Affinage

ATG3

Ubiquitin-like-conjugating enzyme ATG3 · UniProt Q9NT62

Length
314 aa
Mass
35.9 kDa
Annotated
2026-06-09
100 papers in source corpus 32 papers cited in narrative 32 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 9/9 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ATG3 is the E2-like conjugating enzyme of the autophagy machinery, catalyzing covalent attachment of Atg8/LC3/GABARAP-family proteins to phosphatidylethanolamine (PE) on growing phagophore membranes (PMID:17227760, PMID:24747438). Its alpha/beta catalytic core is topologically related to canonical E2 enzymes but carries two functionally distinct insertions: a long flexible region that binds the E1 enzyme ATG7, and an alpha-helical element that engages the Atg8 substrate (PMID:17227760). ATG3 receives activated Atg8 from ATG7 in a noncanonical "in trans" reaction within an (Atg7-Atg3)2 architecture, in which Atg8 is transferred from the catalytic cysteine of one Atg7 protomer to the Atg3 bound to the opposite protomer (PMID:22055190, PMID:23142976). Catalysis is not autonomous: the ATG12-ATG5 conjugate acts as an E3 that reorients ATG3's catalytic cysteine toward a noncanonical catalytic threonine to license PE conjugation (PMID:23503366), and the E1- and E3-binding surfaces in ATG3's flexible region overlap, forming an allosteric E123IR switch that cycles ATG3 between ATG7 and the ATG12-ATG5-ATG16L1 complex while relieving an autoinhibitory intramolecular contact on the catalytic loop (PMID:24186333, PMID:26043688, PMID:31399562, PMID:40628661). Membrane selectivity is conferred by an N-terminal amphipathic helix of unusually low hydrophobicity that senses lipid-packing defects at the highly curved phagophore rim, communicating with the C-terminal catalytic core to position the ATG3~LC3 thioester at the membrane surface near PE (PMID:24747438, PMID:33446636, PMID:37679347, PMID:37352354). Substrate Atg8/LC3 positioning is further governed by a noncanonical LIR/AIM motif in the flexible region that binds the LC3 backside and is required for efficient thioester transfer and lipidation (PMID:20615880, PMID:37252361, PMID:40628661). ATG3 lipidation activity supports phagophore localization and isolation-membrane expansion (PMID:25680528, PMID:25645919) and is essential for mitochondrial homeostasis and remodeling during cell reprogramming (PMID:27575019). Beyond conjugating Atg8 proteins, ATG3 is itself modified by ATG12 in an ATG7-dependent, autocatalytic reaction onto a single lysine, generating an ATG12-ATG3 conjugate that acts independently of starvation autophagy in mitochondrial homeostasis and, via interaction with the ESCRT regulator Alix (PDCD6IP), in late-endosome distribution, exosome biogenesis, and viral budding (PMID:20723759, PMID:25686249). ATG3 abundance and activity are tuned post-translationally: acetylation at K19/K48 promotes membrane binding (PMID:28327644), PTK2/FAK phosphorylation at Y203 drives degradation following DNA damage (PMID:28103122), and HDAC6 deacetylates and ubiquitinates ATG3 at K272 to trigger proteasomal turnover (PMID:40739328); caspase-8 cleavage inactivates ATG3-dependent autophagy during receptor-mediated apoptosis (PMID:22644571).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2007 High

    Establishing how ATG3 could function in conjugation required defining its fold; the crystal structure showed it is an E2-like enzyme with dedicated insertions for binding its E1 and its Atg8 substrate.

    Evidence X-ray crystallography of yeast Atg3 with in vitro and in vivo functional analysis

    PMID:17227760

    Open questions at the time
    • Did not resolve how Atg8 is transferred from E1 or how PE is recognized catalytically
    • Static structure did not capture the active conjugating conformation
  2. 2009 High

    It was unclear how ATG3 selects the PE substrate; the N-terminus, including Leu6, was shown to be essential for Atg8-PE conjugation by mediating PE interaction.

    Evidence In vitro lipidation and in vivo yeast assays with N-terminal deletion and point mutagenesis

    PMID:19285500

    Open questions at the time
    • Did not define the structural basis of membrane sensing
    • Did not distinguish PE binding from general membrane association
  3. 2010 High

    Two distinct ATG3 functions were uncovered: ATG3 is itself a target of ATG12 conjugation forming an ATG12-ATG3 conjugate dispensable for starvation autophagy but required for mitochondrial homeostasis, and ATG3 uses a WEDL AIM motif to position Atg8 for transfer to PE.

    Evidence Co-IP, MS, knockout/knockdown cells, cell death and mitochondrial assays; NMR and in vitro/in vivo lipidation with mutagenesis

    PMID:20615880 PMID:20723759

    Open questions at the time
    • The downstream mitochondrial effectors of ATG12-ATG3 were not identified
    • How the AIM contacts Atg8 structurally was not resolved at this stage
  4. 2012 High

    The geometry of Atg8 transfer was unknown; structures of the (Atg7-Atg3)2 complex revealed noncanonical multisite E1-E2 recognition with in-trans transfer between Atg7 protomers, and caspase-8 cleavage was shown to inactivate ATG3-dependent autophagy during apoptosis.

