (or allotypes) have been detected among the major continental populations based on common missense variants in ERAP2. [16] [19] ERAP2 haplotypes are associated with severe inflammatory conditions (e.g., birdshot chorioretinopathy, Crohn's disease, ankylosing spondylitis, psoriasis) and cancer treatment responses. [20] Interestingly, the alleles from SNVs that strongly predispose to autoimmune conditions (i.e., A allele of rs2248374 and other SNVs in haplotype A) display natural selection in recent human history, which has been suggested to provide higher resistance against severe respiratory illnesses, including the bubonic plague ("Black Death"), pneumonia and COVID-19. [21] [22] [23] Klunk et al. found that individuals with the protective allele (dominant in the present European population) had a fivefold increase in ERAP2 expression in macrophages resulting in reduced replication of Y. pestis.

Structure / Mechanism

Structure

ERAP2 is composed of 4 structural units (I-IV), with the HEXXHX18E zinc-binding motif and the known GAMEN aminopeptidase motif located in domain II, similarly to its closely related enzyme ERAP1. The catalytic site features a single Zn(II) ion and is coordinated by two histidine residues (H370, H374) and a glutamate residue (E393). Domains II and IV, which are linked by domain III, form a large internal cavity close to the catalytic site and exclude the external solvent, in accordance with the “closed” conformation obtained for ERAP1. [24]

Mechanism

ERAP2 selects substrates by sequestering them in its internal cavity and allowing interactions to determine trimming rates, thus combining substrate permissiveness with sequence bias. [25] A crystal structure of ERAP2 with a peptide product located in this cavity has revealed lack of deep specificity pockets and lack of a cavity that interacts with the peptide C- terminus, which justify the limited selectivity of this enzyme and the differences in length selection compared to ERAP1 (ERAP2 can effectively trim 8-mer peptides, while it is less active with longer substrates [25] [26] ). Interactions between side-chains of a 10-mer phosphinic analogue and residues of the interior of the cavity also appear shallow and opportunistic, further confirming its ability to process a variety of peptide substrates [27] .  In terms of N-terminal residue specificity, ERAP2 prefers basic amino acids, such as arginine. [26]

Interactions

Some experimental evidence has suggested the formation of a heterodimer between ERAP2 and the homologous enzyme ERAP1. Formation of leucine zipper-fused heterodimers of ERAP1 and ERAP2 produces mature epitopes more efficiently than a dilute mixture of the two enzymes. The interaction of ERAP2 with ERAP1 changes basic enzymatic parameters of the latter and improves its substrate-binding affinity. [28] A possible dimerization between ERAP1/ERAP2 could be the basis for enhanced synergism between these two enzymes which helps define the human immunopeptidome. [29]

Therapeutic approaches and pharmacology

Therapeutic approaches for ERAP2 regulation rely mostly on the development of small molecule inhibitors. The most explored classes of inhibitors for ERAP2 are the allosteric site ones.

Figure 1. A. Crystal structure of ERAP2 co-crystallized with hydroxamic acid triazole in the active site. Adapted and recreated from PDB code 7NSK. B. 2D chemical structure of co-crystallized compound. Figure 1. (A) Crystal structure of ERAP2 co-crystallized with hydroxamic acid triazole in the active site. Adapted and recreated from PDB code 7NSK29. (B) 2D chemical structure of co-crystallized compound..png
Figure 1. A. Crystal structure of ERAP2 co-crystallized with hydroxamic acid triazole in the active site. Adapted and recreated from PDB code 7NSK. B. 2D chemical structure of co-crystallized compound.

