Affinage

UFM1

Ubiquitin-fold modifier 1 · UniProt P61960

Length
85 aa
Mass
9.1 kDa
Annotated
2026-06-10
77 papers in source corpus 42 papers cited in narrative 41 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 8/8 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

UFM1 is a ubiquitin-fold modifier that is covalently conjugated to target proteins through a dedicated three-enzyme cascade analogous to ubiquitylation, coupling protein quality control at the endoplasmic reticulum to cellular proteostasis (PMID:15071506). Newly synthesized UFM1 is matured by the cysteine proteases UFSP1 and UFSP2, which cleave its C-terminal extension to expose the conjugation-essential Gly; these same proteases also reverse the modification by releasing UFM1 from substrates (PMID:17182609, PMID:35926457). The exposed Gly is activated by the non-canonical homodimeric E1 enzyme UBA5 through an ATP-dependent thioester mechanism in which UFM1 binds in trans across the dimer interface and stabilizes the dimer to promote ATP loading, then is transthiolated to the E2 enzyme UFC1 (PMID:15071506, PMID:27653677, PMID:29295865). Conjugation to substrates is catalyzed by a trimeric E3 ligase complex of UFL1, UFBP1 (DDRGK1) and CDK5RAP3, which assembles at the ER membrane (PMID:20018847, PMID:21494687). The best-characterized substrate is the 60S ribosomal protein RPL26 (uL24): the E3 complex engages stalled and split 60S subunits as a C-shaped clamp, inserting loops of UFL1 to remodel the peptidyl transferase center, catalyzing UFMylation of uL24 across a large distance, and then remaining bound to ufmylated 60S to release the SEC61 translocon and recycle the subunit—thereby integrating ER-associated ribosome quality control with ER-phagy (PMID:37595036, PMID:38383789, PMID:38383785). Beyond ribosome quality control, UFMylation modifies additional ER and signaling substrates including CYB5R3, where modification drives ER-phagy (PMID:36543799), and the transcriptional regulators ASC1 and ERα, linking ufmylation to estrogen-receptor target-gene activation and hematopoietic transcription (PMID:25219498, PMID:35680375, PMID:26544067). The pathway is transcriptionally induced as part of the ER stress response downstream of Xbp-1, and its disruption activates the unfolded protein response, impairs erythroid and hematopoietic development, and causes neuronal loss (PMID:23152784, PMID:21304510, PMID:25952549, PMID:35931931). Biallelic mutations in UFM1, UBA5, and UFC1 that impair thioester intermediate formation cause severe early-onset encephalopathy with progressive microcephaly, establishing ufmylation as essential for human brain development (PMID:27545674, PMID:27545681, PMID:29868776).

Mechanistic history

Synthesis pass · year-by-year structured walk · 17 steps
  1. 2004 High

    Established UFM1 as a bona fide ubiquitin-like modifier by demonstrating it operates through a three-enzyme conjugation cascade, answering whether this ubiquitin-fold protein is a functional modifier.

    Evidence In vitro reconstitution of thioester intermediates with UBA5/UFC1 and Gly mutagenesis

    PMID:15071506

    Open questions at the time
    • No physiological substrates or E3 ligase identified
    • Cellular processes regulated by UFMylation unknown
  2. 2006 High

    Identified the deconjugating/maturing machinery, showing UFSP1 and UFSP2 both expose the conjugation Gly on pro-UFM1 and reverse the modification, establishing ufmylation as a reversible cycle.

    Evidence Cleavage assays with recombinant proteins, Cys→Ser active-site mutagenesis, and activity-based probe labeling

    PMID:17182609

    Open questions at the time
    • Distinct roles of UFSP1 vs UFSP2 not resolved
    • Substrate specificity of deconjugation undefined
  3. 2008 High

    Structural and biochemical work defined the catalytic chemistry and UFM1-recognition basis of the proteases, explaining how UFSP enzymes engage the UFM1 C-terminus.

    Evidence X-ray crystallography of UfSP1, active-site mutagenesis, ITC and NMR binding mapping (mouse; C. elegans complex in #30)

    PMID:18321862 PMID:29251776

    Open questions at the time
    • Recognition of substrate-conjugated UFM1 versus free UFM1 not distinguished
    • Regulation of protease activity in cells unaddressed
  4. 2009 High

    Identified UFL1 as the first UFM1 E3 ligase and its substrate UFBP1, locating the conjugation machinery at the ER and answering how UFM1 is transferred to substrates.

    Evidence Co-IP, in vitro conjugation acceleration, Uba5 knockout cells, and subcellular localization

    PMID:20018847

    Open questions at the time
    • Full E3 complex composition not yet defined
    • Functional consequence of UFBP1 modification unknown
  5. 2012 Medium

    Placed the UFM1 system within the ER stress response by showing it is a transcriptional target of Xbp-1 and that its loss triggers the UPR, framing ufmylation as an ER proteostasis pathway.

    Evidence Luciferase reporters, ChIP, Xbp-1 knockout MEFs, and siRNA knockdown with UPR readouts

    PMID:23152784

    Open questions at the time
    • Direct molecular targets mediating UPR effects not identified
    • Single-lab transcriptional regulation evidence
  6. 2015 High

    Demonstrated physiological essentiality of the pathway in hematopoiesis, linking E1 (UBA5), E3 (UFL1) and substrate-receptor (UFBP1) loss to ER stress, blocked differentiation, and HSC death.

    Evidence Germline and conditional knockout mice for Uba5, Ufl1, and UFBP1 with ER stress, autophagy, ROS, and ChIP analyses

    PMID:21304510 PMID:25952549 PMID:26544067

    Open questions at the time
    • Molecular substrates driving erythroid phenotypes not pinned to specific UFMylation events
    • Whether phenotypes are conjugation-dependent in every case unresolved
  7. 2016 High

    Resolved the unusual E1 mechanism, showing UBA5 is a homodimer that binds and transfers UFM1 in trans, with a dual LIR/UFIM motif linking activation to autophagy machinery.

