Affinage

EDEM3

ER degradation-enhancing alpha-mannosidase-like protein 3 · UniProt Q9BZQ6

Length
932 aa
Mass
104.7 kDa
Annotated
2026-06-09
12 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

EDEM3 is an ER-resident alpha1,2-mannosidase that catalyzes the second step of N-glycan mannose trimming during glycoprotein ER-associated degradation (ERAD), and its activity directly drives clearance of misfolded glycoproteins (PMID:16431915, PMID:34698634). Purified EDEM3 is the major enzyme converting Man8GlcNAc2 isomer B (M8B) to M7 (M7A/M7C), M6, and M5 oligosaccharides, and it also trims intact glycoproteins, with catalysis depending on the conserved active-site glutamate (E147) (PMID:16431915, PMID:34698634). Full activity requires a covalent partnership with the ER oxidoreductase ERp46, which forms a disulfide bond with the EDEM3 alpha-mannosidase domain and is needed for mannose trimming of substrates such as misfolded TCRalpha (PMID:29784879, PMID:35500441). The protein is organized into discrete functional domains — a catalytic GH47 domain that binds substrate even without trimming, an intermediate (IMD) domain required for GH47 folding, and protease-associated (PA) and intrinsically disordered (IDD) domains that respectively promote and restrain degradation of specific substrates to set ERAD timing (PMID:33671632). Human loss-of-function variants cause a congenital disorder of glycosylation (EDEM3-CDG) marked by defective M8B trimming, accumulation of Glc1Man5GlcNAc2, and a blunted unfolded protein response (PMID:34143952).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2006 High

    Established that EDEM3 is an active mannosidase whose enzymatic activity, not merely lectin binding, is required for its ERAD-promoting function — resolving whether EDEM proteins act catalytically.

    Evidence Wild-type versus E147Q active-site mutant transfection in HEK293 cells with NHK and TCRalpha degradation and mannose-trimming assays

    PMID:16431915

    Open questions at the time
    • Did not define the precise glycan products generated
    • In-cell assay could not exclude contributions from associated factors
    • No purified-protein reconstitution
  2. 2018 High

    Identified ERp46 as a disulfide-bonded partner essential for EDEM3 catalysis, showing the enzyme requires a redox-active cofactor rather than acting alone.

    Evidence Co-IP, disulfide bond mapping, and in vitro reconstitution with purified recombinant proteins from HEK293 cells

    PMID:29784879

    Open questions at the time
    • Single lab
    • Mechanism by which the disulfide bond activates the GH47 domain not structurally resolved
    • Generality across substrates beyond TCRalpha not established
  3. 2021 High

    Defined EDEM3 as the major enzyme for the second mannose-trimming step in gpERAD by reconstituting the full M8B-to-M7/M6/M5 reaction with purified protein and defined glycans.

    Evidence In vitro mannosidase assays with purified recombinant EDEM3 and pyridylamine-labeled M8B and glycoprotein substrates

    PMID:34698634

    Open questions at the time
    • Kinetic determinants of product distribution not detailed
    • Did not address in vivo cofactor requirement
  4. 2021 Medium

    Mapped EDEM3 into four functional domains and assigned distinct roles, explaining how a single enzyme tunes ERAD timing for different substrates.

    Evidence EDEM3-knockout cells complemented with domain-deletion mutants, NHK and tyrosinase degradation assays, and LC/MS interactome analysis

    PMID:33671632

    Open questions at the time
    • Mechanism of IDD-mediated negative modulation unknown
    • Single lab
    • Domain effects shown for limited substrate set
  5. 2021 Medium

    Connected EDEM3 catalytic function to human disease, demonstrating that loss-of-function variants cause a CDG and impair the unfolded protein response in vivo.

    Evidence Exome sequencing, patient fibroblast/plasma and mouse glycan profiling, and tunicamycin-induced UPR assays

    PMID:34143952

    Open questions at the time
    • Link between glycan defect and UPR impairment mechanistically unresolved
    • No in vitro reconstitution of variant enzymes
  6. 2022 Medium

    Refined substrate specificity by showing EDEM3 acts on asparagine-linked but not glycine-linked oligomannose glycans and that ERp46 enhances activity, indicating glycan-protein linkage context matters.