ERAP2 catalytic site inhibitors

Although most of the phosphinic pseudopeptide analogs disclosed by Kokkala et al. in 2016 were non-selective ERAP inhibitors, compound 1 displayed nanomolar potency towards ERAP2 (IC50 = 129 nM) with a highly improved selectivity against ERAP1, and was active in modulating the immunopeptidome of cancer cells. [31] [32]

In 2022, the first nanomolar selective ERAP2 inhibitors were discovered by kinetic-target guided synthesis (KTGS). A central core structure of hydroxamic acid triazoles targets the zinc ion in the catalytic site. Further investigations to optimize the activity led to nanomolar inhibitor BDM88952 (IC50 = 3.9 nM) with the relative protein-ligand interactions studied by ERAP2 X-ray co-crystallography (Figure 1). [30]

Two hits of carboxylic acid derivatives were identified via high-throughput screening (HTS) against ERAP2, from an in-house library of 1920 compounds. Compound 3 was amongst those selected for their potency (ERAP2, IC50 = 22 nM) and selectivity. Docking studies revealed that the carboxylic acid is predicted to coordinate the catalytic zinc ion within ERAP2. Several analogues were designed and synthesized. [33]

ERAP2 allosteric site inhibitors

Sulfonamide compound 4 was identified as a potential allosteric inhibitor against ERAP2 in 2022 by Arya et al.. [34] This compound targets ERAP2 through an uncompetitive manner (IC50 = 44 μM) by inhibiting the hydrolysis of peptide substrates. At the same time it acts as a competitive inhibitor against ERAP1 (IC50 = 73 μM). [34]

Table 1. Representative examples of reported ERAP2 inhibitors. *IC50 value measured on long-peptide assay. Table1Representative examples of reported ERAP2 inhibitors..png
Table 1. Representative examples of reported ERAP2 inhibitors. *IC50 value measured on long-peptide assay.

Related Research Articles

<span class="mw-page-title-main">Antigen</span> Molecule triggering an immune response (antibody production) in the host

In immunology, an antigen (Ag) is a molecule, moiety, foreign particulate matter, or an allergen, such as pollen, that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response.

<span class="mw-page-title-main">Calreticulin</span> Soluble protein

Calreticulin also known as calregulin, CRP55, CaBP3, calsequestrin-like protein, and endoplasmic reticulum resident protein 60 (ERp60) is a protein that in humans is encoded by the CALR gene.

<span class="mw-page-title-main">Major histocompatibility complex</span> Cell surface proteins, part of the acquired immune system

The major histocompatibility complex (MHC) is a large locus on vertebrate DNA containing a set of closely linked polymorphic genes that code for cell surface proteins essential for the adaptive immune system. These cell surface proteins are called MHC molecules.

<span class="mw-page-title-main">Human leukocyte antigen</span> Genes on human chromosome 6

The human leukocyte antigen (HLA) system is a complex of genes on chromosome 6 in humans that encode cell-surface proteins responsible for regulation of the immune system. The HLA system is also known as the human version of the major histocompatibility complex (MHC) found in many animals.

<span class="mw-page-title-main">MHC class I</span> Protein of the immune system

MHC class I molecules are one of two primary classes of major histocompatibility complex (MHC) molecules and are found on the cell surface of all nucleated cells in the bodies of vertebrates. They also occur on platelets, but not on red blood cells. Their function is to display peptide fragments of proteins from within the cell to cytotoxic T cells; this will trigger an immediate response from the immune system against a particular non-self antigen displayed with the help of an MHC class I protein. Because MHC class I molecules present peptides derived from cytosolic proteins, the pathway of MHC class I presentation is often called cytosolic or endogenous pathway.

Cross-presentation is the ability of certain professional antigen-presenting cells (mostly dendritic cells) to take up, process and present extracellular antigens with MHC class I molecules to CD8 T cells (cytotoxic T cells). Cross-priming, the result of this process, describes the stimulation of naive cytotoxic CD8+ T cells into activated cytotoxic CD8+ T cells. This process is necessary for immunity against most tumors and against viruses that infect dendritic cells and sabotage their presentation of virus antigens. Cross presentation is also required for the induction of cytotoxic immunity by vaccination with protein antigens, for example, tumour vaccination.

<span class="mw-page-title-main">Birdshot chorioretinopathy</span> Medical condition

Birdshot chorioretinopathy, now commonly named birdshot uveitis or HLA-A29 uveitis, is a rare form of bilateral posterior uveitis affecting both eyes. It causes severe, progressive inflammation of both the choroid and retina.