    Evidence Crystal and NMR structures of UBA5–UFM1, mutagenesis, and in vitro/cellular transfer assays

    PMID:26929408 PMID:27653677

    Open questions at the time
    • Functional significance of LC3/GABARAP binding to ufmylation outputs incomplete
    • Regulation of dimerization in cells unaddressed
  8. 2016 High

    Established UFM1 ufmylation as essential for human development by linking biallelic UBA5 hypomorphic mutations to abnormal ER and CNS phenotypes across model organisms.

    Evidence In vitro thioester assay of mutant UBA5, patient fibroblasts, Ufm1 CNS-specific knockout mice, and C. elegans/zebrafish models

    PMID:27545674 PMID:27545681

    Open questions at the time
    • Substrate(s) whose mis-ufmylation drives neuropathology not identified
    • Tissue-selective vulnerability mechanism unknown
  9. 2018 High

    Confirmed UFM1 and UFC1 mutations cause severe encephalopathy by impairing thioester intermediate formation, cementing ufmylation as essential for brain development.

    Evidence Thioester formation assays with mutant proteins, cellular ufmylation assays, and clinical genetics

    PMID:29868776

    Open questions at the time
    • Genotype–phenotype relationship not mechanistically explained at substrate level
  10. 2018 Medium

    Refined the catalytic logic of UFM1 activation, showing UFM1 binding stabilizes the UBA5 dimer to enhance ATP binding and that an N-terminal extension tunes ATP stoichiometry and transfer.

    Evidence Biochemical binding/dimerization assays and crystal structures of the UBA5 long isoform with ATP

    PMID:29295865 PMID:30412706

    Open questions at the time
    • In-cell relevance of isoform-specific ATP handling untested
    • Some claims rest on single-lab biochemistry
  11. 2018 High

    Extended physiological roles to the heart and identified substrate-specificity logic in the protease layer, linking UFL1 loss to ER-stress cardiomyopathy and UFSP1/2 to differential UFM1 maturation and RPL26 deufmylation.

    Evidence Cardiac-specific Ufl1 knockout mice with PERK signaling analysis and pharmacological rescue; UFSP1/UFSP2 double-knockout cells

    PMID:30354401 PMID:35926457

    Open questions at the time
    • Cardiac substrates mediating ER stress not identified
    • Regulation of UFSP1 non-canonical translation in vivo unaddressed
  12. 2021 High

    Defined the molecular basis of UFM1 transfer from E1 to E2, showing a short linear UBA5 C-terminal sequence binds UFC1 and a separate UBA5 region compensates for a missing UFC1 active-site loop.

    Evidence X-ray and NMR structures of UFC1–UBA5 peptide complexes with mutational transfer assays

    PMID:34299007 PMID:34588452

    Open questions at the time
    • How transfer is coupled to E3 handoff not structurally resolved
  13. 2014 High

    Identified transcriptional substrates of ufmylation, showing UFMylation of ASC1 (and later ERα) regulates estrogen-receptor target gene activation and stability, expanding ufmylation beyond the ER membrane.

    Evidence Co-IP, ufmylation assays, ChIP, site-specific Lys-to-Arg mutants, stability assays, and tumor formation assays

    PMID:25219498 PMID:35680375

    Open questions at the time
    • How nuclear UFMylation is spatially coordinated with ER-localized E3 unclear
    • Generality across nuclear receptors untested
  14. 2022 High

    Identified ER-membrane substrates linking ufmylation to organelle turnover, showing CYB5R3 UFMylation inactivates it and targets it for lysosomal ER-phagy via UFBP1 recognition and CDK5RAP3.

    Evidence Substrate identification, UFL1/UFBP1 dependency, in vitro ufmylation, Atg7-dependent degradation, and ufmylation-defective Cyb5r3 knock-in mice

    PMID:36543799

    Open questions at the time
    • Selectivity of CYB5R3 among ER substrates not explained
    • Link between CYB5R3 ER-phagy and microcephaly phenotype mechanistic gap
  15. 2023 High

    Defined the central ribosomal substrate pathway, showing the UFL1-UFBP1-CDK5RAP3 E3 complex UFMylates RPL26 on colliding/disome 60S and that UFBP1 reads ufmylated RPL26 to drive ER-ribosome quality control.

    Evidence Co-IP, ribosome pulldown, disome analysis, and mutational disruption of UFBP1–UFM1 interaction with ER-RQC reporters

    PMID:37595036

    Open questions at the time
    • Trigger coupling collision sensing to E3 recruitment incompletely defined
  16. 2024 High

    Provided the structural mechanism of ribosomal UFMylation, showing the E3 complex clamps split 60S as a C-shaped writer/reader that remodels the PTC, UFMylates uL24 at long range, and releases SEC61 for subunit recycling.

    Evidence Cryo-EM structures of UREL–60S complexes and sequential snapshots with biochemical validation and 60S-SEC61 accumulation upon loss of function

    PMID:38383785 PMID:38383789

    Open questions at the time
    • How the reader function feeds into downstream ER-phagy/recycling steps not fully traced
    • Regulation of writer-to-reader transition unclear
  17. 2025 Medium

    Connected ufmylation to additional substrates and processes—DNA double-strand break repair (Ku70/NHEJ), antiviral RIG-I/MAVS signaling (14-3-3ε), and cancer metabolism—and dissected neuronal UPR consequences of UFM1 loss with pharmacological rescue.

