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Information on EC 6.2.1.64 - E1 NEDD8-activating enzyme
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6.2.1.64 E1 NEDD8-activating enzymeIUBMB Comments
Some RING-type E3 ubiquitin transferase (EC 2.3.2.27) are not able to bind a substrate protein directly. Instead, they form complexes with a cullin scaffold protein and a substrate recognition module, which are known as CRL (Cullin-RING-Ligase) complexes. The cullin protein needs to be activated by the ubiquitin-like protein NEDD8 in a process known as neddylation. Like ubiquitin, the NEDD8 protein ends with two glycine residues. The E1 NEDD8-activating enzyme activates NEDD8 in an ATP-dependent reaction by forming a high-energy thioester intermediate between NEDD8 and one of its cysteine residues. The activated NEDD8 is subsequently transferred to a cysteine residue of EC 2.3.2.34, E2 NEDD8-conjugating enzyme, and is eventually conjugated to a lysine residue of specific substrates in the presence of the appropriate E3 transferase (EC 2.3.2.32, cullin-RING-type E3 NEDD8 transferase).
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Word Map
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
+
+
=
+
+
+
[NEDD8 protein]
+
[E1 NEDD8-activating enzyme]-L-cysteine
=
+
+
[E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Synonyms
nedd8-activating enzyme, app-bp1, nedd8 activating enzyme, appbp1-uba3, appbp1, nedd8 e1, nedd8 activating enzyme e1, e1 nedd8-activating enzyme, nedd8's e1, nedd8 e1 activating enzyme, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
APPBP1
APPBP1-UBA3 complex
NAE
NAE1
-
-
-
-
NEDD-activating enzyme E1
-
-
-
-
NEDD8 activating enzyme E1
NEDD8-activating enzyme
Uba3
Uba3
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
-
-
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SYSTEMATIC NAME
IUBMB Comments
[NEDD8 protein]:[E1 NEDD8-activating enzyme] ligase (AMP-forming)
Some RING-type E3 ubiquitin transferase (EC 2.3.2.27) are not able to bind a substrate protein directly. Instead, they form complexes with a cullin scaffold protein and a substrate recognition module, which are known as CRL (Cullin-RING-Ligase) complexes. The cullin protein needs to be activated by the ubiquitin-like protein NEDD8 in a process known as neddylation. Like ubiquitin, the NEDD8 protein ends with two glycine residues. The E1 NEDD8-activating enzyme activates NEDD8 in an ATP-dependent reaction by forming a high-energy thioester intermediate between NEDD8 and one of its cysteine residues. The activated NEDD8 is subsequently transferred to a cysteine residue of EC 2.3.2.34, E2 NEDD8-conjugating enzyme, and is eventually conjugated to a lysine residue of specific substrates in the presence of the appropriate E3 transferase (EC 2.3.2.32, cullin-RING-type E3 NEDD8 transferase).
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
-
-
-
-
r
ATP + ubiquitin + [ubiquitin-activating protein UBA1]-L-cysteine
AMP + diphosphate + [ubiquitin-activating protein UBA1]-S-ubiquitinyl-L-cysteine
-
-
-
?
ATP + ubiquitin + [ubiquitin-activating protein Uba3]-L-cysteine
AMP + diphosphate + [ubiquitin-activating protein Uba3]-S-ubiquitinyl-L-cysteine
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [UBC12]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
?
ATP + [NEDD8 protein] + [Ubc12]-L-cysteine
AMP + diphosphate + [Ubc12]-S-[NEDD8 protein]-yl-L-cysteine
ATP + [Ubc12]-L-Cys + [NEDD8 protein]
ADP + diphosphate + [Ubc12]-S-[NEDD8 protein]-yl-L-cysteine
Q13564; Q8TBC4
-
-
-
-
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
r
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Q8TBC4; Q13564
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Q13564; Q8TBC4
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
?
ATP + [NEDD8 protein] + [Ubc12]-L-cysteine
AMP + diphosphate + [Ubc12]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
?
ATP + [NEDD8 protein] + [Ubc12]-L-cysteine
AMP + diphosphate + [Ubc12]-S-[NEDD8 protein]-yl-L-cysteine
Q8TBC4; Q13564
-
-
-
?
additional information
?