<span class="mw-page-title-main">HLA-DR</span> Subclass of HLA-D antigens that consist of alpha and beta chains

HLA-DR is an MHC class II cell surface receptor encoded by the human leukocyte antigen complex on chromosome 6 region 6p21.31. The complex of HLA-DR and peptide, generally between 9 and 30 amino acids in length, constitutes a ligand for the T-cell receptor (TCR). HLA were originally defined as cell surface antigens that mediate graft-versus-host disease. Identification of these antigens has led to greater success and longevity in organ transplant.

<span class="mw-page-title-main">Aminopeptidase</span> Class of enzymes

Aminopeptidases are enzymes that catalyze the cleavage of amino acids from the N-terminus (beginning), of proteins or peptides. They are found in many organisms; in the cell, they are found in many organelles, in the cytosol, and as membrane proteins. Aminopeptidases are used in essential cellular functions, and are often zinc metalloenzymes, containing a zinc cofactor.

<span class="mw-page-title-main">Bare lymphocyte syndrome</span> Medical condition

Bare lymphocyte syndrome is a condition caused by mutations in certain genes of the major histocompatibility complex or involved with the processing and presentation of MHC molecules. It is a form of severe combined immunodeficiency.

<span class="mw-page-title-main">Insulin regulated aminopeptidase</span>

Insulin regulated aminopeptidase (IRAP) is a protein that in humans is encoded by the leucyl and cystinyl aminopeptidase (LNPEP) gene. IRAP is a type II transmembrane protein which belongs to the oxytocinase subfamily of M1 aminopeptidases, alongside ERAP1 and ERAP2. It is also known as oxytocinase, leucyl and cystinyl aminopeptidase, placental leucine aminopeptidase (P-LAP), cystinyl aminopeptidase (CAP), and vasopressinase. IRAP is expressed in different cell types, mainly located in specialized regulated endosomes that can be recruited to the cell surface upon cell type-specific receptor activation.

<span class="mw-page-title-main">Antigen presentation</span> Vital immune process that is essential for T cell immune response triggering

Antigen presentation is a vital immune process that is essential for T cell immune response triggering. Because T cells recognize only fragmented antigens displayed on cell surfaces, antigen processing must occur before the antigen fragment can be recognized by a T-cell receptor. Specifically, the fragment, bound to the major histocompatibility complex (MHC), is transported to the surface of the antigen-presenting cell, a process known as presentation. If there has been an infection with viruses or bacteria, the antigen-presenting cell will present an endogenous or exogenous peptide fragment derived from the antigen by MHC molecules. There are two types of MHC molecules which differ in the behaviour of the antigens: MHC class I molecules (MHC-I) bind peptides from the cell cytosol, while peptides generated in the endocytic vesicles after internalisation are bound to MHC class II (MHC-II). Cellular membranes separate these two cellular environments - intracellular and extracellular. Each T cell can only recognize tens to hundreds of copies of a unique sequence of a single peptide among thousands of other peptides presented on the same cell, because an MHC molecule in one cell can bind to quite a large range of peptides. Predicting which antigens will be presented to the immune system by a certain MHC/HLA type is difficult, but the technology involved is improving.

<span class="mw-page-title-main">HLA-A</span> Protein-coding gene in the species Homo sapiens

HLA-A is a group of human leukocyte antigens (HLA) that are encoded by the HLA-A locus, which is located at human chromosome 6p21.3. HLA is a major histocompatibility complex (MHC) antigen specific to humans. HLA-A is one of three major types of human MHC class I transmembrane proteins. The others are HLA-B and HLA-C. The protein is a heterodimer, and is composed of a heavy α chain and smaller β chain. The α chain is encoded by a variant HLA-A gene, and the β chain (β2-microglobulin) is an invariant β2 microglobulin molecule. The β2 microglobulin protein is encoded by the B2M gene, which is located at chromosome 15q21.1 in humans.