    Evidence UFM1-deficient and UFM1-R81C knock-in neurons with UPR/translation/synapse readouts and Trazodone rescue; preprint probe/proteomics studies of Ku70, 14-3-3ε, and metabolic substrates

    PMID:41731076 PMID:bio_10.1101_2025.03.19.644084 PMID:bio_10.1101_2025.06.02.657324 PMID:bio_10.1101_2025.06.16.659844

    Open questions at the time
    • Several substrates rest on single-lab preprint evidence awaiting peer review
    • Whether non-ribosomal substrates are direct E3 targets in vivo not fully established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How substrate selection is partitioned between the dominant ribosomal UFMylation pathway and the growing list of non-ribosomal substrates, and which substrates underlie the neurodevelopmental and hematopoietic disease phenotypes, remains unresolved.
  • No unifying model for E3 substrate targeting outside the ribosome
  • Causal substrate(s) for human encephalopathy not identified
  • Cell-type-specific vulnerability mechanisms undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0031386 protein tag activity 5 GO:0140096 catalytic activity, acting on a protein 4
Localization
GO:0005783 endoplasmic reticulum 5 GO:0005840 ribosome 4 GO:0005634 nucleus 3
Pathway
R-HSA-392499 Metabolism of proteins 4 R-HSA-8953897 Cellular responses to stimuli 4 R-HSA-8953854 Metabolism of RNA 3 R-HSA-9612973 Autophagy 1
Partners
CDK5RAP3RPL26UBA5UFBP1UFC1UFL1UFSP1UFSP2
Complex memberships
UFM1 E3 ligase complex (UFL1-UFBP1-CDK5RAP3)

