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Information on EC 6.2.1.45 - E1 ubiquitin-activating enzyme

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EC Tree
     6 Ligases
         6.2 Forming carbon-sulfur bonds
             6.2.1 Acid-thiol ligases
                6.2.1.45 E1 ubiquitin-activating enzyme
IUBMB Comments
Catalyses the ATP-dependent activation of ubiquitin through the formation of a thioester bond between the C-terminal glycine of ubiquitin and the sulfhydryl side group of a cysteine residue in the E1 protein. The two-step reaction consists of the ATP-dependent formation of an E1-ubiquitin adenylate intermediate in which the C-terminal glycine of ubiquitin is bound to AMP via an acyl-phosphate linkage, then followed by the conversion to an E1-ubiquitin thioester bond via the cysteine residue on E1 in the second step.
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UNIPROT: Q9GZZ9
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Word Map
The enzyme appears in viruses and cellular organisms
Reaction Schemes
+
+
[E1 ubiquitin-activating enzyme]-L-cysteine
=
+
+
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
Synonyms
ubiquitin-conjugating enzyme, ube1l, ubiquitin-activating enzyme, ubiquitin-activating enzyme e1, ubiquitin-activating enzyme (e1), ubiquitin activating enzyme, sumo e1, e1 ubiquitin-activating enzyme, ubiquitin e1, ubiquitin activating enzyme e1, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
UBE1DC1A
isoform
UBE1DC1B
isoform
ubiquitin-activating enzyme 5
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ubiquitin-activating enzyme E1 domain-containing protein 1
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ubiquitin-activating enzyme E1-domain containing 1
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ubiquitin-like modifier-activating enzyme 5
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
show the reaction diagram
modeling of a cis-binding mechanism of UFM1 to UBA5, trans-binding mechanism of UFM1 transfer to the E2, UFC1, and UFM1-UBA5 adenylation domain interactions, overview. Although the active site Cys in the UBA5 apo structure is located at the N terminus of helix H, this Cys is no longer part of a helical structure in the complex with UFM1. Conformational changes in UBA5 are required to bring the active site Cys into the vicinity of UFM1-AMP mixed anhydride bond, leading to formation of the thioester bond
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
ubiquitin:[E1 ubiquitin-activating enzyme] ligase (AMP-forming)
Catalyses the ATP-dependent activation of ubiquitin through the formation of a thioester bond between the C-terminal glycine of ubiquitin and the sulfhydryl side group of a cysteine residue in the E1 protein. The two-step reaction consists of the ATP-dependent formation of an E1-ubiquitin adenylate intermediate in which the C-terminal glycine of ubiquitin is bound to AMP via an acyl-phosphate linkage, then followed by the conversion to an E1-ubiquitin thioester bond via the cysteine residue on E1 in the second step.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + SUMO2 + [ubiquitin-activating protein UBA5]-L-cysteine
AMP + diphosphate + [ubiquitin-activating protein UBA5]-S-SUMO2-L-cysteine
show the reaction diagram
SUMO2, small ubiquitin-like modifier2, an ubiquitin-like protein
enzyme greatly activates SUMO2 in the nucleus or transfers activated SUMO2 to the nucleus after it conjugated SUMO2 in the cytoplasm
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?
ATP + ubiquitin + SUMO2
?
show the reaction diagram
UBE1DC1 greatly activates SUMO2 in the nucleus or transfers activated-SUMO2 to nucleus after conjugation of SUMO2 in the cytoplasm
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-
?
ATP + ubiquitin + ubiquitin-fold modifier 1
?
show the reaction diagram
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-
-
?
ATP + ubiquitin + Ufm1
?
show the reaction diagram
-
-
-
?
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine
AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
show the reaction diagram
-
-
-
?
ATP + ubiquitin + [ubiquitin-activating enzyme Uba5]-L-cysteine
AMP + diphosphate + [ubiquitin-activating enzyme Uba5]-S-ubiquitinyl-L-cysteine
show the reaction diagram
the catalytic cysteine residue of isoform Uba5 is part of the adenylation domain in a alpha-helical motif
-
-
?
ATP + ubiquitin fold modifier1 + [ubiquitin-activating enzyme Uba5]-L-cysteine
AMP + diphosphate + [ubiquitin-activating enzyme Uba5]-S-(ubiquitin fold modifier1)-L-cysteine
show the reaction diagram
the catalytic cysteine residue of isoform Uba5 is part of the adenylation domain in a alpha-helical motif
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-
?