<span class="mw-page-title-main">Minor histocompatibility antigen</span>

Minor histocompatibility antigen are peptides presented on the cellular surface of donated organs that are known to give an immunological response in some organ transplants. They cause problems of rejection less frequently than those of the major histocompatibility complex (MHC). Minor histocompatibility antigens (MiHAs) are diverse, short segments of proteins and are referred to as peptides. These peptides are normally around 9-12 amino acids in length and are bound to both the major histocompatibility complex (MHC) class I and class II proteins. Peptide sequences can differ among individuals and these differences arise from SNPs in the coding region of genes, gene deletions, frameshift mutations, or insertions. About a third of the characterized MiHAs come from the Y chromosome. Prior to becoming a short peptide sequence, the proteins expressed by these polymorphic or diverse genes need to be digested in the proteasome into shorter peptides. These endogenous or self peptides are then transported into the endoplasmic reticulum with a peptide transporter pump called TAP where they encounter and bind to the MHC class I molecule. This contrasts with MHC class II molecules's antigens which are peptides derived from phagocytosis/endocytosis and molecular degradation of non-self entities' proteins, usually by antigen-presenting cells. MiHA antigens are either ubiquitously expressed in most tissue like skin and intestines or restrictively expressed in the immune cells.

Human leukocyte histocompatibility complex DO (HLA-DO) is an intracellular, dimeric non-classical Major Histocompatibility Complex (MHC) class II protein composed of α- and β-subunits which interact with HLA-DM in order to fine tune immunodominant epitope selection. As a non-classical MHC class II molecule, HLA-DO is a non-polymorphic accessory protein that aids in antigenic peptide chaperoning and loading, as opposed to its classical counterparts, which are polymorphic and involved in antigen presentation. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian body—namely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cells—indicate that it may be of physiological importance and has inspired further research. Although HLA-DM can be found without HLA-DO, HLA-DO is only found in complex with HLA-DM and exhibits instability in the absence of HLA-DM. The evolutionary conservation of both DM and DO, further denote its biological significance and potential to confer evolutionary benefits to its host.

<span class="mw-page-title-main">CD74</span> Mammalian protein found in humans

HLA class II histocompatibility antigen gamma chain also known as HLA-DR antigens-associated invariant chain or CD74, is a protein that in humans is encoded by the CD74 gene. The invariant chain is a polypeptide which plays a critical role in antigen presentation. It is involved in the formation and transport of MHC class II peptide complexes for the generation of CD4+ T cell responses. The cell surface form of the invariant chain is known as CD74. CD74 is a cell surface receptor for the cytokine macrophage migration inhibitory factor (MIF).

<span class="mw-page-title-main">HLA-F</span> Protein-coding gene in the species Homo sapiens

HLA class I histocompatibility antigen, alpha chain F is a protein that in humans is encoded by the HLA-F gene. It is an empty intracellular molecule that encodes a non-classical heavy chain anchored to the membrane and forming a heterodimer with a β-2 microglobulin light chain. It belongs to the HLA class I heavy chain paralogues that separate from most of the HLA heavy chains. HLA-F is localized in the endoplasmic reticulum and Golgi apparatus, and is also unique in the sense that it exhibits few polymorphisms in the human population relative to the other HLA genes; however, there have been found different isoforms from numerous transcript variants found for the HLA-F gene. Its pathways include IFN-gamma signaling and CDK-mediated phosphorylation and removal of the Saccharomycescerevisiae Cdc6 protein, which is crucial for functional DNA replication.

<span class="mw-page-title-main">ERAP1</span> Protein-coding gene in the species Homo sapiens

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an enzyme that in humans is encoded by the ERAP1 gene. This M1 zinc aminopeptidase is involved in the antigen processing and presentation pathway. ERAP1 is mainly located in the endoplasmic reticulum (ER), where it trims peptides at their N-terminus, adapting them for presentation by MHC class I molecules (MHC-I).

<span class="mw-page-title-main">Peptide loading complex</span>

The peptide-loading complex (PLC) is a short-lived, multisubunit membrane protein complex that is located in the endoplasmic reticulum (ER). It orchestrates peptide translocation and selection by major histocompatibility complex class I (MHC-I) molecules. Stable peptide-MHC I complexes are released to the cell surface to promote T-cell response against malignant or infected cells. In turn, T-cells recognize the activated peptides, which could be immunogenic or non-immunogenic.

<span class="mw-page-title-main">Margarita del Val</span> Spanish chemist

Margarita del Val Latorre is a Spanish chemist, immunologist, and virologist. She coordinates the Salud Global platform run by the Spanish National Research Council (CSIC).

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