Evidence

Reading pass · 41 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2004 UFM1 is a novel ubiquitin-fold modifier that undergoes C-terminal cleavage to expose a conserved Gly residue, which is essential for conjugation. The exposed Gly is then activated by E1-like enzyme UBA5 via a high-energy thioester bond, and transferred to E2-like enzyme UFC1 in a similar thioester linkage, forming a three-enzyme conjugation cascade analogous to ubiquitylation. Biochemical reconstitution of thioester intermediates, C-terminal processing assays, in vitro conjugation assays, mutagenesis of the conserved Gly residue The EMBO journal High 15071506
2006 Two UFM1-specific proteases, UfSP1 and UfSP2, cleave the C-terminal extension of UFM1 to expose the Gly residue required for conjugation, and also release UFM1 from UFM1-conjugated cellular proteins. Both are thiol proteases sensitive to sulfhydryl-blocking agents; mutation of the active-site Cys to Ser abolishes activity, and Ufm1-vinylmethylester labels the active-site Cys. Biochemical cleavage assays with recombinant proteins, active-site mutagenesis (Cys→Ser), activity-based probe labeling with Ufm1-vinylmethylester, inhibitor studies The Journal of biological chemistry High 17182609
2007 Crystal structure of human UFC1 (the UFM1 E2-conjugating enzyme) was determined at 1.6 Å resolution. The structure reveals a canonical E2 domain plus an additional N-terminal domain. The UBA5-binding site on UFC1 was mapped by structural comparison with Ubc12 and mutational analysis; the N-terminal domain contributes to thermal stability. X-ray crystallography (1.6 Å), structural comparison, mutational analysis Biochemical and biophysical research communications High 17825256
2008 Crystal structure of mouse UfSP1 at 1.7 Å resolution reveals it is a novel cysteine protease with a papain-like fold. The catalytic triad is formed by Cys53, Asp175, and His177 in a Asp-Pro-His configuration; Tyr41 participates in the oxyanion hole. NMR data indicate that the loop between β3 and α2, plus the C-terminal region of UFM1, are important for UFM1-UfSP1 binding (KD ~1.6 μM by ITC). X-ray crystallography (1.7 Å), active-site mutagenesis, isothermal titration calorimetry, NMR binding mapping The Journal of biological chemistry High 18321862
2009 UFL1 (also called RCAD) was identified as the first E3 ligase for UFM1. UFL1 covalently conjugates UFM1 to the substrate C20orf116 (UFBP1/DDRGK1); this conjugation is greatly accelerated by UFL1, reversed by UFM1-specific proteases, and abolished in Uba5 knockout cells. UFL1 and UFBP1 localize mainly to the endoplasmic reticulum. Co-immunoprecipitation, in vitro conjugation assays, Uba5 knockout cells, subcellular fractionation, immunofluorescence localization The Journal of biological chemistry High 20018847
2011 UFBP1 (C20orf116) and CDK5RAP3 interact with UFM1. UFM1 co-localizes with UFBP1 at the endoplasmic reticulum, and this ER co-localization depends on UFBP1. siRNA knockdown of UFM1, UFBP1, or UFL1 enhances apoptosis upon ER stress in INS-1E beta cells, indicating that UFM1-UFBP1 conjugation is required to prevent ER stress-induced apoptosis. Co-immunoprecipitation, immunofluorescence co-localization, siRNA knockdown, apoptosis assays under ER stress PloS one High 21494687
2011 Uba5 (UFM1 E1 activating enzyme) is indispensable for erythroid differentiation in mice. Uba5 knockout mice exhibit severe anaemia and die in utero. Genetic loss impairs development of megakaryocyte and erythroid progenitors from common myeloid progenitors in a cell-autonomous manner, as transgenic Uba5 expression restricted to erythroid lineage rescues the anaemia. Uba5 knockout mouse model, erythroid-specific transgenic rescue, hematopoietic progenitor analysis Nature communications High 21304510
2012 The UFM1 system is transcriptionally upregulated in response to ER stress and inhibition of vesicle trafficking. Using luciferase reporter and ChIP assays, UFM1 was identified as a transcriptional target of Xbp-1. Conversely, knockdown of the UFM1 system in U2OS cells triggered the unfolded protein response and amplification of the ER network. RCAD/Ufl1 and its binding partner C53/LZAP are involved in ufmylation of endogenous targets. Luciferase reporter assays, ChIP assays, Xbp-1 knockout MEFs, siRNA knockdown with UPR readouts PloS one Medium 23152784
2014 Ufmylation of the nuclear receptor coactivator ASC1 is required for ERα transactivation. In the absence of E2-estradiol, UfSP2 binds ASC1 and keeps it deufmylated. E2 binding causes ERα to associate with ASC1 and displace UfSP2, leading to polyufmylation of ASC1, which enhances association of p300, SRC1, and ASC1 at promoters of ERα target genes. Co-immunoprecipitation, ufmylation assays, ChIP, knockdown of UBA5 and UFSP2, ufmylation-deficient ASC1 mutant expression, in vivo tumor formation assays Molecular cell High 25219498
2014 Uba5 activates UFM1 via a two-step mechanism forming a binary Uba5~UFM1 thioester (unlike the three-step ternary complex of Uba1/ubiquitin). Uba5 shows random ordered binding with UFM1 and ATP; its transthiolation of UFM1 to UFC1 requires ATP binding to the Uba5~UFM1 thioester complex. The pan-E1 inhibitor adenosine 5'-sulfamate forms a covalent Ufm1-ADS adduct in Uba5's active site. In vitro kinetic assays, thioester formation assays, ATP-PPi exchange assays, mechanism-based inhibitor studies in cells The Journal of biological chemistry High 24966333
