| 1997 |
NEDD8 is a ubiquitin-like protein that is covalently conjugated to other proteins; its C-terminus is cleaved to expose Gly-76, which is required for conjugation. NEDD8 is enriched in the nucleus relative to ubiquitin, and mutational analysis showed Gly-76 is essential for conjugation. |
Mutational analysis, immunocytochemistry, Western blot of HA-tagged NEDD8 in COS cells |
The Journal of biological chemistry |
High |
9353319
|
| 1998 |
The NEDD8 conjugation pathway uses a dedicated E1-like heterodimeric complex (APP-BP1/hUba3) to activate NEDD8, followed by transfer to the E2 conjugating enzyme hUbc12, with the major identified substrate being cullin-4A (Cul-4A). |
In vitro biochemical reconstitution with purified components, identification of Cul-4A as neddylation substrate |
Genes & development |
High |
9694792
|
| 1998 |
Crystal structure of human NEDD8 at 1.6-Å resolution shows close structural similarity to ubiquitin. A single conserved residue, Ala-72 (Arg in ubiquitin), prevents NEDD8 from being efficiently activated by the ubiquitin E1 enzyme, thereby maintaining pathway specificity. NEDD8 can be transferred from E1 to E2-25K, which adds it to polyubiquitin chains, and chimeric NEDD8-containing tetramers bind the 26S proteasome. |
X-ray crystallography (1.6 Å), in vitro activation assay with ubiquitin E1, mutational analysis of Ala-72 |
The Journal of biological chemistry |
High |
9857030
|
| 1998 |
UCH-L3 (but not UCH-L1) cleaves the C-terminus of NEDD8 in vitro and binds NEDD8 directly, identifying UCH-L3 as a C-terminal hydrolase/processing enzyme for NEDD8. |
Yeast two-hybrid screen, GST pull-down, in vitro cleavage assay |
Biochemical and biophysical research communications |
Medium |
9790970
|
| 1999 |
Human UBA3 forms the catalytic subunit of the NEDD8-activating E1 complex (with APP-BP1) and forms a beta-mercaptoethanol-sensitive (thioester) conjugate with NEDD8. Human UBC12 forms a thiol-ester linkage with NEDD8 in the presence of the activating enzyme, identifying both E1 and E2 components of the NEDD8 pathway. |
GST pulldown (UBA3 with NEDD8 vs. ubiquitin/sentrin-1), thioester conjugate formation assay, co-precipitation |
The Journal of biological chemistry |
High |
10207026
|
| 2000 |
Nedd8 modification of Cul-1 is required for SCF(β-TrCP)-mediated ubiquitination of IκBα. The Nedd8-conjugated form of Cul-1 is selectively enriched in active SCF complexes in vivo, and a K720R Cul-1 mutant that cannot be neddylated shows markedly reduced IκBα ubiquitination activity. |
In vivo co-immunoprecipitation, in vitro ubiquitination assay with dominant-negative Ubc12, K720R Cul-1 mutant analysis |
Molecular and cellular biology |
High |
10713156
|
| 2000 |
The Nedd8 conjugation pathway is required for SCF(Skp2)-mediated ubiquitination and subsequent proteasomal degradation of p27Kip1. A dominant-negative UBC12(C111S) mutant blocks p27 ubiquitination and degradation in cell extracts, and recombinant SCF(Skp2) requires Nedd8 pathway components for p27 ubiquitination activity. |
In vitro ubiquitination assay with cell extracts and recombinant SCF(Skp2), dominant-negative UBC12(C111S) |
Proceedings of the National Academy of Sciences of the United States of America |
High |
10781063
|
| 2000 |
UBC12(C111S), a dominant-negative mutant of the NEDD8 E2 conjugating enzyme, sequesters NEDD8 by forming a stable non-reducible heterodimeric conjugate, thereby inhibiting NEDD8 transfer to substrates including cullin-1 and cullin-2. Overexpression of this mutant inhibits cell growth in U2OS and HEK293 cells. |
Co-expression, SDS-PAGE under denaturing conditions, cell growth assay |
The Journal of biological chemistry |
Medium |
10828074
|
| 2001 |
NUB1 (NEDD8 Ultimate Buster-1), an interferon-inducible protein, interacts with NEDD8 and recruits NEDD8 and its conjugates to the 26S proteasome via binding to the S5a subunit (PA700), leading to proteasomal degradation of NEDD8 conjugates. Proteasome inhibitors block this NUB1-mediated down-regulation. |