    Evidence X-ray crystallography, SAXS, crosslinking and transfer assays; in vitro caspase cleavage with site mutagenesis and autophagy flux in cells

    PMID:22055190 PMID:22644571 PMID:23142976

    Open questions at the time
    • Did not explain how the catalytic site becomes competent for PE conjugation
    • Physiological contexts coupling apoptosis to ATG3 cleavage were not mapped
  5. 2013 High

    How conjugase activity is switched on was resolved: the ATG12-ATG5 E3 reorients ATG3's catalytic cysteine toward a noncanonical catalytic threonine, and the overlapping E1/E3 binding sites in ATG3's flexible region imply cycling between ATG7 and the E3 complex.

    Evidence Structure-guided mutagenesis and in vitro lipidation; crystallography of ATG12-ATG3; peptide-inhibition and binding-competition assays

    PMID:23503366 PMID:24186333 PMID:24191030

    Open questions at the time
    • Kinetics of the E1-to-E3 handoff in cells were not measured
    • Medium-confidence competition data (idx 8) used peptides rather than full complexes
  6. 2014 High

    The basis for spatial restriction of lipidation to the phagophore was established: an N-terminal amphipathic helix makes ATG3 act preferentially on highly curved, packing-defect-rich membranes.

    Evidence In vitro lipidation on curved membranes, amphipathic helix mutagenesis, and rescue in Atg3-KO cells

    PMID:24747438

    Open questions at the time
    • Did not show how curvature sensing is communicated to the distant catalytic core
    • In vivo membrane curvature at the rim was inferred
  7. 2015 High

    Localization, the human E1/E3 binding overlap, and a second moonlighting role were defined: ATG3 acts at the isolation membrane via its AIM, RIA7 mediates mutually exclusive ATG7/E3 binding in humans, and ATG12-ATG3 controls Alix-dependent endosome/exosome/viral-budding processes.

    Evidence Live-cell imaging with GFP-Atg3 and AIM mutagenesis; NMR mapping of RIA7 with transfer assays; reciprocal Co-IP with Alix and trafficking/exosome/budding assays

    PMID:25645919 PMID:25680528 PMID:25686249 PMID:26043688

    Open questions at the time
    • Mechanism by which ATG12-ATG3 regulates Alix activity was not detailed
    • ATG3-ECM adhesion switching between autophagy and apoptosis (idx 13) lacked a defined apoptotic effector
  8. 2017 High

    Post-translational control of ATG3 membrane binding and abundance was extended: acetylation at K19/K48 promotes PE/ER membrane binding, and PTK2/FAK phosphorylation at Y203 drives ATG3 degradation while ATG3-BAG3 binding promotes DNA-damage-induced mitotic catastrophe independent of autophagy.

    Evidence Semisynthetic diacetylated ATG3 in reconstituted lipidation and liposome binding; MS phosphosite mapping, PTK2 inhibition/siRNA, Y203 mutagenesis in KO MEFs, and Co-IP with BAG3

    PMID:28103122 PMID:28327644

    Open questions at the time
    • Enzymes adding the K19/K48 acetylation in cells were not identified
    • How the BAG3 interaction promotes mitotic catastrophe mechanistically was not resolved
  9. 2019 High

    The unifying activation principle was defined as the E123IR allosteric switch, whose intramolecular contacts autoinhibit the catalytic loop until E1 or E3 binding conformationally activates ATG3.

    Evidence NMR, X-ray crystallography, in vitro lipidation, and in vivo yeast genetics

    PMID:31399562

    Open questions at the time
    • Did not quantify how the switch couples temporally to membrane engagement
    • Conservation of the precise switch contacts across the human enzyme was inferred
  10. 2021 High

    The link from curvature sensing to catalysis and a non-autophagic metabolic role were resolved: an N-terminal conserved region relays membrane information from the amphipathic helix to the catalytic core, while hepatic ATG3 knockdown ameliorates steatosis via JNK1-SIRT1-CPT1a independent of canonical autophagy.

    Evidence NMR in solution and bicelles, in vitro lipidation, KO-cell rescue with mutagenesis; in vivo mouse and hepatocyte knockdown/overexpression with SIRT1/CPT1a epistasis

    PMID:33446636 PMID:34296398 PMID:34555423

    Open questions at the time
    • Direct molecular link between ATG3 and JNK1 regulation was not established
    • Membrane-bound conformation was structurally characterized only in bicelles
  11. 2023 High

    High-resolution mechanism of membrane-coupled catalysis emerged: the dynamic C-terminal catalytic regions cooperate with the low-hydrophobicity amphipathic helix to dock the ATG3~LC3 thioester at the membrane near PE, and a noncanonical beta-strand LIR binds the LC3 backside to drive thioester formation and lipidation.

    Evidence NMR, MD simulations, live-cell imaging, helix and LIR mutagenesis, lipidation/thioester assays; crystallography of ATG3-LIR/LC3 with CRISPR mutagenesis

    PMID:37252361 PMID:37352354 PMID:37679347

    Open questions at the time
    • The exact catalytic chemistry of PE attack was not fully defined
    • Coordination between LIR backside binding and the active site during transfer was inferred
  12. 2025 High

    Substrate backside binding and degradative control were refined: GABARAP binds the ATG3 E2-domain backside in a noncanonical mode overlapping the LIR site and is required for PE conjugation, while HDAC6 deacetylates and ubiquitinates ATG3 at K272 to drive proteasomal turnover.