2015 RCAD/Ufl1 (UFM1 E3 ligase) is essential for hematopoietic stem cell survival and erythroid differentiation. Both germ-line and somatic deletion impaired hematopoietic development resulting in severe anaemia. Loss of RCAD/Ufl1 elevated ER stress, evoked UPR, blocked autophagic degradation, increased mitochondrial mass and reactive oxygen species, and led to DNA damage response and p53 activation in HSCs. Germ-line and conditional knockout mouse models, bone marrow cell analysis, ER stress markers, autophagy assays, ROS measurement Cell death and differentiation High 25952549
2015 UFBP1 is indispensable for embryonic development and hematopoiesis. UFBP1 deficiency causes elevated ER stress and UPR activation leading to HSC/progenitor cell death, and suppresses expression of erythroid transcription factors GATA-1 and KLF1. ASC1 was found to associate with GATA-1 and Klf1 promoters in a UFBP1-dependent manner. Germ-line and conditional UFBP1 knockout mice, ChIP, K562 cell knockdowns, ER stress marker analysis PLoS genetics High 26544067
2016 Crystal structure of the non-canonical homodimeric E1 UBA5 in complex with UFM1 reveals that UFM1 interacts with distinct sites in both subunits of the UBA5 dimer via a trans-binding mechanism. UFM1 transfer from UBA5 to UFC1 also occurs via a trans mechanism requiring UBA5 homodimerization. A C-terminal region outside the adenylation domain recruits UFM1 to the active site of the adjacent subunit. X-ray crystallography, biochemical assays of trans-binding mechanism, mutagenesis Cell reports High 27653677
2016 A combined LIR/UFM1-interacting motif (LIR/UFIM) at the C-terminus of UBA5 mediates binding to both UFM1 and LC3/GABARAP. This motif is required for full biological activity of UBA5 and for effective transfer of UFM1 to UFC1 and downstream protein substrates both in vitro and in cells. NMR structure, mutational analysis, in vitro UFM1 transfer assays, cellular ufmylation assays The Journal of biological chemistry High 26929408
2016 Biallelic mutations in UBA5 impair ufmylation, resulting in abnormal endoplasmic reticulum structure. The UBA5 p.Ala371Thr variant is hypomorphic with attenuated ability to transfer activated UFM1 to UFC1 (shown by in vitro thioester formation assay). CNS-specific knockout of Ufm1 in mice causes neonatal death with microcephaly and neuronal apoptosis. In C. elegans, knockout of uba-5 alters cholinergic but not glutamatergic neurotransmission. In vitro thioester formation assay with mutant UBA5, patient fibroblast studies, Ufm1 CNS-specific knockout mice, C. elegans knockout, zebrafish uba5 silencing American journal of human genetics High 27545674 27545681
2018 Biallelic mutations in UFM1 and UFC1 impair formation of UFM1-UBA5 and UFM1-UFC1 thioester intermediates, causing widespread reduction of cellular ufmylation. This establishes that mutations in the UFM1 modifier itself and its E2 enzyme cause severe early-onset encephalopathy with progressive microcephaly, demonstrating the essential role of ufmylation in human brain development. Thioester intermediate formation assays with mutant proteins, cellular ufmylation assays, clinical genetics Brain : a journal of neurology High 29868776
2018 Ufl1 (UFM1 E3 ligase) deficiency in cardiac-specific knockout mice leads to age-dependent cardiomyopathy and heart failure, with excessive ER stress preceding and worsening with disease progression. Mechanistically, Ufl1 depletion impairs PERK (PKR-like ER-resident kinase) signaling and aggravates cardiomyocyte death after ER stress. Chemical ER chaperone tauroursodeoxycholic acid treatment alleviates the cardiac dysfunction. Cardiac-specific knockout mice, transcriptome analysis, ER stress markers, PERK signaling assays, pharmacological rescue Circulation. Heart failure High 30354401
2018 Trans-binding of UFM1 to UBA5 stabilizes the UBA5 homodimer, which in turn enhances ATP binding to UBA5. Dimerization of UBA5 is required for ATP binding; UFM1 binding promotes dimerization and thereby stimulates ATP binding necessary for UFM1 activation. Biochemical binding assays, dimerization analysis, ATP binding assays FASEB journal Medium 29295865
2018 The N-terminal extension present in the long isoform of UBA5 is directly involved in ATP binding and affects how the adenylation domain interacts with ATP, changing the stoichiometry from 1:2 to 1:1 ATP:UBA5. The N-terminus also significantly increases ATP affinity and stimulates UFM1 transfer from UBA5 to UFC1, though it is not directly involved in E2 binding. Crystal structures of UBA5 long isoform with ATP and UFM1, ATP binding assays, UFC1 transfer assays Journal of molecular biology High 30412706
2019 The UFM1 cascade controls cell cycle entry at the G2/M transition in Drosophila neuroblasts. Disruption of ufmylation increases the mitotic index and extends G2/M phase. Impaired E3 ligase Ufl1 function causes premature mitotic entry and failed cellularization. The UFM1 cascade alters the phosphorylation level of Tyr15 on CDK1 (pY15-CDK1), a negative regulator of the G2-to-M transition. Drosophila neuroblast genetic knockdown/knockout, live imaging, mitotic index analysis, phosphorylation assays for CDK1-pY15 FASEB journal Medium 31914610
2021 Crystal structure of UFC1 bound to the C-terminus of UBA5 reveals that UBA5 interacts with UFC1 via a short linear sequence not observed in other E1-E2 complexes. A region of UBA5 outside the adenylation domain, dispensable for UFC1 binding, is critical for UFM1 transfer by compensating for a missing loop in UFC1's active site. X-ray crystallography of UFC1-UBA5 C-terminal peptide complex, mutational analysis of transfer Nature communications High 34588452