GST pull-down with S5a, co-immunoprecipitation, proteasome inhibitor treatment |
The Journal of biological chemistry |
Medium |
11585840
|
| 2001 |
The NEDD8 system is essential for cell cycle progression in both mitotic and endoreduplicative cycles in mice. Uba3 knockout mice die at peri-implantation, with inner cell mass apoptosis and failure of trophoblastic cells to enter S phase, accompanied by aberrant cyclin E and p57(Kip2) expression. β-catenin, a SCF substrate, accumulates in the cytoplasm and nucleus of Uba3−/− cells, confirming loss of SCF-mediated degradation. |
Gene knockout (Uba3−/−) in mice, cell cycle analysis, immunostaining for cyclin E, p57, β-catenin |
The Journal of cell biology |
High |
11696557
|
| 2002 |
The NEDD8 pathway is required for proteasome-mediated degradation of estrogen receptor alpha (ERα). Uba3 co-expression increases ERα turnover via the 26S proteasome; inhibition of NEDD8 activation reduces ERα polyubiquitination and stabilizes the receptor. Loss of the NEDD8 pathway impairs ICI 182,780-induced ERα degradation and antiproliferative activity in MCF7 cells. |
Co-expression and proteasome inhibitor assays, dominant-negative NEDD8 pathway, cell proliferation assay |
Molecular endocrinology (Baltimore, Md.) |
Medium |
12554766
|
| 2002 |
The NEDD8 pathway is required for SCF(β-TrCP)-mediated ubiquitination and processing of the NF-κB precursor p105. In cell-free and reconstituted systems, all three NEDD8 pathway components (E1, E2, NEDD8) stimulate p105 ubiquitination, and a non-neddylatable Cul-1 K720R mutant cannot support p105 ubiquitination/processing. |
Cell-free ubiquitination assay, reconstituted system, dominant-negative UBC12, Cul-1 K720R mutant |
The Journal of biological chemistry |
High |
11953428
|
| 2002 |
The Nedd8 pathway in C. elegans regulates cytoskeletal organization: Nedd8 conjugation negatively regulates microfilament cortical contractility during pronuclear migration and cytokinesis, and is required to down-regulate katanin (a microtubule-severing complex) to permit assembly of the large mitotic spindle, likely via cullin-based E3 ligase-mediated degradation of katanin. |
Genetic analysis (RNAi and loss-of-function) in C. elegans embryos, live imaging of cytoskeletal dynamics |
Science (New York, N.Y.) |
High |
11847342
|
| 2003 |
ASPP2 specifically interacts with APP-BP1 (the non-catalytic subunit of the NEDD8 E1 complex), inhibits APP-BP1-mediated NEDD8 conjugation to cullin-1, and blocks APP-BP1-induced cell proliferation and neuronal apoptosis, identifying ASPP2 as a negative regulator of the neddylation pathway. |
Co-immunoprecipitation in non-transfected cells, neddylation assay of cullin-1, functional proliferation/apoptosis assays |
Journal of neurochemistry |
Medium |
12694406
|
| 2003 |
Roc1 (a RING-finger protein in SCF) binds Ubc12 (NEDD8 E2) via its RING domain and functions as a NEDD8 E3 ligase toward Cul1 in vitro. A RING mutant (H77A) abolishes Ubc12 binding. Neddylation of Cul1 also triggers its own ubiquitination and proteasomal degradation; non-neddylatable Cul1-K720R is more stable than wild-type. |
In vitro neddylation assay with bacterially expressed Cul1/Roc1, Roc1 RING mutant, pulse-chase degradation assay |
Biochemical and biophysical research communications |
Medium |
12565873
|
| 2004 |
Mdm2 acts as an E3 ligase for NEDD8 modification of p53, and Mdm2-dependent neddylation of p53 inhibits its transcriptional activity. Using a temperature-sensitive NEDD8 conjugation pathway cell line and a p53 mutant (3NKR) that cannot be neddylated, neddylation was shown to suppress p53-dependent transcription. Mdm2 itself is also modified with NEDD8. |
Temperature-sensitive cell line (TS-41) with mutant NEDD8 conjugation, 3NKR p53 mutant, transcriptional reporter assays, Western blot |