    Evidence Crystallography, NMR, mutagenesis, AlphaFold modeling, PE conjugation assay; Co-IP, deacetylation/ubiquitination assays, K272 mutagenesis, autophagy flux

    PMID:40628661 PMID:40739328

    Open questions at the time
    • How backside GABARAP binding is coordinated with thioester transfer in time was not resolved
    • Cellular signals directing HDAC6 to ATG3 were not defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • A complete, time-resolved description of how the membrane-docked ATG12-ATG5-ATG16L1/ATG3 complex coordinates curvature sensing, allosteric activation, substrate backside binding, and the chemical step of LC3-PE bond formation in living phagophores remains to be assembled.
  • No experimentally confirmed identity of the catalytic residue(s) attacking PE; histidine roles are simulation-inferred (idx 26)
  • How the multiple regulatory PTMs are integrated in vivo is unknown
  • Structural intermediates of the full membrane-bound conjugation reaction are unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0008289 lipid binding 4 GO:0016740 transferase activity 4 GO:0031386 protein tag activity 1
Localization
GO:0005829 cytosol 2 GO:0005783 endoplasmic reticulum 1
Pathway
R-HSA-9612973 Autophagy 5 R-HSA-392499 Metabolism of proteins 4 R-HSA-5357801 Programmed Cell Death 2 R-HSA-5653656 Vesicle-mediated transport 1
Partners
ATG12ATG5ATG7ATG8BAG3GABARAPLC3PDCD6IP
Complex memberships
ATG12-ATG3 conjugateATG12-ATG5-ATG16L1 conjugation complexATG7-ATG3 (E1-E2) complex