2022 NADH-cytochrome b5 reductase 3 (CYB5R3) on the ER membrane is a UFM1 substrate. Ufmylation of CYB5R3 depends on the E3 components UFL1 and UFBP1, converts CYB5R3 into its inactive form, and is recognized by UFBP1 through a UFM1-interacting motif on UFBP1. Ufmylated CYB5R3 is degraded in lysosomes in an Atg7- and CDK5RAP3-dependent manner, promoting ER-phagy. Ufmylation-defective Cyb5r3 knock-in mice exhibit microcephaly. Identification of ufmylation substrate, UFL1/UFBP1 dependency assays, in vitro ufmylation, lysosomal degradation assays, Atg7 dependency, Cyb5r3 ufmylation-defective knock-in mice Nature communications High 36543799
2022 ERα (estrogen receptor α) is directly ufmylated at Lys171 and Lys180. UFMylation of ERα increases its stability by inhibiting ubiquitination and proteasomal degradation. UfSP2 knockdown increases ERα stability, while UBA5 silencing decreases it. Ufmylation-deficient ERα (2KR mutant) shows reduced stability, abolished E2-induced transactivity, and cannot form anchorage-independent colonies. Site-specific mutagenesis (Lys to Arg), ubiquitination assays, stability assays with UBA5/UFSP2 manipulation, ERα target gene expression analysis, colony formation assays Molecules and cells High 35680375
2022 UFSP1 is translated from a non-canonical start site and acts as an active protease that matures UFM1 (cleaves pro-UFM1) and cleaves a potential autoinhibitory modification on UFC1 to control activation of UFMylation. Cells lacking both UFSP1 and UFSP2 show complete loss of UFMylation due to absence of mature UFM1. UFSP2, but not UFSP1, removes UFM1 from ribosomal subunit RPL26, revealing distinct substrate specificities. UFSP1/UFSP2 double-knockout cells, identification of non-canonical start site, UFM1 maturation assays, UFC1 deufmylation assays, RPL26 deufmylation assays Cell reports High 35926457
2022 PLAC8 is post-translationally modified by UFM1 (ufmylated), and this modification maintains PLAC8 protein stability in triple-negative breast cancer cells. PLAC8 in turn regulates PD-L1 levels by affecting PD-L1 ubiquitination. Co-immunoprecipitation, ufmylation assays, protein stability assays Journal for immunotherapy of cancer Medium 36543379
2022 UFL1 and CDK5RAP3/C53 associate with γ-tubulin ring complex proteins. Knockout of UFL1 or CDK5RAP3 in human osteosarcoma cells induces ER stress and boosts centrosomal microtubule nucleation with γ-tubulin accumulation. CDK5RAP3, which is stabilized by UFL1, associates with the centrosome and rescues microtubule nucleation in UFL1-lacking cells. Knockout of UFL1 and CDK5RAP3, immunofluorescence, γ-tubulin complex co-immunoprecipitation, microtubule nucleation assays Cells Medium 35159364
2022 Neuron-specific deletion of either UFL1 or UFBP1 (UFM1 E3 ligase components) leads to significant neuronal loss in adult mice, elevated inflammatory response, and seizure-like events upon loss of one UFBP1 allele, demonstrating the indispensable role of the UFM1 E3 ligase in mature neuron survival. Neuron-specific conditional knockout mice for UFL1 and UFBP1, histological analysis, inflammatory marker measurement Molecular neurobiology High 35931931
2023 The UFM1 E3 complex (UFL1-UFBP1-CDK5RAP3) interacts with UFC1 (E2), then CDK5RAP3 acts as an adaptor for ufmylation of ribosomal subunit RPL26. Upon disome formation (colliding ribosomes), the E3 complex associates with ufmylated RPL26 on the 60S subunit through the UFM1-interacting region of UFBP1. Loss of E3 components or disruption of UFBP1-ufmylated RPL26 interaction impairs ER-ribosome quality control. Co-immunoprecipitation, ribosome pulldown, disome analysis, mutational disruption of UFBP1-UFM1 interaction, ER-RQC reporter assays Science advances High 37595036
2024 Cryo-EM structures of the UFM1 E3 ligase complex (UREL, comprising UFL1-UFBP1-CDK5RAP3) bound to 60S ribosomes reveal a C-shaped clamp architecture. UFL1 loops insert into and remodel the peptidyl transferase center. UREL functions as both a 'writer' (catalyzing UFMylation of RPL26/uL24) and subsequently a 'reader' of ufmylated 60S. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating UFMylation is necessary for releasing SEC61 from 60S subunits. Cryo-EM structures, biochemical reconstitution, genetic loss-of-function accumulation of 60S-SEC61 complexes Nature High 38383785 38383789
2024 Sequential cryo-EM snapshots show the UFM1 E3 ligase (E3(UFM1)) engages its substrate uL24 (RPL26) on free 60S ribosomes. E3(UFM1) binds the L1 stalk, empty tRNA-binding sites, and the peptidyl transferase center through C-terminal domains of UFL1, catalyzing UFM1 transfer to uL24 more than 150 Å away. After catalysis, E3(UFM1) remains stably bound to ufmylated 60S, forming the C-shaped clamp, suggesting a role in post-termination recycling of the large ribosomal subunit from the ER membrane. Cryo-EM (sequential snapshots), biochemical analysis of E3 binding and catalysis, substrate engagement mapping Nature High 38383785
2018 Structural basis for UFM1 recognition by C. elegans UfSP: the structure reveals that the conserved Pro88-Val92 residues (P6-P2 positions from the cleavage site) plus extended β-structure at the UFM1 C-terminus are important for specific recognition of UFM1 by UfSP. X-ray crystallography of cUFM1-cUfSP complex FEBS letters Medium 29251776