    Evidence In vitro mannosidase assays with purified EDEM3 and synthetic N-linked versus glycine-linked M9 substrates, with and without ERp46

    PMID:35500441

    Open questions at the time
    • Single method, no mutagenesis validation
    • Structural basis of linkage discrimination unknown
  7. 2020 Medium

    Revealed a physiological consequence of EDEM3 activity beyond protein quality control, linking it to LRP1 surface glycosylation and lipoprotein metabolism.

    Evidence EDEM3-knockout cells and mice with VLDL uptake, LRP1 expression, cell-surface glycoprotein profiling, and metabolomics

    PMID:32213464

    Open questions at the time
    • Direct glycan changes on LRP1 not mapped
    • Single lab
  8. 2017 Low

    Began mapping the EDEM3 interaction network, placing it among ERAD cargo-recognition and ubiquitination machinery sensitive to glycan-processing state.

    Evidence IP-mass spectrometry with Western validation and glycan-processing inhibitor treatments

    PMID:28366632

    Open questions at the time
    • Single Co-IP/MS with only partial validation
    • Direct versus indirect interactions not distinguished
    • UBA1/UBA2 functional relevance unconfirmed
  9. 2025 Low

    Implicated COPB2 in controlling EDEM3 ER localization and activity, suggesting trafficking-level regulation of EDEM3 function in cancer cells.

    Evidence Co-IP, glycoproteomics, and COPB2 knockdown/overexpression in ovarian cancer cells with xenografts

    PMID:40736660

    Open questions at the time
    • Single Co-IP without reciprocal validation
    • No in vitro reconstitution
    • Direct effect on EDEM3 catalysis versus localization not separated

Open questions

Synthesis pass · forward-looking unresolved questions
  • How EDEM3's domain architecture and the ERp46 disulfide bond are structurally coordinated to set substrate-specific trimming kinetics in the cell remains unresolved.
  • No experimental structure of EDEM3 or the EDEM3-ERp46 complex in the corpus
  • Mechanism of IDD-mediated turnover restraint unknown
  • Regulation of EDEM3 by trafficking factors not reconstituted

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016787 hydrolase activity 3 GO:0140098 catalytic activity, acting on RNA 3
Localization
GO:0005783 endoplasmic reticulum 2
Pathway
R-HSA-392499 Metabolism of proteins 2 R-HSA-8953897 Cellular responses to stimuli 1
Partners
COPB2ERP46