Evidence

Reading pass · 32 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 Crystal structure of yeast Atg3 at 2.5 Å resolution revealed an alpha/beta-fold with a core region topologically similar to canonical E2 enzymes, two unique inserted regions (one ~80-residue random coil responsible for Atg7 binding, one long alpha-helical structure responsible for Atg8 binding), and a sulfate ion near the catalytic cysteine suggesting a binding site for the phosphate moiety of PE. X-ray crystallography (2.5 Å); in vivo and in vitro functional analyses The Journal of biological chemistry High 17227760
2009 The N-terminal region of yeast Atg3 (first 7 residues, including Leu6) is essential for Atg8-PE conjugation by mediating interaction with the substrate phosphatidylethanolamine; truncation or Leu6-to-Asp mutation severely impairs lipidation both in vivo and in vitro. In vitro lipidation assay; in vivo yeast autophagy assay; N-terminal deletion and point mutagenesis FEBS letters High 19285500
2010 ATG3 is identified as a substrate for ATG12 conjugation; ATG12-ATG3 complex formation requires ATG7 as E1 enzyme and ATG3 autocatalytic activity as E2, resulting in covalent linkage of ATG12 onto a single lysine on ATG3. The ATG12-ATG3 conjugate is not required for starvation-induced autophagy but is required for mitochondrial homeostasis and mitochondria-mediated cell death. Co-immunoprecipitation; mass spectrometry; ATG3 and ATG7 knockout/knockdown cell lines; cell death assays; mitochondrial mass measurement Cell High 20723759
2010 Atg3 directly interacts with Atg8 through a WEDL sequence (AIM motif) that resembles the Atg8-family interacting motif (AIM) found in autophagic receptors. This AIM is essential for transfer of Atg8 from the Atg8~Atg3 thioester to PE (but not for thioester intermediate formation), and is required for the Cvt pathway but not for starvation-induced autophagy. NMR; in vitro lipidation assay; in vivo yeast Cvt/autophagy assays; mutagenesis The Journal of biological chemistry High 20615880
2011 Atg7's unique N-terminal domain (Atg7NTD) recruits a 'flexible region' (FR) of Atg3 via hydrophobic contacts. Structure of the Atg7NTD-Atg3FR complex shows Atg8 is transferred in trans: from the catalytic cysteine of one Atg7 protomer to Atg3 bound to the N-terminal domain of the opposite Atg7 protomer within the homodimer. X-ray crystallography; SAXS; crosslinking; biochemical transfer assays; mutagenesis Molecular cell High 22055190
2012 Caspase-8 cleaves Atg3 during receptor-mediated (TNF-α and TRAIL) cell death; mutation of the caspase-8 cleavage site on Atg3 abolished cleavage in vitro and in vivo, and overexpression of non-cleavable Atg3 reestablished autophagic activity during apoptosis, demonstrating that Atg3 cleavage by caspase-8 inactivates autophagy. In vitro caspase cleavage assay; site-directed mutagenesis; cell death assays; autophagy flux measurement Apoptosis High 22644571
2012 Crystallographic and mutational analyses of yeast (Atg7-Atg3)2 complex reveal noncanonical multisite E1-E2 recognition: Atg7's unique N-terminal domain recruits distinctive elements from the Atg3 'backside', and E1/E2 conformational variability allows presentation of the Atg3 active site to the catalytic cysteine of the opposite Atg7 protomer. X-ray crystallography of (Atg7-Atg3)2 complex; mutagenesis; biochemical assays Nature structural & molecular biology High 23142976
2013 The Atg12-Atg5 conjugate functions as an E3 enzyme by rearranging Atg3's catalytic site: Atg3 uses a threonine (rather than canonical asparagine) for catalysis, and its catalytic cysteine is normally suppressed by orientation; Atg12-Atg5 induces reorientation of the cysteine toward the threonine, enhancing Atg3 conjugase activity. Biochemical assays; structural information-guided mutagenesis; in vitro lipidation assays Nature structural & molecular biology High 23503366
2013 The E3-binding site on human Atg3 overlaps with the E1 (Atg7)-binding site in its flexible region; E3 (Atg12~Atg5-Atg16) competes with Atg7 for binding to Atg3, implying Atg3 cycles between E1 and E3 binding during LC3 lipidation. Short peptides from this region inhibit LC3 lipidation in vitro. Bioinformatic mapping; peptide inhibition of in vitro lipidation; binding competition assays Protein science Medium 24186333
2013 Crystal structure of the ATG12-ATG3 interaction reveals that 13 residues of ATG3's flexible region form a short beta-strand and alpha-helix on an exclusive surface area of ATG12; four critical ATG3 residues contact ATG12 and are required for E3 interaction and LC3 lipidation. The ATG3-binding surface on ATG12 contains a hydrophobic pocket corresponding to the LC3-LIR binding pocket. X-ray crystallography; mutational analysis; LC3 lipidation assay Proceedings of the National Academy of Sciences of the United States of America High 24191030