-
-
first, the enzyme associates with the Ublp and catalyses adenylation of the carboxy terminus of the ubiquitin-like protein. Second, the enzyme forms a thioester between its catalytic cysteine and the ubiquitin-like protein. Next, the enzyme is loaded with a second ubiquitin-like protein molecule, adenylating the C terminus of this second ubiquitin-like protein while still carrying the first thioester-bound ubiquitin-like protein. Last, the enzyme binds E2 and promotes ubiquitin-like protein transfer to the catalytic cysteine of E2 enzyme
-
-
-
additional information
?
-
Q8TBC4; Q13564
NEDD8 activation requires only one of two E1 subunits, UBA3. The other subunit, APPBP1, only contributes by accelerating the activation reaction rate
-
-
-
additional information
?
-
-
the enzyme catalyzes NEDD8 activation by a multistep mechanism. In step 1, ATP and NEDD8 bind the enzyme to form a NEDD8-acyl adenylate intermediate and release diphosphate. In step 2, NEDD8-AMP reacts with the enzyme active-site thiol to form an enzyme-NEDD8 thioester (with high-energy bond). In step 3, a second ATP and NEDD8 bind the enzyme as in the first step to form a ternary complex containing two NEDD8 molecules bound to the enzyme. This enzyme form is competent for transfer of the thioester-bound NEDD8 to a pathway-specific E2 (primarily UBC12; step 4) and is required for the downstream functions of NEDD8 conjugation
-
-
-
additional information
?
-
-
the enzyme exhibits very low activity with ubiquitin, SUMO1, SUMO2, MAPLC3A, GABRAP, GATE-16, Ufm-1, FAT10 and ISG-15
-
-
-
additional information
?
-
-
proteins But1 and But2 proteins bind to the catalytic subunit Uba3
-
-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
-
-
-
-
r
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [UBC12]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
r
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Q8TBC4; Q13564
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Q13564; Q8TBC4
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
-
?
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine
AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0045
ATP
chimeric Ub1, pH not specified in the publication, temperature not specified in the publication
0.0054
ATP
mutant DELTA946, pH not specified in the publication, temperature not specified in the publication
0.0055
ATP
wild-type, pH not specified in the publication, temperature not specified in the publication
0.02
ATP
mutant DELTA348, pH not specified in the publication, temperature not specified in the publication
0.02
ATP
mutant enzyme I310N, pH and temperature not specified in the publication
0.027
ATP
mutant enzyme Y352H, pH and temperature not specified in the publication
0.08
ATP
wild type enzyme, pH and temperature not specified in the publication
0.103
ATP
wild-type, pH not specified in the publication, temperature not specified in the publication
0.005
diphosphate
wild type enzyme, pH and temperature not specified in the publication
0.0109
diphosphate
mutant enzyme Y352H, pH and temperature not specified in the publication
0.0511
diphosphate
mutant enzyme I310N, pH and temperature not specified in the publication
0.0006
ubiquitin
mutant DELTA946, pH not specified in the publication, temperature not specified in the publication
0.0008
ubiquitin
wild-type, pH not specified in the publication, temperature not specified in the publication
0.0012
ubiquitin
chimeric Ub1, pH not specified in the publication, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000075
ATP
chimeric Ub1, pH not specified in the publication, temperature not specified in the publication
0.00013
ATP
mutant DELTA946, pH not specified in the publication, temperature not specified in the publication
3.1
ATP
mutant DELTA348, pH not specified in the publication, temperature not specified in the publication
3.4
ATP
wild-type, pH not specified in the publication, temperature not specified in the publication
3.5
ATP
wild-type, pH not specified in the publication, temperature not specified in the publication
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
-