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 EDEM3 has alpha1,2-mannosidase activity in vivo, accelerating mannose trimming from misfolded glycoproteins and total glycoproteins. Mutation of the conserved active-site residue E147Q abolishes mannose trimming and greatly reduces ERAD stimulation, demonstrating that mannosidase activity is required for EDEM3's ERAD function. Transfection of HEK293 cells with wild-type and E147Q catalytic mutant EDEM3; degradation assays of misfolded alpha1-antitrypsin NHK and TCRα; mannose trimming assays The Journal of biological chemistry High 16431915
2018 ERp46, an ER-resident oxidoreductase, stably associates with EDEM3 via a disulfide bond between ERp46 redox-active cysteine residues and the EDEM3 alpha-mannosidase domain. This covalent interaction is required for EDEM3 mannose-trimming activity toward misfolded TCRα substrate, as reconstituted in a defined in vitro system with purified recombinant proteins. Co-immunoprecipitation, in vitro reconstitution with purified recombinant proteins from HEK293 cells, disulfide bond analysis, mannose-trimming activity assay The Journal of biological chemistry High 29784879
2021 Purified EDEM3 alone is the major alpha1,2-mannosidase responsible for the second step of N-glycan trimming in gpERAD, converting M8B to M7 (M7A and M7C), M6, and M5 oligosaccharides. EDEM3 also efficiently trims M8B from intact glycoproteins. In vitro mannosidase assay with purified recombinant EDEM3 and pyridylamine-labeled M8B glycan substrates; glycoprotein substrate trimming assays eLife High 34698634
2021 EDEM3 consists of four functional domains: GH47 (mannosidase), intermediate (IMD), protease-associated (PA), and intrinsically disordered (IDD). The GH47 domain mediates substrate binding even without mannose trimming; IMD is required for GH47 folding; PA domain positively modulates ERAD of specific substrates; IDD domain negatively modulates substrate turnover, providing unique ERAD timing. EDEM3 knockout cell line complemented with domain-deletion mutants; ERAD substrate degradation assays for NHK and soluble tyrosinase mutant; LC/MS interactome analysis International journal of molecular sciences Medium 33671632
2021 Loss-of-function EDEM3 variants in humans cause a congenital disorder of glycosylation (EDEM3-CDG) characterized by decreased trimming of Man8GlcNAc2 isomer B to Man7GlcNAc2, and impaired Man5GlcNAc2-to-Man4GlcNAc2 conversion with accumulation of Glc1Man5GlcNAc2, confirming EDEM3's enzymatic role in vivo. Loss of EDEM3 also impairs the unfolded protein response (reduced PERK/EIF2AK3 induction upon ER stress). Exome sequencing; glycan profiling in patient fibroblasts, human plasma, and mouse plasma/brain tissue; tunicamycin-induced UPR assay in human fibroblasts American journal of human genetics Medium 34143952
2022 EDEM3 exhibits in vitro alpha1,2-mannosidase activity toward asparagine-linked (N-linked) oligomannose glycans, converting M9 to M8 and M7, but not toward glycine-linked M9 glycan. ERp46 co-incubation enhances this activity. In vitro mannosidase assay with purified EDEM3 and synthetic asparagine-linked vs. glycine-linked M9 glycan substrates; activity measured with and without ERp46 Biochemical and biophysical research communications Medium 35500441
2017 EDEM3 interacts with ER-resident proteins including components of the ERAD cargo recognition and targeting machinery, as well as UBA1 and UBA2 ubiquitinating enzymes. This interaction network is sensitive to perturbation of early ER N-glycan processing by kifunensine and NB-DNJ. Immunoprecipitation coupled with mass spectrometry; Western blot validation; glycan processing inhibitor treatments Biochemical and biophysical research communications Low 28366632
2020 EDEM3 deficiency increases LRP1 cell-surface expression and VLDL uptake by upregulating surface mannose-containing glycoproteins, thereby reducing plasma triglyceride levels. EDEM3 deletion upregulates RNA and ER protein processing/transport pathways. EDEM3 knockout cell and mouse models; VLDL uptake assays; LRP1 expression analysis; cell-surface glycoprotein profiling; metabolomics iScience Medium 32213464
2025 COPB2 physically interacts with EDEM3 and enhances its ER localization and mannose-trimming activity. COPB2 depletion impairs EDEM3 function, causing glycan processing defects and ER stress accumulation. Co-immunoprecipitation; protein interaction analysis; glycoproteomic analysis; COPB2 knockdown and overexpression in ovarian cancer cells; xenograft models Cellular oncology (Dordrecht, Netherlands) Low 40736660

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 EDEM3, a soluble EDEM homolog, enhances glycoprotein endoplasmic reticulum-associated degradation and mannose trimming. The Journal of biological chemistry 199 16431915
2007 Glycoprotein folding and the role of EDEM1, EDEM2 and EDEM3 in degradation of folding-defective glycoproteins. FEBS letters 112 17499246
2018 ER-resident protein 46 (ERp46) triggers the mannose-trimming activity of ER degradation-enhancing α-mannosidase-like protein 3 (EDEM3). The Journal of biological chemistry 33 29784879
2021 Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation. American journal of human genetics 19 34143952
2021 Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD. eLife 15 34698634
2022 Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer. International journal of molecular sciences 11 35897761
2021 EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning. International journal of molecular sciences 11 33671632
2020 EDEM3 Modulates Plasma Triglyceride Level through Its Regulation of LRP1 Expression. iScience 9 32213464
2022 In vitro mannosidase activity of EDEM3 against asparagine-linked oligomannose-type glycans. Biochemical and biophysical research communications 7 35500441
2025 Disrupting EDEM3-induced M2-like macrophage trafficking by glucose restriction overcomes resistance to PD-1/PD-L1 blockade. Clinical and translational medicine 6 39754316
2017 Inhibition of N-glycan processing modulates the network of EDEM3 interactors. Biochemical and biophysical research communications 6 28366632
2025 COPB2 facilitates EDEM3-mediated mannose trimming to sustain ER homeostasis in ovarian cancer. Cellular oncology (Dordrecht, Netherlands) 0 40736660

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