2014 The E2-like enzyme Atg3 facilitates LC3/GABARAP lipidation only on membranes exhibiting local lipid-packing defects (high curvature). This requires an N-terminal amphipathic helix; tuning its hydrophobicity promotes or inhibits lipidation in vitro and in Atg3-knockout cell rescue experiments, implying Atg3 is designed to work at the highly curved rim of the growing phagophore. In vitro lipidation assays on curved membranes; amphipathic helix mutagenesis; rescue experiments in Atg3-KO cells Nature cell biology High 24747438
2015 ATG12-ATG3 conjugate interacts with the ESCRT-associated protein Alix (PDCD6IP); this interaction controls multiple Alix-dependent processes including late endosome distribution, exosome biogenesis, and viral budding. ATG12-ATG3 also promotes basal but not starvation-induced autophagic flux. Co-immunoprecipitation; genetic KO/KD of ATG12-ATG3; late endosome trafficking assays; exosome quantification; viral budding assay Nature cell biology High 25686249
2015 Atg3 localizes to the pre-autophagosomal structure (PAS) and isolation membrane (IM) in yeast. Mutations in the AIM motif of Atg3 impair PAS/IM localization and result in inefficient isolation membrane expansion, suggesting AIM-mediated membrane localization facilitates active Atg8-PE production on autophagic membranes. Live-cell fluorescence microscopy with GFP-Atg3; AIM mutagenesis; quantitative autophagy assays FEBS letters Medium 25680528
2015 ATG3 upregulation contributes to detachment-induced autophagy in nonmalignant intestinal epithelial cells, but when overexpressed in attached cells (where other autophagy-promoting events are absent), ATG3 triggers autophagy-independent apoptosis; cell-ECM adhesion context switches ATG3 function between autophagy and apoptosis promotion. siRNA knockdown; lentiviral overexpression; autophagy flux assays; apoptosis assays; cell detachment model Autophagy Medium 26061804
2015 In yeast, GFP-Atg3 forms a transient dot on the vacuolar membrane during autophagy that colocalizes with Atg8, and is localized to the isolation membrane by fine-localization analysis, establishing the isolation membrane as the site of Atg8 lipidation by Atg3. Live-cell fluorescence microscopy; functional GFP-Atg3 insertion; colocalization with Atg8 The Journal of biological chemistry Medium 25645919
2015 NMR data precisely define the region in the flexible region of human ATG3 that interacts with ATG7 (RIA7); this region partially overlaps with the E3-interacting region, providing the mechanistic basis for mutually exclusive E1-E2 and E2-E3 binding in the human system. Mutagenesis of RIA7 residues impairs GABARAP transfer. NMR; mutagenesis; GABARAP transfer assays Biochemical and biophysical research communications Medium 26043688
2017 Acetylation of Atg3 at K19 and K48 promotes its binding to phosphatidylethanolamine-containing liposomes and to the ER membrane, thereby promoting Atg8 lipidation; demonstrated using semisynthetically produced homogeneous K19/K48-diacetylated Atg3 in vitro reconstitution experiments. Semisynthesis via native chemical ligation; in vitro lipidation reconstitution; liposome-binding assay; ER membrane binding assay Nature communications High 28327644
2017 PTK2 (FAK) phosphorylates ATG3 at tyrosine 203 in response to DNA-damaging agents (etoposide, cisplatin), leading to ATG3 degradation. ATG3 has an autophagy-independent function: it promotes DNA damage-induced mitotic catastrophe by binding to BAG3 (a crucial protein in mitosis). PTK2 inhibition sustains ATG3 levels and sensitizes cancer cells to DNA-damaging agents. Mass spectrometry identification of pY203; phospho-specific antibody; PTK2 inhibitor and siRNA; ATG3 Y203E/Y203F mutagenesis in KO MEFs; Co-immunoprecipitation with BAG3 Autophagy High 28103122
2018 The translation initiation factor eIF5A is required for efficient translation of ATG3; a specific amino acid motif in ATG3 confers eIF5A-dependency. Loss of eIF5A reduces ATG3 protein levels, impairs LC3B and paralog lipidation, and blocks autophagosome formation. This is evolutionarily conserved. High-throughput screen; eIF5A knockdown; LC3 lipidation assay; autophagosome quantification; motif mutagenesis; conservation analysis EMBO reports Medium 29712776
2019 An element in Atg3 termed E123IR (E1, E2, and E3-interacting region) functions as an allosteric switch: in the absence of enzymatic partners, E123IR makes intramolecular contacts that restrain Atg3's catalytic loop; E1 (Atg7) and E3 (Atg12-Atg5-Atg16) enzymes directly bind this region to conformationally activate Atg3 and promote Atg8 lipidation in vitro and in vivo. NMR; X-ray crystallography; biochemical lipidation assays; genetic analysis in yeast Nature communications High 31399562
2021 NMR studies of human Atg3 in bicelles reveal structural rearrangement of the hAtg3 N-terminus upon membrane interaction, establishing that the N-terminal region adopts a different conformation when membrane-bound versus in solution. NMR in aqueous solution and in bicelles Biomolecular NMR assignments Medium 34296398
2021 An N-terminal conserved region of human ATG3 communicates information from the N-terminal amphipathic helix (membrane curvature sensor) to the C-terminal catalytic core; mutations in this communication region abolish LC3-PE conjugation in vitro and in vivo and alter membrane-bound conformation as shown by NMR. NMR; in vitro lipidation assay; in vivo rescue in ATG3-KO cells; mutagenesis Nature communications High 33446636
