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Protein

Ubiquitin-conjugating enzyme E2 D3

Gene

Ube2d3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein 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).By similarity

Catalytic activityi

ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.PROSITE-ProRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei85 – 851Glycyl thioester intermediatePROSITE-ProRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ligase activity Source: UniProtKB-KW
  3. ubiquitin conjugating enzyme activity Source: MGI
  4. ubiquitin-protein transferase activity Source: UniProtKB

GO - Biological processi

  1. apoptotic process Source: UniProtKB-KW
  2. DNA repair Source: UniProtKB-KW
  3. proteasome-mediated ubiquitin-dependent protein catabolic process Source: UniProtKB
  4. protein K11-linked ubiquitination Source: UniProtKB
  5. protein K48-linked ubiquitination Source: UniProtKB
  6. protein monoubiquitination Source: MGI
  7. protein polyubiquitination Source: UniProtKB
  8. protein ubiquitination Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Apoptosis, DNA damage, DNA repair, Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiREACT_198532. Negative regulators of RIG-I/MDA5 signaling.
REACT_199108. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
REACT_220505. Signaling by BMP.
REACT_220566. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_226192. IKK complex recruitment mediated by RIP1.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 D3 (EC:6.3.2.19)
Alternative name(s):
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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 3

Organism-specific databases

MGIiMGI:1913355. Ube2d3.

Subcellular locationi

Cell membrane By similarity; Peripheral membrane protein By similarity. Endosome membrane By similarity; Peripheral membrane protein By similarity

GO - Cellular componenti

  1. endosome membrane Source: UniProtKB-SubCell
  2. extracellular vesicular exosome Source: MGI
  3. plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Endosome, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 147147Ubiquitin-conjugating enzyme E2 D3PRO_0000082467Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi21 ↔ 107By similarity

Post-translational modificationi

Phosphorylated by AURKB.1 Publication

Keywords - PTMi

Disulfide bond, Phosphoprotein

Proteomic databases

MaxQBiP61079.
PRIDEiP61079.

PTM databases

PhosphoSiteiP61079.

Expressioni

Gene expression databases

BgeeiP61079.
ExpressionAtlasiP61079. baseline and differential.
GenevestigatoriP61079.

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.1 Publication

Protein-protein interaction databases

BioGridi211216. 6 interactions.
IntActiP61079. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliP61079.
SMRiP61079. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000233455.
HOVERGENiHBG063308.
InParanoidiP61079.
KOiK06689.
OMAiMATKRIN.
OrthoDBiEOG7PCJGX.
PhylomeDBiP61079.
TreeFamiTF101108.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P61079-1 [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
AK004001 mRNA. Translation: BAB23116.1.
AK032885 mRNA. Translation: BAC28070.1.
AK049906 mRNA. Translation: BAC33981.1.
AK077666 mRNA. Translation: BAC36940.1.
AK088448 mRNA. Translation: BAC40357.1.
BC057941 mRNA. Translation: AAH57941.1.
CCDSiCCDS38644.1.
RefSeqiNP_079632.1. NM_025356.4.
XP_006501936.1. XM_006501873.1.
XP_006501937.1. XM_006501874.1.
XP_006501938.1. XM_006501875.1.
XP_006501939.1. XM_006501876.1.
UniGeneiMm.391601.
Mm.471976.
Mm.49884.

Genome annotation databases

EnsembliENSMUST00000106291; ENSMUSP00000101898; ENSMUSG00000078578.
ENSMUST00000166033; ENSMUSP00000130096; ENSMUSG00000078578.
GeneIDi66105.
KEGGimmu:66105.
UCSCiuc008rln.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK004001 mRNA. Translation: BAB23116.1.
AK032885 mRNA. Translation: BAC28070.1.
AK049906 mRNA. Translation: BAC33981.1.
AK077666 mRNA. Translation: BAC36940.1.
AK088448 mRNA. Translation: BAC40357.1.
BC057941 mRNA. Translation: AAH57941.1.
CCDSiCCDS38644.1.
RefSeqiNP_079632.1. NM_025356.4.
XP_006501936.1. XM_006501873.1.
XP_006501937.1. XM_006501874.1.
XP_006501938.1. XM_006501875.1.
XP_006501939.1. XM_006501876.1.
UniGeneiMm.391601.
Mm.471976.
Mm.49884.

3D structure databases

ProteinModelPortaliP61079.
SMRiP61079. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi211216. 6 interactions.
IntActiP61079. 1 interaction.

PTM databases

PhosphoSiteiP61079.

Proteomic databases

MaxQBiP61079.
PRIDEiP61079.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000106291; ENSMUSP00000101898; ENSMUSG00000078578.
ENSMUST00000166033; ENSMUSP00000130096; ENSMUSG00000078578.
GeneIDi66105.
KEGGimmu:66105.
UCSCiuc008rln.1. mouse.

Organism-specific databases

CTDi7323.
MGIiMGI:1913355. Ube2d3.

Phylogenomic databases

HOGENOMiHOG000233455.
HOVERGENiHBG063308.
InParanoidiP61079.
KOiK06689.
OMAiMATKRIN.
OrthoDBiEOG7PCJGX.
PhylomeDBiP61079.
TreeFamiTF101108.

Enzyme and pathway databases

UniPathwayiUPA00143.
ReactomeiREACT_198532. Negative regulators of RIG-I/MDA5 signaling.
REACT_199108. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
REACT_220505. Signaling by BMP.
REACT_220566. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_226192. IKK complex recruitment mediated by RIP1.

Miscellaneous databases

ChiTaRSiUbe2d3. mouse.
NextBioi320638.
PROiP61079.
SOURCEiSearch...

Gene expression databases

BgeeiP61079.
ExpressionAtlasiP61079. baseline and differential.
GenevestigatoriP61079.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J and NOD.
    Tissue: Hippocampus and Thymus.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Mammary tumor.
  3. Cited for: INTERACTION WITH DAPK3.
  4. "The Aurora B kinase and the Polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes."
    Frangini A., Sjoberg M., Roman-Trufero M., Dharmalingam G., Haberle V., Bartke T., Lenhard B., Malumbres M., Vidal M., Dillon N.
    Mol. Cell 51:647-661(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION.

Entry informationi

Entry nameiUB2D3_MOUSE
AccessioniPrimary (citable) accession number: P61079
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: April 26, 2004
Last modified: March 4, 2015
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.