2014 In C. elegans, UfSP2 (odr-8) forms a physical complex with ODR-4 at the ER membrane in chemosensory neurons. This complex promotes GPCR (ODR-10) maturation and ER export independently of UfSP2's catalytic activity and independently of UFM1, since catalytically dead UfSP2 rescues all odr-8 mutant phenotypes and deletion of ufm-1 does not alter chemoreceptor trafficking. Genetic epistasis in C. elegans, co-immunoprecipitation of ODR-4/ODR-8, catalytic-dead mutant rescue, ufm-1 null mutant analysis PLoS genetics Medium 24603482
2021 The NMR structure of UFC1 bound to a peptide spanning the last 20 residues of UBA5 reveals the molecular basis of UBA5-UFC1 interaction. These last 20 residues are pivotal for UFC1 binding and accelerate UFM1 transfer to UFC1; a proposed regulatory role involves the C-terminal unstructured region controlling cellular localization and interaction of ufmylation cascade elements. NMR structure of UFC1-UBA5 peptide complex, ITC binding assays, UFM1 transfer assays International journal of molecular sciences High 34299007
2021 The UFM1 pathway impacts ER-associated protein degradation (ERAD). A genome-wide CRISPR/Cas9 screen using US2-mediated HLA-I degradation as ERAD model identified the UFM1 pathway. Interference with the UFM1 pathway inhibits ER-to-cytosol dislocation of HLA-I specifically; no UFMylation of HLA-I was detected, suggesting UFM1 impacts ERAD indirectly. Ribosomal proteins are a major class of UFMylated proteins in US2-expressing cells. Genome-wide CRISPR/Cas9 screen, mass spectrometry, HLA-I dislocation assays Molecules (Basel, Switzerland) Medium 33430125
2023 UfSP1 binds to the ubiquitin-associated (UBA) domain of p62/SQSTM1 and promotes the interaction between p62 and ubiquitinated proteins, thereby increasing p62 body formation. This function is independent of UfSP1's protease activity, as both catalytically active and inactive UfSP1 promote p62 body formation through the same mechanism. Proximity labeling (TurboID), co-immunoprecipitation, immunofluorescence co-localization, catalytic-dead mutant analysis Journal of proteome research Medium 37285312
2022 UFM1 suppresses gastric cancer cell invasion by increasing ubiquitination of PDK1 (decreasing PDK1 protein level), thereby inhibiting AKT phosphorylation at Ser473 and the PI3K/AKT signaling pathway. The effect of UFM1 on cancer cell function depends on PDK1 expression. Co-immunoprecipitation, protein kinase array, stable UFM1 overexpression/knockdown, PDK1 ubiquitination assays, AKT phosphorylation analysis Journal of experimental & clinical cancer research Medium 31533855
2025 UFM1 loss in neurons causes ER stress, activation of the unfolded protein response (UPR), and reduced protein translation, leading to impaired neuron development and synapse function. The pathogenic UFM1-R81C variant partially rescues UFM1 loss phenotypes but displays distinct ER stress responses, suggesting it is not merely a loss-of-function variant. The UPR inhibitor Trazodone restores protein translation only in UFM1-R81C-expressing neurons, and increases synapse numbers in both UFM1-KO and R81C neurons. UFM1-deficient mouse neurons, UFM1-R81C knock-in neurons, UPR pathway analysis, protein translation assays, synapse counting, pharmacological rescue with Trazodone EMBO molecular medicine High 41731076
2025 UFMylation promotes non-homologous end-joining (NHEJ) of DNA double-strand breaks. Ku70 is a UFMylation substrate; XRCC4 engages UFMylated Ku70 via non-canonical UFM1-binding regions to promote chromatin assembly of NHEJ factors. Perturbation of UFM1 signaling (via UFSP2 depletion or hypomorphic UBA5 allele in patient fibroblasts) impairs NHEJ. Photo-crosslinkable UFM1 probe, NMR, proximity-dependent proteomics, NHEJ assays, patient fibroblast analysis bioRxivpreprint Medium bio_10.1101_2025.06.16.659844
2025 UFMylation of 14-3-3ε at Lys50 and Lys215 promotes RIG-I/MAVS antiviral signaling. K50R/K215R mutations abolish UFMylation and reduce type I and III interferon induction following RIG-I activation. These mutations do not disrupt the 14-3-3ε-RIG-I interaction but paradoxically enhance RIG-I-MAVS interaction while reducing 14-3-3ε-MAVS interaction, indicating UFMylation controls MAVS signaling complex architecture. In vitro and cellular UFMylation assays, site-specific mutagenesis, co-immunoprecipitation, interferon induction assays bioRxivpreprint Medium bio_10.1101_2025.03.19.644084
2025 Loss of UFMylation reroutes glucose metabolism and promotes prostate cancer cell invasion. Phosphofructokinase (PFKAP) was identified as a UFMylation substrate. Loss of UFMylation reduces glycolytic flux and increases hexosamine biosynthesis, elevating protein glycosylation relevant to invasion. Biotin-based UFMylation proteomics, transcriptomics, metabolic flux analysis, pharmacological pathway inhibition bioRxivpreprint Low bio_10.1101_2025.06.02.657324
2025 Canonical RQC factors associate with ribosomes stalled at the ER. Ribosome splitting is a prerequisite for UFMylation of RPL26. The UFM1 E3 ligase complex binds and UFMylates the 60S-peptidyl-tRNA complex; UFMylation of RPL26 persists without late RQC components (NEMF, LTN1). UFMylation and the canonical RQC pathway act in concert to facilitate clearance of arrested polypeptides at the ER. ER-targeted stalling reporters, ribosome fractionation, UFMylation and RQC factor dependency assays bioRxivpreprint Medium bio_10.1101_2025.01.17.633636