2021 Genetic knockdown of ATG3 in mice and human hepatocytes ameliorates steatosis and improves fatty acid metabolism by reducing JNK1, thereby increasing SIRT1 and CPT1a expression and mitochondrial function; these effects are independent of canonical autophagy activity. In vivo mouse hepatic ATG3 knockdown; primary hepatocyte and cell line knockdown/overexpression; proteomic analysis; SIRT1/CPT1a epistasis knockdown Journal of hepatology Medium 34555423
2023 The C-terminal catalytic regions of human ATG3 are conformationally dynamic and directly interact with membranes in collaboration with the N-terminal curvature-sensitive helix, targeting ATG3's catalytic center to the membrane surface and bringing LC3 and PE substrates into proximity for conjugation. NMR; in vitro conjugation assays; in vivo cellular assays; membrane interaction studies Nature communications High 37679347
2023 The ATG3 amphipathic helix (AHATG3) has low hydrophobicity and contains less bulky residues compared to canonical amphipathic helices; molecular dynamics simulations show AHATG3 regulates dynamics and accessibility of the ATG3~LC3 thioester bond to lipids, enabling covalent LC3 lipidation. Live-cell imaging confirms transient membrane association of ATG3 governed by these unique AHATG3 features. Molecular dynamics simulations; live-cell imaging; amphipathic helix mutagenesis; LC3 lipidation assay Science advances High 37352354
2023 A noncanonical LIR motif in the flexible region of human ATG3 adopts an uncommon beta-sheet structure binding to the backside of LC3; this LIRATG3 is required for LC3 lipidation and ATG3~LC3 thioester formation as shown by CRISPR-enabled in cellulo studies. Disrupting LIRATG3 negatively impacts the rate of thioester transfer from ATG7 to ATG3. Activity-based probes; X-ray crystallography of ATG3-LIR peptide/LC3 complex; protein modeling; CRISPR mutagenesis in cells; LC3 lipidation and thioester assays ACS central science High 37252361
2024 LC3 lipidation occurs via three-step docking of the ATG12-ATG5-ATG16L1/ATG3 complex to the membrane: (i) WIPI2-mediated, (ii) ATG16L1 helix α2-mediated, and (iii) a membrane-interacting surface on ATG3. PE lipids concentrate around the ATG3-LC3 thioester bond, and two conserved histidines near the thioester may participate in catalytic transfer of LC3 to PE. Molecular dynamics simulations; in vitro lipidation experiments; in cellulo assays Science advances Medium 38324698
2025 HDAC6 interacts with ATG3, deacetylates it, and also ubiquitinates ATG3 at lysine 272 via its E3 ligase activity, leading to ATG3 proteasomal degradation. Lysine 272 is targeted by both deacetylation and ubiquitination by HDAC6, and HDAC6-mediated ATG3 degradation regulates autophagic flux. Co-immunoprecipitation; deacetylation assay; ubiquitination assay; K272 mutagenesis; autophagy flux measurement Cell death and differentiation Medium 40739328
2025 GABARAP binds noncovalently to the backside of ATG3's catalytic E2 domain through a binding mode distinct from canonical Ub/Ubl-E2 backside interactions; the GABARAP backside-binding surface overlaps the LIR motif-binding site. NMR confirms this interaction, and mutagenesis of the interface impairs PE conjugation. Additionally, NMR reveals an intramolecular contact between a segment of ATG3's flexible region and its catalytic core that suppresses conjugation in the apo state. X-ray crystallography; solution NMR; targeted mutagenesis; PE conjugation assay; AlphaFold modeling Biochemistry High 40628661
2011 In Toxoplasma gondii, TgAtg3 is essential for TgAtg8 conjugation to autophagosomal membranes; conditional depletion of TgAtg3 impairs TgAtg8 lipidation, causes pronounced mitochondrial fragmentation, and produces severe growth defects, establishing ATG3-dependent autophagy as regulating mitochondrial homeostasis in T. gondii cell division. Conditional TgAtg3 knockout; TgAtg8 lipidation assay; fluorescence microscopy of mitochondria; growth assays PLoS pathogens Medium 22144900
2016 ATG3-dependent autophagy is required for mitochondrial remodeling during somatic cell reprogramming to iPSCs and for mitochondrial homeostasis in mouse ESCs; Atg3-null ESCs accumulate aberrant mitochondria with enhanced ROS and defective ATP, and these defects are rescued by wild-type but not lipidation-deficient Atg3. Atg3 knockout mouse ESCs; iPSC reprogramming assays; mitochondrial ROS and ATP measurements; rescue with WT vs. lipidation-deficient Atg3 Autophagy High 27575019
2014 Atg3 expression is required for IRG and Gbp proteins to dock to pathogen-containing vacuoles (PVs) of Chlamydia and Toxoplasma; a dominant-active GTP-locked IRG protein variant rescues the PV-targeting defect in Atg3-deficient cells. IFN-induced cell-autonomous resistance to C. trachomatis requires Atg3 (alongside Atg5, IRG proteins, and Gbp proteins). Atg3-deficient mouse cells; IRG/Gbp localization by fluorescence microscopy; genetic epistasis with dominant-active IRG; infection resistance assays PloS one Medium 24466199