Cell |
High |
15242646
|
| 2005 |
Crystal structure of NEDP1 (the NEDD8-specific deconjugating cysteine protease of the Ulp family) in isolation and in a transition-state complex with NEDD8 at atomic resolution. NEDD8 binding induces a dramatic conformational change in a flexible loop that locks the NEDD8 C-terminus in an extended β-structure for catalysis. A single residue difference between NEDD8 and ubiquitin C-termini underlies NEDP1's ability to discriminate between them. NEDP1 processes pre-NEDD8 and deconjugates NEDD8 from substrates including p53 and cullins. |
X-ray crystallography (transition-state complex), site-directed mutagenesis, biochemical deconjugation assay, in vivo analysis of NEDP1 mutants |
The EMBO journal |
High |
15775960
|
| 2006 |
Mdm2 promotes NEDD8 modification of TAp73 (but not ΔNp73) in an Mdm2-dependent manner. The deNEDDylating enzyme NEDP1 reverses this modification. Neddylated TAp73 is preferentially localized to the cytoplasm, and blocking the NEDD8 pathway increases TAp73 transactivation activity. |
Co-expression with NEDP1, subcellular fractionation, transcriptional reporter assay |
The Journal of biological chemistry |
Medium |
16980297
|
| 2006 |
The ubiquitin ligase c-Cbl mediates NEDD8 modification of the EGF receptor (EGFR). EGF stimulates receptor neddylation at multiple lysines in the kinase domain, which enhances subsequent ubiquitylation and lysosomal sorting/degradation of EGFR. Clathrin coat-associated ubiquitin-binding proteins also bind Nedd8. |
Co-immunoprecipitation, mutational analysis, lysosomal degradation assay |
The Journal of biological chemistry |
Medium |
16735510
|
| 2009 |
MLN4924 is a potent and selective inhibitor of NEDD8-activating enzyme (NAE) that acts as an adenosine sulfamate analog, disrupts cullin-RING ligase-mediated protein turnover, and induces apoptosis in cancer cells via deregulation of S-phase DNA synthesis. |
Enzymatic inhibition assay, cell-based assays, mouse xenograft models |
Nature |
High |
19360080
|
| 2009 |
UBE2F is a second NEDD8-conjugating E2 enzyme, distinct from UBE2M (UBC12). Structural and biochemical analyses show that UBE2M/RBX1 and UBE2F/RBX2 have distinct cullin substrate specificities, establishing hierarchical E2-E3 (RING) specificity in the NEDD8 conjugation cascade. |
In vitro NEDD8 conjugation assay, structural analysis (crystallography), biochemical specificity assays |
Molecular cell |
High |
19250909
|
| 2009 |
Poly-NEDD8 chain formation on Cullin-1 occurs via buildup on the catalytic Cys of Ubc12, and ROC1 is essential for transfer of the poly-NEDD8 chain from Ubc12 to Cul-1 (but not for chain formation itself). A ROC1 ubiquitin ligase-inactive mutant enhances poly-NEDD8 chain formation. |
In vitro reconstituted NEDD8 conjugation system with purified components, ROC1 mutant analysis |
Biochemical and biophysical research communications |
Medium |
19245792
|
| 2010 |
The bacterial effector CHBP (and the related Cif from EPEC) functions as a deamidase that specifically deamidates Gln40 in both ubiquitin and NEDD8 in vitro and during infection. Deamidation of NEDD8 at Gln40 abolishes the activity of neddylated cullin-RING ligases (CRLs), blocking ubiquitination and degradation of multiple CRL substrates. |
In vitro deamidation assay, infection experiments, ubiquitination assays, mass spectrometry |
Science (New York, N.Y.) |
High |
20688984
|
| 2010 |
The bacterial effector Cif targets NEDD8-conjugated cullins, co-localizing with NEDD8 in the host nucleus and inducing accumulation of neddylated cullins. Cif directly inhibits neddylated CUL1-associated ubiquitin ligase activity in an in vitro ubiquitylation assay, modulating turnover of multiple CRL substrates (including p21 and p27). |
Yeast two-hybrid, co-immunoprecipitation, in vitro ubiquitylation assay, cell infection |
PLoS pathogens |
High |
20941356
|
| 2011 |