Source papers

Stage 0 corpus · 77 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2004 A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier. The EMBO journal 349 15071506
2009 A novel type of E3 ligase for the Ufm1 conjugation system. The Journal of biological chemistry 217 20018847
2014 Modification of ASC1 by UFM1 is crucial for ERα transactivation and breast cancer development. Molecular cell 186 25219498
2006 Two novel ubiquitin-fold modifier 1 (Ufm1)-specific proteases, UfSP1 and UfSP2. The Journal of biological chemistry 172 17182609
2011 Ubiquitin fold modifier 1 (UFM1) and its target UFBP1 protect pancreatic beta cells from ER stress-induced apoptosis. PloS one 167 21494687
2015 RCAD/Ufl1, a Ufm1 E3 ligase, is essential for hematopoietic stem cell function and murine hematopoiesis. Cell death and differentiation 160 25952549
2015 UFBP1, a Key Component of the Ufm1 Conjugation System, Is Essential for Ufmylation-Mediated Regulation of Erythroid Development. PLoS genetics 150 26544067
2011 The Ufm1-activating enzyme Uba5 is indispensable for erythroid differentiation in mice. Nature communications 150 21304510
2012 Transcriptional regulation of the Ufm1 conjugation system in response to disturbance of the endoplasmic reticulum homeostasis and inhibition of vesicle trafficking. PloS one 108 23152784
2016 Biallelic Variants in UBA5 Reveal that Disruption of the UFM1 Cascade Can Result in Early-Onset Encephalopathy. American journal of human genetics 104 27545681
2016 Biallelic Variants in UBA5 Link Dysfunctional UFM1 Ubiquitin-like Modifier Pathway to Severe Infantile-Onset Encephalopathy. American journal of human genetics 101 27545674
2018 Biallelic UFM1 and UFC1 mutations expand the essential role of ufmylation in brain development. Brain : a journal of neurology 98 29868776
2018 Ufm1-Specific Ligase Ufl1 Regulates Endoplasmic Reticulum Homeostasis and Protects Against Heart Failure. Circulation. Heart failure 81 30354401
2022 The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. Nature communications 79 36543799
2014 The ufm1 cascade. Cells 73 24921187
2016 Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation. The Journal of biological chemistry 67 26929408
2019 UFM1 suppresses invasive activities of gastric cancer cells by attenuating the expres7sion of PDK1 through PI3K/AKT signaling. Journal of experimental & clinical cancer research : CR 62 31533855
2022 Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation. Cell reports 59 35926457
2023 The UFM1 system: Working principles, cellular functions, and pathophysiology. Molecular cell 56 38141606
2016 Trans-Binding Mechanism of Ubiquitin-like Protein Activation Revealed by a UBA5-UFM1 Complex. Cell reports 55 27653677
2024 The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Nature 53 38383789
2020 Decrypting UFMylation: How Proteins Are Modified with UFM1. Biomolecules 50 33066455
2008 Structural basis for Ufm1 processing by UfSP1. The Journal of biological chemistry 50 18321862
2017 UFM1 founder mutation in the Roma population causes recessive variant of H-ABC. Neurology 49 28931644
2024 UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature 48 38383785
2023 Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control. Science advances 48 37595036
2022 Modification of PLAC8 by UFM1 affects tumorous proliferation and immune response by impacting PD-L1 levels in triple-negative breast cancer. Journal for immunotherapy of cancer 47 36543379
2014 An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. PLoS genetics 46 24603482
2007 Crystal structure of Ufc1, the Ufm1-conjugating enzyme. Biochemical and biophysical research communications 44 17825256
2014 Mechanistic study of Uba5 enzyme and the Ufm1 conjugation pathway. The Journal of biological chemistry 43 24966333
2012 Deletion of mitochondrial associated ubiquitin fold modifier protein Ufm1 in Leishmania donovani results in loss of β-oxidation of fatty acids and blocks cell division in the amastigote stage. Molecular microbiology 41 22897198
2021 Structural basis for UFM1 transfer from UBA5 to UFC1. Nature communications 38 34588452
2018 An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. Journal of molecular biology 35 30412706
2019 Ufl1/RCAD, a Ufm1 E3 ligase, has an intricate connection with ER stress. International journal of biological macromolecules 33 31129212
2008 NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. Journal of structural and functional genomics 32 19101823
2018 Generation of the UFM1 Toolkit for Profiling UFM1-Specific Proteases and Ligases. Angewandte Chemie (International ed. in English) 31 30188611
2017 Ufm1 inhibits LPS-induced endothelial cell inflammatory responses through the NF-κB signaling pathway. International journal of molecular medicine 31 28393202
2015 A selective inhibitor of the UFM1-activating enzyme, UBA5. Bioorganic & medicinal chemistry letters 30 27520940
2017 Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. Scientific reports 29 28360427
2013 The ubiquitin-fold modifier 1 (Ufm1) cascade of Caenorhabditis elegans. The Journal of biological chemistry 29 23449979
2021 Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma. Biomolecules 26 33578803
2022 Deficiency of Murine UFM1-Specific E3 Ligase Causes Microcephaly and Inflammation. Molecular neurobiology 25 35931931
2016 Essential role of Ufm1 conjugation in the hematopoietic system. Experimental hematology 25 27033164
2022 Modification of ERα by UFM1 Increases Its Stability and Transactivity for Breast Cancer Development. Molecules and cells 24 35680375
2019 The UFM1 cascade times mitosis entry associated with microcephaly. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 21 31914610
2018 Trans-binding of UFM1 to UBA5 stimulates UBA5 homodimerization and ATP binding. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 21 29295865
2022 Facile Preparation of UFMylation Activity-Based Probes by Chemoselective Installation of Electrophiles at the C-Terminus of Recombinant UFM1. ACS central science 20 35756382
2022 C53 Interacting with UFM1-Protein Ligase 1 Regulates Microtubule Nucleation in Response to ER Stress. Cells 19 35159364
2022 Emerging role of protein modification by UFM1 in cancer. Biochemical and biophysical research communications 18 36344165
2023 The UFM1 conjugation system in mammalian development. Developmental dynamics : an official publication of the American Association of Anatomists 17 36932998
2014 Deletion of ubiquitin fold modifier protein Ufm1 processing peptidase Ufsp in L. donovani abolishes Ufm1 processing and alters pathogenesis. PLoS neglected tropical diseases 17 24587462
2021 A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1. International journal of molecular sciences 15 34299007
2021 The UFM1 Pathway Impacts HCMV US2-Mediated Degradation of HLA Class I. Molecules (Basel, Switzerland) 14 33430125
2021 The lncRNA B3GALT5-AS1 Functions as an HCC Suppressor by Regulating the miR-934/UFM1 Axis. Journal of oncology 14 34721576
2022 UFM1 inhibits the activation of the pyroptosis in LPS-induced goat endometritis. Theriogenology 13 36395577
2015 UFM1 Protects Macrophages from oxLDL-Induced Foam Cell Formation Through a Liver X Receptor α Dependent Pathway. Journal of atherosclerosis and thrombosis 13 26040753
2021 Ufbp1, a Key Player of Ufm1 Conjugation System, Protects Against Ketosis-Induced Liver Injury via Suppressing Smad3 Activation. Frontiers in cell and developmental biology 12 34307359
2021 Four New Cases of Hypomyelinating Leukodystrophy Associated with the UFM1 c.-155_-153delTCA Founder Mutation in Pediatric Patients of Roma Descent in Hungary. Genes 12 34573312
2018 Structural basis for Ufm1 recognition by UfSP. FEBS letters 11 29251776
2023 Proximity Proteomics and Biochemical Analysis Reveal a Noncanonical Function for UFM1-Specific Protease 1 in the p62 Body Formation. Journal of proteome research 10 37285312
2022 Dynamic recruitment of UFM1-specific peptidase 2 to the DNA double-strand breaks regulated by WIP1. Genome instability & disease 10 36042814
2023 Hypomyelination with Atrophy of Basal Ganglia and Cerebellum (HABC) Due to UFM1 Mutation in Roma Patients - Severe Early Encephalopathy with Stridor and Severe Hearing and Visual Impairment. A Single Center Experience. CNS & neurological disorders drug targets 8 35189806
2023 Preparation of UFM1-Derived Probes through Highly Optimized Total Chemical Synthesis. Chemistry (Weinheim an der Bergstrasse, Germany) 6 37080930
2014 Characterization, crystallization and preliminary X-ray crystallographic analysis of the Uba5 fragment necessary for high-efficiency activation of Ufm1. Acta crystallographica. Section F, Structural biology communications 5 24915089
2024 UFM1 inhibits hypoxia-induced angiogenesis via promoting proteasome degradation of HIF-1α. Molecular and cellular biochemistry 4 38722467
2023 Characterization of a silkworm UFM1 homolog in regulating Bombyx mori unfolded protein response and nucleopolyhedrovirus replication. Biochemical and biophysical research communications 4 37478772
2021 Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism. Journal of structural biology 4 34508858
2025 UFM1 at the endoplasmic reticulum: linking ER stress, ribosome quality control, and ER-phagy. Essays in biochemistry 2 41065375
2023 Screening UFMylation-associated genes in heart tissues of Ufm1-transgenic mice. BMC cardiovascular disorders 2 37980507
2025 Flexible Semi-synthesis of UFM11-82-Propargylamine by Aminolysis with Valine-Propargylamine. Organic letters 1 39899039
2025 RNA-binding protein HuR interacts with UFM1 mRNA to ameliorate chondrocyte inflammation, apoptosis and extracellular matrix degradation. Functional & integrative genomics 1 40289171
2026 Encephalopathy-linked UFM1 variants impede neuronal protein translation, development, and function. EMBO molecular medicine 0 41731076
2026 The UFM1 Conjugation System: A Master Regulator of Cellular Stress Surveillance in Human Disease. Biology 0 41823810
2026 UFM1 suppresses VSMCs phenotypic switching and attenuates atherosclerosis by inhibiting AKT phosphorylation. Biochemical pharmacology 0 41974329
2026 UFM1 regulates ferroptosis in oral squamous cell carcinoma by stabilizing SLC7A11. American journal of cancer research 0 42004070
2025 UBA5 missense variants disrupt UFM1 activation: Structural, dynamic, and functional dissection. International journal of biological macromolecules 0 41360240
2022 Probing Protein-protein Interactions and Druggable Site Identification: Mechanistic Binding Events Between Ubiquitin and Zinc Finger with UFM1-specific Peptidase Domain Protein (ZUFSP). Combinatorial chemistry & high throughput screening 0 33538664

Missed literature

Know a paper Affinage missed for UFM1? Flag it for the maintainers and the community.

No submissions yet.