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 ATG12-ATG3 interacts with Alix to promote basal autophagic flux and late endosome function. Nature cell biology 259 25686249
2010 ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death. Cell 241 20723759
2014 Lipidation of the LC3/GABARAP family of autophagy proteins relies on a membrane-curvature-sensing domain in Atg3. Nature cell biology 218 24747438
2013 Uba1 functions in Atg7- and Atg3-independent autophagy. Nature cell biology 156 23873149
2015 Cytoplastic Glyceraldehyde-3-Phosphate Dehydrogenases Interact with ATG3 to Negatively Regulate Autophagy and Immunity in Nicotiana benthamiana. The Plant cell 154 25829441
2011 Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the autophagy pathway. Molecular cell 146 22055190
2012 Cleavage of Atg3 protein by caspase-8 regulates autophagy during receptor-activated cell death. Apoptosis : an international journal on programmed cell death 138 22644571
2016 The long noncoding RNA HOTAIR activates autophagy by upregulating ATG3 and ATG7 in hepatocellular carcinoma. Molecular bioSystems 136 27301338
2013 Atg12-Atg5 conjugate enhances E2 activity of Atg3 by rearranging its catalytic site. Nature structural & molecular biology 129 23503366
2007 The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation. The Journal of biological chemistry 122 17227760
2018 Mycobacterium tuberculosis-induced miR-155 subverts autophagy by targeting ATG3 in human dendritic cells. PLoS pathogens 110 29300789
2019 LncRNA NEAT1 promotes autophagy via regulating miR-204/ATG3 and enhanced cell resistance to sorafenib in hepatocellular carcinoma. Journal of cellular physiology 101 31549407
2011 Autophagy protein Atg3 is essential for maintaining mitochondrial integrity and for normal intracellular development of Toxoplasma gondii tachyzoites. PLoS pathogens 94 22144900
2012 Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Nature structural & molecular biology 93 23142976
2017 Upregulation of the lncRNA Meg3 induces autophagy to inhibit tumorigenesis and progression of epithelial ovarian carcinoma by regulating activity of ATG3. Oncotarget 90 28423647
2010 Autophagy-related protein 8 (Atg8) family interacting motif in Atg3 mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-to-vacuole targeting pathway. The Journal of biological chemistry 90 20615880
2013 Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12. Proceedings of the National Academy of Sciences of the United States of America 89 24191030
2016 ATG3-dependent autophagy mediates mitochondrial homeostasis in pluripotency acquirement and maintenance. Autophagy 85 27575019
2018 eIF5A is required for autophagy by mediating ATG3 translation. EMBO reports 81 29712776
2018 Effect of the LncRNA GAS5-MiR-23a-ATG3 Axis in Regulating Autophagy in Patients with Breast Cancer. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 80 30007957
2014 The E2-like conjugation enzyme Atg3 promotes binding of IRG and Gbp proteins to Chlamydia- and Toxoplasma-containing vacuoles and host resistance. PloS one 77 24466199
2019 Long non-coding RNA PVT1 promotes autophagy as ceRNA to target ATG3 by sponging microRNA-365 in hepatocellular carcinoma. Gene 72 30794914
2022 A novel long noncoding RNA SP100-AS1 induces radioresistance of colorectal cancer via sponging miR-622 and stabilizing ATG3. Cell death and differentiation 66 35978049
2019 Long Noncoding RNA KCNQ1OT1 Promotes the Progression of Non-Small Cell Lung Cancer via Regulating miR-204-5p/ATG3 Axis. OncoTargets and therapy 57 31849486
2018 RETRACTED: Long noncoding RNA RMRP upregulation aggravates myocardial ischemia-reperfusion injury by sponging miR-206 to target ATG3 expression. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 56 30551524
2009 The amino-terminal region of Atg3 is essential for association with phosphatidylethanolamine in Atg8 lipidation. FEBS letters 51 19285500
2021 Binding Features and Functions of ATG3. Frontiers in cell and developmental biology 47 34235149
2015 ATG12-ATG3 connects basal autophagy and late endosome function. Autophagy 46 25998418
2006 Atg8L/Apg8L is the fourth mammalian modifier of mammalian Atg8 conjugation mediated by human Atg4B, Atg7 and Atg3. The FEBS journal 46 16704426
2012 Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction. Journal of structural biology 44 22982544
2014 Identification of an Atg8-Atg3 protein-protein interaction inhibitor from the medicines for Malaria Venture Malaria Box active in blood and liver stage Plasmodium falciparum parasites. Journal of medicinal chemistry 40 24786226
2019 A switch element in the autophagy E2 Atg3 mediates allosteric regulation across the lipidation cascade. Nature communications 38 31399562
2012 Combination erlotinib-cisplatin and Atg3-mediated autophagy in erlotinib resistant lung cancer. PloS one 38 23119048
2021 Inhibition of ATG3 ameliorates liver steatosis by increasing mitochondrial function. Journal of hepatology 37 34555423
2019 ATG3, a Target of miR-431-5p, Promotes Proliferation and Invasion of Colon Cancer via Promoting Autophagy. Cancer management and research 37 31849517
2017 A semisynthetic Atg3 reveals that acetylation promotes Atg3 membrane binding and Atg8 lipidation. Nature communications 37 28327644
2014 Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast. Autophagy 37 24879155
2017 Human ATG3 binding to lipid bilayers: role of lipid geometry, and electric charge. Scientific reports 36 29142222
2023 Multifaceted membrane interactions of human Atg3 promote LC3-phosphatidylethanolamine conjugation during autophagy. Nature communications 35 37679347
2015 Localization of Atg3 to autophagy-related membranes and its enhancement by the Atg8-family interacting motif to promote expansion of the membranes. FEBS letters 34 25680528
2013 Structures of Atg7-Atg3 and Atg7-Atg10 reveal noncanonical mechanisms of E2 recruitment by the autophagy E1. Autophagy 34 23388412
2018 Knockdown of Long Non-Coding RNA GAS5 Increases miR-23a by Targeting ATG3 Involved in Autophagy and Cell Viability. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 32 30078013
2021 An N-terminal conserved region in human Atg3 couples membrane curvature sensitivity to conjugase activity during autophagy. Nature communications 30 33446636
2024 Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore. Science advances 28 38324698
2011 Vaccinia virus leads to ATG12–ATG3 conjugation and deficiency in autophagosome formation. Autophagy 28 22024753
2015 Visualization of Atg3 during autophagosome formation in Saccharomyces cerevisiae. The Journal of biological chemistry 25 25645919
2015 Upregulation of ATG3 contributes to autophagy induced by the detachment of intestinal epithelial cells from the extracellular matrix, but promotes autophagy-independent apoptosis of the attached cells. Autophagy 25 26061804
2011 Atg3-mediated lipidation of Atg8 is involved in encystation of Acanthamoeba. The Korean journal of parasitology 25 21738264
2021 Platinum complexes inhibit HER-2 enriched and triple-negative breast cancer cells metabolism to suppress growth, stemness and migration by targeting PKM/LDHA and CCND1/BCL2/ATG3 signaling pathways. European journal of medicinal chemistry 24 34293698
2021 VDR/Atg3 Axis Regulates Slit Diaphragm to Tight Junction Transition via p62-Mediated Autophagy Pathway in Diabetic Nephropathy. Diabetes 23 34376476