Inhibition of NAE by siRNA or MLN4924 leads to CDT1 accumulation, which is the primary mediator of the DNA rereplication phenotype observed upon NAE inhibition. siRNA knockdown of cullins responsible for CDT1 turnover recapitulates rereplication, while CDT1 knockdown suppresses it. |
siRNA knockdown, cell cycle analysis, synchrony experiments |
Cancer research |
High |
21159650 21487042
|
| 2012 |
The ubiquitin E1 enzyme Ube1 (not the canonical NEDD8 E1) mediates NEDD8 conjugation under stress conditions (proteasome inhibition, heat shock, oxidative stress). This is triggered by depletion of free ubiquitin. Under stress, NEDDylated proteins are simultaneously ubiquitinated and mixed NEDD8-ubiquitin chains form. NEDD8 modification of p53 upon stress is mainly mediated through Ube1. |
Ube1 siRNA knockdown, mass spectrometry of NEDD8 proteome, immunoprecipitation, free ubiquitin depletion experiments |
Cell cycle (Georgetown, Tex.) |
Medium |
22370482
|
| 2012 |
The p97 cofactor UBXD7 (and its yeast ortholog Ubx5) selectively associates with the active, NEDD8-modified form of cullins through its ubiquitin-interacting motif (UIM), linking neddylated CRL activity to the p97 pathway for substrate extraction/degradation. Disruption of the UIM abolishes CRL binding and impedes degradation of a Cul3 substrate. |
Co-immunoprecipitation (selective for neddylated cullin), UIM mutation, yeast substrate degradation assay |
Nature structural & molecular biology |
High |
22466964
|
| 2012 |
Crystal structures of two Cif/NEDD8 complexes reveal the conserved molecular interface for enzyme-substrate recognition at Gln40 of NEDD8. Shape complementarity rather than specific individual contacts drives recognition. The 'occluding loop' in Cif forces a conformational change in the NEDD8 C-terminus to position Gln40 in the active site. |
X-ray crystallography of Cif/NEDD8 complexes, mutagenesis, native PAGE activity assay |
Proceedings of the National Academy of Sciences of the United States of America |
High |
22691497
|
| 2012 |
NAE inhibition by MLN4924 increases cellular sensitivity to DNA interstrand cross-linking agents by suppressing FANCD2 monoubiquitination and CHK1 phosphorylation, thereby inhibiting the Fanconi anemia DNA repair pathway. |
siRNA knockdown of NEDD8 conjugating enzymes, MLN4924 treatment, immunoblot for FANCD2 monoubiquitination and CHK1 phosphorylation |
Molecular cancer research : MCR |
Medium |
22219386
|
| 2014 |
The HECT E3 ubiquitin ligase Smurf1 is activated by neddylation. Smurf1 physically interacts with Nedd8 and Ubc12, forms a Nedd8-thioester intermediate, and catalyzes its own neddylation on multiple lysines via its active site Cys426. Neddylation of Smurf1 enhances ubiquitin E2 recruitment and augments Smurf1 ubiquitin ligase activity. This activation mechanism is conserved in yeast Rsp5. |
Co-immunoprecipitation, thioester intermediate assay, active-site mutant (C426A), neddylation assay, ubiquitin E2 recruitment assay |
Nature communications |
High |
24821572
|
| 2016 |
DCN-like (DCNL) proteins form stable stoichiometric complexes with CAND1 and cullins and function as NEDD8 E3 ligases that can only neddylate cullins in the presence of a substrate adaptor. Different DCNL proteins have distinct subcellular localizations, determining which subpopulation of a given cullin they neddylate. |
Biochemical complex purification, in vitro neddylation assay, subcellular localization experiments |
Journal of cell science |
Medium |
26906416
|
| 2017 |
SENP8/DEN1 deconjugates auto-neddylation of Ubc12 (the NEDD8 E2 conjugating enzyme). Loss of SENP8 leads to aberrant neddylation of Ubc12 and other NEDD8 conjugation pathway components, resulting in accumulation of CRL substrates and defective cell cycle progression. |
Deconjugation-resistant NEDD8 mutant, SENP8-deficient cells, identification of Ubc12 auto-neddylation, cell cycle analysis |
eLife |
High |
28475037
|
