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Protein

Ubiquitin-conjugating enzyme E2 D3

Gene

Ube2d3

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2 CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination of NFKBIA leading to its subsequent proteasomal degradation. Acts as an initiator E2, priming the phosphorylated NFKBIA target at positions 'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain elongation is then performed by CDC34, building ubiquitin chains from the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator E2, in conjunction with RNF8, for the priming of PCNA. Monoubiquitination of PCNA, and its subsequent polyubiquitination, are essential events in the operation of the DNA damage tolerance (DDT) pathway that is activated after DNA damage caused by UV or chemical agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase complex to perform ubiquitination at DNA damage sites following ionizing radiation leading to DNA repair. Targets DAPK3 for ubiquitination which influences promyelocytic leukemia protein nuclear body (PML-NB) formation in the nucleus. In conjunction with the MDM2 and TOPORS E3 ligases, functions ubiquitination of p53/TP53. Supports NRDP1-mediated ubiquitination and degradation of ERBB3 and of BRUCE which triggers apoptosis. In conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination at the plasma membrane as well as during its internalization and transport on endosomes. In conjunction with the STUB1 E3 quality control E3 ligase, ubiquitinates unfolded proteins to catalyze their immediate destruction.By similarity

Catalytic activityi

S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine.PROSITE-ProRule annotationBy similarity
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N6-monoubiquitinyl-[acceptor protein]-L-lysine.By similarity

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.PROSITE-ProRule annotation
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei85Glycyl thioester intermediatePROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionTransferase
Biological processApoptosis, DNA damage, DNA repair, Ubl conjugation pathway
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-RNO-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-RNO-201451 Signaling by BMP
R-RNO-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-RNO-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-RNO-8951664 Neddylation
R-RNO-9033241 Peroxisomal protein import
R-RNO-983168 Antigen processing: Ubiquitination & Proteasome degradation
UniPathwayiUPA00143

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 D3 (EC:2.3.2.23)
Alternative name(s):
(E3-independent) E2 ubiquitin-conjugating enzyme D3 (EC:2.3.2.24)
E2 ubiquitin-conjugating enzyme D3
Phosphoarginine phosphatase
Short name:
PAPase
Ubiquitin carrier protein D3
Ubiquitin-conjugating enzyme E2(17)KB 3
Ubiquitin-conjugating enzyme E2-17 kDa 3
Ubiquitin-protein ligase D3
Gene namesi
Name:Ube2d3
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 2

Organism-specific databases

RGDi619912 Ube2d3

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell membrane, Endosome, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000824681 – 147Ubiquitin-conjugating enzyme E2 D3Add BLAST147

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi21 ↔ 107By similarity

Post-translational modificationi

Phosphorylated by AURKB.By similarity

Keywords - PTMi

Disulfide bond, Phosphoprotein

Proteomic databases

PaxDbiP61078
PeptideAtlasiP61078
PRIDEiP61078

PTM databases

iPTMnetiP61078
PhosphoSitePlusiP61078
SwissPalmiP61078

Expressioni

Gene expression databases

BgeeiENSRNOG00000013741
ExpressionAtlasiP61078 baseline and differential
GenevisibleiP61078 RN

Interactioni

Subunit structurei

Interacts with SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex; when Cullin is neddylated, the interaction between the E2 and the SCF complex is strengthened. Interacts with DAPK3. Interacts with BRCA1; the DNA damage checkpoint promotes the association with BRCA1 after ionizing radiation. Interacts non-covalently with ubiquitin. Interacts with E3 ubiquitin-protein ligase CBLC. Interacts with UBTD1 (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000060962

Structurei

3D structure databases

ProteinModelPortaliP61078
SMRiP61078
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ubiquitin-conjugating enzyme family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0417 Eukaryota
COG5078 LUCA
GeneTreeiENSGT00910000143990
HOGENOMiHOG000233455
HOVERGENiHBG063308
InParanoidiP61078
KOiK06689
OMAiLAQEWTT
OrthoDBiEOG091G0GF8
PhylomeDBiP61078

Family and domain databases

CDDicd00195 UBCc, 1 hit
Gene3Di3.10.110.10, 1 hit
InterProiView protein in InterPro
IPR000608 UBQ-conjugat_E2
IPR023313 UBQ-conjugating_AS
IPR016135 UBQ-conjugating_enzyme/RWD
PfamiView protein in Pfam
PF00179 UQ_con, 1 hit
SUPFAMiSSF54495 SSF54495, 1 hit
PROSITEiView protein in PROSITE
PS00183 UBIQUITIN_CONJUGAT_1, 1 hit
PS50127 UBIQUITIN_CONJUGAT_2, 1 hit

Sequencei

Sequence statusi: Complete.

P61078-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF
60 70 80 90 100
FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDILR SQWSPALTIS
110 120 130 140
KVLLSICSLL CDPNPDDPLV PEIARIYKTD RDKYNRISRE WTQKYAM
Length:147
Mass (Da):16,687
Last modified:April 26, 2004 - v1
Checksum:iADD74A8A708EFEE3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U13177 mRNA Translation: AAA85102.1
U13175 mRNA Translation: AAA85100.1
AB006852 mRNA Translation: BAA87330.1
BC072696 mRNA Translation: AAH72696.1
PIRiS53358
RefSeqiNP_112516.1, NM_031237.1
XP_006233398.1, XM_006233336.3
XP_006233399.1, XM_006233337.2
XP_006233400.1, XM_006233338.2
UniGeneiRn.2778

Genome annotation databases

EnsembliENSRNOT00000066204; ENSRNOP00000060962; ENSRNOG00000013741
GeneIDi81920
KEGGirno:81920

Similar proteinsi

Entry informationi

Entry nameiUB2D3_RAT
AccessioniPrimary (citable) accession number: P61078
Secondary accession number(s): P47986
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: April 26, 2004
Last modified: May 23, 2018
This is version 114 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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