2021 Cancer-Derived Exosomal miR-651 as a Diagnostic Marker Restrains Cisplatin Resistance and Directly Targets ATG3 for Cervical Cancer. Disease markers 23 34567283
2023 Unique amphipathic α helix drives membrane insertion and enzymatic activity of ATG3. Science advances 22 37352354
2016 MicroRNA-495 regulates starvation-induced autophagy by targeting ATG3. FEBS letters 21 26910393
2014 Depletion of autophagy-related genes ATG3 and ATG5 in Tenebrio molitor leads to decreased survivability against an intracellular pathogen, Listeria monocytogenes. Archives of insect biochemistry and physiology 21 25403020
2021 Propofol protects cardiomyocytes from hypoxia/reoxygenation injury via regulating MALAT1/miR-206/ATG3 axis. Journal of biochemical and molecular toxicology 20 34383354
2020 Let-7c-3p Regulates Autophagy under Oxidative Stress by Targeting ATG3 in Lens Epithelial Cells. BioMed research international 20 32258130
2016 Atg3 Overexpression Enhances Bortezomib-Induced Cell Death in SKM-1 Cell. PloS one 20 27391105
2013 Binding to E1 and E3 is mutually exclusive for the human autophagy E2 Atg3. Protein science : a publication of the Protein Society 19 24186333
2017 PTK2-mediated degradation of ATG3 impedes cancer cells susceptible to DNA damage treatment. Autophagy 18 28103122
2016 Virtual Screening and Experimental Validation Identify Novel Inhibitors of the Plasmodium falciparum Atg8-Atg3 Protein-Protein Interaction. ChemMedChem 18 26748931
2018 Atg12-Atg3 Coordinates Basal Autophagy, Endolysosomal Trafficking, and Exosome Release. Molecular & cellular oncology 17 30263931
2018 Salinomycin-induced autophagy blocks apoptosis via the ATG3/AKT/mTOR signaling axis in PC-3 cells. Life sciences 15 29966607
2023 Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3. ACS central science 14 37252361
2021 ATG3 Is Important for the Chorion Ultrastructure During Oogenesis in the Insect Vector Rhodnius prolixus. Frontiers in physiology 14 33613326
2019 Autophagy Related Gene (ATG3) is a Key Regulator for Cell Growth, Development, and Virulence of Fusarium oxysporum. Genes 14 31466418
2021 Autophagy Inhibition by ATG3 Knockdown Remits Oxygen-Glucose Deprivation/Reoxygenation-Induced Injury and Inflammation in Brain Microvascular Endothelial Cells. Neurochemical research 13 34379294
2019 Allosteric regulation through a switch element in the autophagy E2, Atg3. Autophagy 13 31690182
2018 Characterization of Plasmodium Atg3-Atg8 Interaction Inhibitors Identifies Novel Alternative Mechanisms of Action in Toxoplasma gondii. Antimicrobial agents and chemotherapy 13 29158278
2023 Identifying a selective inhibitor of autophagy that targets ATG12-ATG3 protein-protein interaction. Autophagy 12 37184247
2021 Multiple structural rearrangements mediated by high-plasticity regions in Atg3 are key for efficient conjugation of Atg8 to PE during autophagy. Autophagy 11 34338142
2025 Betaine inhibits the stem cell-like properties of hepatocellular carcinoma by activating autophagy via SAM/m6A/YTHDF1-mediated enhancement on ATG3 stability. Theranostics 10 39897540
2021 Knockdown of long non-coding RNA RMRP protects cerebral ischemia-reperfusion injury via the microRNA-613/ATG3 axis and the JAK2/STAT3 pathway. The Kaohsiung journal of medical sciences 10 33560543
2021 Metabolic Rewiring Is Essential for AML Cell Survival to Overcome Autophagy Inhibition by Loss of ATG3. Cancers 10 34885250
2018 Structure-based drug design, synthesis and biological assays of P. falciparum Atg3-Atg8 protein-protein interaction inhibitors. Journal of computer-aided molecular design 10 29383466
2018 EIF5A mediates autophagy via translation of ATG3. Autophagy 10 29973124
2018 Characterization of the molecular mechanism of the autophagy-related Atg8-Atg3 protein interaction in Toxoplasma gondii. The Journal of biological chemistry 9 30026233
2015 Identification and characterization of the linear region of ATG3 that interacts with ATG7 in higher eukaryotes. Biochemical and biophysical research communications 9 26043688
2023 Redox-mediated activation of ATG3 promotes ATG8 lipidation and autophagy progression in Chlamydomonas reinhardtii. Plant physiology 8 37772945
2021 Long non-coding RNA ANRIL mitigates neonatal hypoxic-ischemic brain damage via targeting the miR-378b/ATG3 axis. American journal of translational research 8 34786084
2018 ERK-mediated autophagy promotes inactivated Sendai virus (HVJ-E)-induced apoptosis in HeLa cells in an Atg3-dependent manner. Cancer cell international 8 30534001
2014 Lentiviral vector-mediate ATG3 overexpression inhibits growth and promotes apoptosis of human SKM-1 cells. Molecular biology reports 8 24420857
2024 Curcumin enhances ATG3-dependent autophagy and inhibits metastasis in cervical carcinoma. Cell division 7 39609925
2022 Silencing the Autophagy-Related Genes ATG3 and ATG9 Promotes SRBSDV Propagation and Transmission in Sogatella furcifera. Insects 7 35447836
2021 miR-651-3p Enhances the Sensitivity of Hepatocellular Carcinoma to Cisplatin via Targeting ATG3-Mediated Cell Autophagy. Journal of oncology 7 34457004
2019 The combination of lonafarnib and sorafenib induces cyclin D1 degradation via ATG3-mediated autophagic flux in hepatocellular carcinoma cells. Aging 7 31409760
2006 Crystallization and preliminary X-ray analysis of Atg3. Acta crystallographica. Section F, Structural biology and crystallization communications 5 17012800
2021 Identification of novel Atg3-Atg8 inhibitors using virtual screening for autophagy modulation. Bioorganic chemistry 4 34147881
2025 Role of Atg3, Atg5 and Atg12 in the crosstalk between apoptosis and autophagy in the posterior silk gland of Bombyx mori. Insect molecular biology 3 39910402
2024 Menthol induces extracellular vesicle regulation of apoptosis via ATG3 and caspase-3 in acute leukemic cells. Heliyon 3 39021955
2023 Japanese Flounder pol-miR-155 Is Involved in Edwardsiella tarda Infection via ATG3. Genes 3 37239318
2012 Role of ATG3 in the parasite Toxoplasma gondii: autophagy in an early branching eukaryote. Autophagy 3 22361579
2025 Histone deacetylase 6 deacetylates and ubiquitinates ATG3 to regulate autophagy. Cell death and differentiation 2 40739328
2025 Targeting the ATG12-ATG3 protein-protein interaction: From structural insights to therapeutic opportunities in autophagy modulation. Pathology, research and practice 2 40763565
2025 Draper-ATG3 Interaction Positively Regulates Autophagy to Mediate Silk Gland Degradation in Bombyx mori. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2 40953285
2024 Structure-activity relationship study of small-molecule inhibitor of Atg12-Atg3 protein-protein interaction. Bioorganic & medicinal chemistry letters 2 39218407
2025 ATG-3 limits Orsay virus infection in C. elegans through regulation of collagen pathways. bioRxiv : the preprint server for biology 1 39868230
2025 ATG-3 limits Orsay virus infection in C. elegans and regulates collagen pathways. PLoS pathogens 1 41252446
2021 NMR resonance assignments of human Atg3 in aqueous solution and bicelles. Biomolecular NMR assignments 1 34296398
2025 Structural Insights into the GABARAP-ATG3 Backside Interaction and Apo ATG3 Conformation. Biochemistry 0 40628661
2023 ATG3 proteins possess a unique amphipathic α-helix essential for the Atg8/LC3 lipidation reaction. Autophagy 0 37679935

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