| 2017 |
Nedd8 modification of Cullin-5 following LPS exposure induces Cul-5 interaction with TRAF6, promoting TRAF6 polyubiquitination and NF-κB activation. Cul-5-deficient mice show reduced lung injury in response to LPS, linking NEDD8-dependent CRL activation to TLR4-TRAF6 inflammatory signaling. |
Cul-5 knockout mice, LPS challenge model, co-immunoprecipitation (neddylated Cul-5 with TRAF6), cytokine measurement |
American journal of physiology. Lung cellular and molecular physiology |
Medium |
28522566
|
| 2019 |
Upon DNA damage, the deneddylating enzyme NEDP1 is induced and restricts formation of NEDD8 chains (mainly K11/K48-linked). The resulting balance shift from poly- to mono-NEDDylation is sensed by HSP70, which binds NEDD8. In vitro, conversion of NEDD8 chains to mono-NEDD8 stimulates HSP70 ATPase activity, promoting APAF1 oligomerization and apoptosis induction. |
In vitro ATPase assay with NEDD8 chain vs. monomer, NEDP1 knockout/knockdown, APAF1 oligomerization assay |
Cell reports |
Medium |
31577950
|
| 2019 |
Unanchored trimeric NEDD8 (tri-NEDD8), which accumulates upon oxidative stress (H2O2) due to NEDP1 inhibition, specifically binds the second zinc finger domain of PARP-1 and attenuates PARP-1 activation. In NEDP1-deleted cells, constitutive tri-NEDD8 inhibits PARP-1 and protects from PARP-1-dependent cell death. The NEDD8 trimers are additionally acetylated, and de-acetylase overexpression reduces tri-NEDD8 binding to PARP-1. |
Pull-down with PARP-1 zinc finger domain, NEDP1 deletion, H2O2 treatment, mass spectrometry for acetylation, PARP-1 activity assay |
The EMBO journal |
High |
30804002
|
| 2020 |
Cryo-EM structure of the ubiquitylation intermediate reveals how neddylated CRL1β-TRCP catalyzes ubiquitin transfer from UBE2D to phosphorylated IκBα. NEDD8 acts as a nexus, binding disparate cullin elements and RING-activated ubiquitin-linked UBE2D. Local NEDD8 structural remodeling combined with large-scale CRL domain movements juxtapose substrate and active site, explaining how NEDD8 activates CRL ubiquitylation activity. |
Cryo-electron microscopy structure of chemically trapped ubiquitylation intermediate |
Nature |
High |
32051583
|
| 2021 |
NEDD8 can be phosphorylated at S65 (the same site as ubiquitin). S65 phosphorylation alters NEDD8's structural dynamics similarly to pUb. Both pNEDD8 and pUb can allosterically activate Parkin, but pNEDD8 has a distinct protein interactome including HSP70 family members. pNEDD8 stimulates HSP70 ATPase activity more strongly than unmodified NEDD8, independent of conjugation to other proteins. |
NMR structural analysis, in vitro Parkin activation assay, mass spectrometry interactome, HSP70 ATPase assay |
Nature communications |
High |
34642328
|
| 2021 |
CUL5-linked NEDD8 activates ARIH2 via an allosteric mechanism distinct from CUL1-linked NEDD8. While CUL1-linked NEDD8 directly recruits ARIH1, CUL5-linked NEDD8 does not bind ARIH2 directly; instead, it contacts CUL5 and induces conformational rearrangements that expose cryptic ARIH2-binding sites. This reveals cullin-specific allosteric regulation by NEDD8. |
Cryo-EM/X-ray structures of E3-E3 assemblies, biochemical binding and ubiquitylation assays |
Nature chemical biology |
High |
34518685
|
| 2021 |
Proteome-wide identification of 1,101 unique NEDDylation sites on 620 proteins using NEDD8 R74K mutant combined with anti-diGly antibodies reveals distinct proteomes for canonical (NEDD8-specific enzymes; targets include spliceosome/mRNA surveillance/DNA replication components) versus atypical (ubiquitin enzymes; targets include ribosome/proteasome) NEDDylation. Poly-NEDD8, hybrid NEDD8-ubiquitin, and NEDD8-SUMO-2 chains were identified; NEDD8-SUMO-2 chains are induced by proteotoxic stress via K11 NEDDylation of SUMO-2. |
NEDD8 R74K mutant, anti-diGly antibody enrichment, mass spectrometry, bioinformatics |
Cell reports |
High |
33472076
|