when neddylation is blocked by the enzyme inhibitor MLN4924, the cellular and organismal antiviral response is suppressed. enzyme gene disruption increases the sensitivity of zebrafish to spring viremia of carp virus infection
metabolism
-
APPBP1 and UBA3 are homologous to the amino and carboxyl regions of the ubiquitin-activating enzyme, respectively. APPBP1-UBA3 first catalyzes the adenylation of C-terminal Gly76 of NEDD8 in the presence of Mg2+ and ATP and subsequently forms a thioester intermediate between its catalytic cysteine (Cys216 on UBA3) and the C terminus of NEDD8. The APPBP1-UBA3 complex ultimately binds the E2 of NEDD8, Ubc12, and promotes the transfer of NEDD8 onto the catalytic cysteine of Ubc12
Show AA Sequence and Transmembrane Helices (4501 entries)
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
heterodimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPBP1-UBA3 complex bound to NEDD8 mutant A72Q, hanging drop vapor diffusion method, using 0.1 M Tris, 0.4 M ammonium acetate, 9-10% (w/v) PEG 10K, 5 mM dithiothreitol, pH 7.0-8.0
Q13564; Q8TBC4
quaternary complex between human APPBP1-UBA3, a heterodimeric E1, NEDD8 and ATP, hanging drop vapor diffusion method, using 10.5-10.7% (w/v) PEG 10k, 0.1 M Tris, 0.4 M NaCl, 10% (w/v) PEG400, 5 mM dithiothreitol (pH 8.0-8.5)
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
DELTA946
I310N
the mutations in the catalytic subunit UBA3 increases the enzyme's affinity for ATP while decreasing its affinity for NEDD8. This mutation effectively contributes to decreased MLN4924 potency in vitro while providing for sufficient enzyme function for leukemia cell survival
Y352H
the mutations in the catalytic subunit UBA3 increases the enzyme's affinity for ATP while decreasing its affinity for NEDD8. This mutation effectively contributes to decreased MLN4924 potency in vitro while providing for sufficient enzyme function for leukemia cell survival
additional information
DELTA946
truncation of the Uba1 carboxyl-terminal beta-grasp domain reduces cognate Ubc2b binding by 31-fold and kcat by 33500-fold
DELTA946
truncation of the Uba3 carboxyl-terminal beta-grasp domain, no effect on cognate Ubc12 thiolester formation
additional information
generation of a chimeric Ub1 isoform carrying the beta-grasp domain of Uba3. Ternary complex stoichiometries for wild type and chimeric Uba1 are identical showing that the beta-grasp domain is not required in the Uba1 catalytic cycle
additional information
generation of a chimeric Ub1 isoform carrying the beta-grasp domain of Uba3. Ternary complex stoichiometries for wild type and chimeric Uba1 are identical showing that the beta-grasp domain is not required in the Uba1 catalytic cycle
additional information
-
generation of a chimeric Ub1 isoform carrying the beta-grasp domain of Uba3. Ternary complex stoichiometries for wild type and chimeric Uba1 are identical showing that the beta-grasp domain is not required in the Uba1 catalytic cycle
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
glutathione affinity chromatography, and anion exchange chromatography and gel filtration
-
HisTrap column chromatography, HiTrap Q column chromatography and Superdex 75 gel filtration
-
Ni Sepharose 6 column chromatography and Talon affinity resin column chromatography, and glutathione Sepharose 4 column chromatography
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Tokgoez, Z.; Siepmann, T.J.; Streich, F.; Kumar, B.; Klein, J.M.; Haas, A.L.
E1-E2 interactions in ubiquitin and Nedd8 ligation pathways
J. Biol. Chem.
287
311-321
2012
Homo sapiens (P22314), Homo sapiens (Q8TBC4), Homo sapiens
brenda
Bruzzese, F.J.; Tsu, C.A.; Ma, J.; Loke, H.K.; Wu, D.; Li, Z.; Tayber, O.; Dick, L.R.
Development of a charcoal paper adenosine triphosphate pyrophosphate exchange assay kinetic characterization of NEDD8 activating enzyme
Anal. Biochem.
394
24-29
2009
Homo sapiens
brenda
Yashiroda, H.; Tanaka, K.
But1 and But2 proteins bind to Uba3, a catalytic subunit of E1 for neddylation, in fission yeast
Biochem. Biophys. Res. Commun.
311
691-695
2003
Schizosaccharomyces pombe
brenda
Ohki, Y.; Funatsu, N.; Konishi, N.; Chiba, T.