ATP + Ufm1 + [ubiquitin-activating protein UBA5]-L-cysteine
AMP + diphosphate + [ubiquitin-activating protein UBA5]-S-Ufm1-L-cysteine
show the reaction diagram
Ufm1, ubiquitin-fold modifier 1, an ubiquitin-like protein
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-
?
additional information
?
-
the non-canonical E1, UBA5, binds to the ubiquitin-like protein UFM1 using a trans-binding mechanism in which UFM1 interacts with distinct sites in both subunits of the UBA5 dimer. Mechanism of UFM1 activation by UBA5 and trans-binding mechanism of UFM1 transfer to the E2, UFC1. UFM1 contains a C-terminal Val-Gly dipeptide instead of the canonical Gly-Gly dipeptide present in ubiquitin and other ubiquitin-like proteins
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine
AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
required
Zinc
isoform UBA5 maintains a zinc-binding site that is coordinated by four cysteines with tetrahedral geometry
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
fetal brain
Manually annotated by BRENDA team
embryonic kidney
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
UBA5 is the smallest and structurally simplest E1. The active site Cys of UBA5 (Cys 250) is located within the adenylation domain, but this domain is not sufficient for the formation of a thioester bond between the UFM1 C terminus and the UBA5 catalytic Cys. Modeling of a cis-binding mechanism of UFM1 to UBA5. Trans-binding mechanism of UFM1 transfer to the E2, UFC1. Homodimerization of UBA5 is essential for activating UFM1
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
UBA5_HUMAN
404
0
44863
Swiss-Prot
-
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
homodimer
dimerization of UBA5 is required for UFM1 activation. The active site Cys of UBA5 (Cys 250) is located within the adenylation domain
monomer
analytical ultracentrifugation analysis, forms primarily dimers with 1.85:1 dimers to monomers ratio
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
enzyme exists in two splice variants. To obtain high resolution crystals of UBA5, the N-terminal region of the long isoform, residues 1–56, are deleted and residues 330–404 of the C-terminal domain are also removed. The removal of the CTD thus does not abrogate formation of the UBA5-UFM1 thioester intermediate. Crystals to 2.0 A resolution, and molecular replacement based on PDB structure 1ZFN. Structure shows similarities to both E1 and E1-like enzymes and is composed of an ATP-binding domain that consists of an eight-stranded beta-sheet surrounded by seven alpha-helices. UBA5 maintains a zinc-binding site that is coordinated by four cysteines with tetrahedral geometry
purified UBA5-UFM1 complex, containing both the adenylation domain and the UIS of UBA5, X-ray diffraction structure determination and analysis at 1.85-2.10 A
to 2.0 A resolution using molecular replacement based on PDB entry 1ZFN. UBA5 structure shows similarities to both E1 and E1-like enzymes and is composed of an ATP-binding domain that consists of an eight-stranded beta-sheet surrounded by seven alpha-helices. UBA5 maintains a zinc-binding site that is coordinated by four cysteines with tetrahedral geometry
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D290K/C250A
in this heterodimer, the UBA5 subunit that can form the thioester bond with UFM1 is missing the UFC1 binding site. In the UBA5 (D290K)-UBA5 (K271D/C250A DELTADUIS) heterodimer, binding to the UIS and charging can only take place on the same monomer, thereby supporting a cis-binding mechanism
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography
recombinant N-terminally His6-tagged enzyme UBA5 from Escherichia coli by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli Rosetta cells and in AD-293 cells
expression in BL-21 cell
recombinant expression of N-terminally His6-tagged enzyme UBA5 in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Zheng, M.; Gu, X.; Zheng, D.; Yang, Z.; Li, F.; Zhao, J.; Xie, Y.; Ji, C.; Mao, Y.
UBE1DC1, an ubiquitin-activating enzyme, activates two different ubiquitin-like proteins
J. Cell. Biochem.
104
2324-2334
2008
Homo sapiens (Q9GZZ9)
Manually annotated by BRENDA team
Bacik, J.P.; Walker, J.R.; Ali, M.; Schimmer, A.D.; Dhe-Paganon, S.
Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme
J. Biol. Chem.
285
20273-20280
2010
Homo sapiens (Q9GZZ9), Homo sapiens
Manually annotated by BRENDA team
Oweis, W.; Padala, P.; Hassouna, F.; Cohen-Kfir, E.; Gibbs, D.R.; Todd, E.A.; Berndsen, C.E.; Wiener, R.
Trans-binding mechanism of ubiquitin-like protein activation revealed by a UBA5-UFM1 complex
Cell Rep.
16
3113-3120
2016
Homo sapiens (Q9GZZ9)
Manually annotated by BRENDA team