The mechanism of poly-NEDD8 chain formation in vitro
Biochem. Biophys. Res. Commun.
381
443-447
2009
Mus musculus
brenda
Souphron, J.; Waddell, M.; Paydar, A.; Tokgoez-Gromley, Z.; Martine F Roussel, O.; Schulman, B.
Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8s E1
Biochemistry
47
8961-8969
2008
Homo sapiens (Q13564 and Q8TBC4)
brenda
Muraoka, H.; Yoshimura, C.; Kawabata, R.; Tsuji, S.; Hashimoto, A.; Ochiiwa, H.; Nakagawa, F.; Fujioka, Y.; Matsuo, K.; Ohkubo, S.
Activity of TAS4464, a novel NEDD8 activating enzyme E1 inhibitor, against multiple myeloma via inactivation of nuclear factor ?B pathways
Cancer Sci.
110
3802-3810
2019
Homo sapiens
brenda
Yang, X.; Brownell, J.E.; Xu, Q.; Zhu, F.; Ma, J.; Loke, H.K.; Rollins, N.; Soucy, T.A.; Minissale, J.J.; Thomas, M.P.; Mallender, W.D.; Dick, L.R.; Li, P.; Liao, H.
Absolute quantification of E1, ubiquitin-like proteins and Nedd8-MLN4924 adduct by mass spectrometry
Cell Biochem. Biophys.
67
139-147
2013
Homo sapiens
brenda
Yu, G.; Liu, X.; Tang, J.; Xu, C.; Ouyang, G.; Xiao, W.
Neddylation facilitates the antiviral response in zebrafish
Front. Immunol.
10
1432
2019
Danio rerio
brenda
Osaka, F.; Kawasaki, H.; Aida, N.; Saeki, M.; Chiba, T.; Kawashima, S.; Tanaka, K.; Kato, S.
A new NEDD8-ligating system for cullin-4A
Genes Dev.
12
2263-2268
1998
Homo sapiens
brenda
Gong, L.; Yeh, E.
Identification of the activating and conjugating enzymes of the NEDD8 conjugation pathway
J. Biol. Chem.
274
12036-12042
1999
Saccharomyces cerevisiae (Q99344), Saccharomyces cerevisiae
brenda
Huang, D.; Schulman, B.
Expression, purification, and characterization of the E1 for human NEDD8, the heterodimeric APPBP1-UBA3 complex
Methods Enzymol.
398
9-20
2005
Homo sapiens
brenda
Bruzzese, F.J.; Milhollen, M.A.; Gavin, J.M.; Josephine, H.R.; Brownell, J.E.
Identification and application of NEDD8 E1 inhibitors
Methods Mol. Biol.
832
577-588
2012
Homo sapiens
brenda
Walden, H.; Podgorski, M.; Huang, D.; Miller, D.; Howard, R.; Minor Jr., D.; Holton, J.; Schulman, B.
The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1
Mol. Cell.
12
1427-1437
2003
Homo sapiens
brenda
Walden, H.; Podgorski, M.; Schulman, B.
Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8
Nature
422
330-334
2003
Homo sapiens
brenda
Xu, G.W.; Toth, J.I.; da Silva, S.R.; Paiva, S.L.; Lukkarila, J.L.; Hurren, R.; Maclean, N.; Sukhai, M.A.; Bhattacharjee, R.N.; Goard, C.A.; Medeiros, B.; Gunning, P.T.; Dhe-Paganon, S.; Petroski, M.D.; Schimmer, A.D.
Mutations in UBA3 confer resistance to the NEDD8-activating enzyme inhibitor MLN4924 in human leukemic cells
PLoS ONE
9
e93530
2014
Homo sapiens (Q8TBC4), Homo sapiens
brenda
Malik-Chaudhry, H.; Gaieb, Z.; Saavedra, A.; Reyes, M.; Kung, R.; Le, F.; Morikis, D.; Liao, J.
Dissecting distinct roles of NEDDylation E1 ligase heterodimer APPBP1 and UBA3 reveals potential evolution process for activation of ubiquitin-related pathways
Sci. Rep.
8
10108
2018
Homo sapiens (Q8TBC4 and Q13564)
brenda
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