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P61079

- UB2D3_MOUSE

UniProt

P61079 - UB2D3_MOUSE

Protein

Ubiquitin-conjugating enzyme E2 D3

Gene

Ube2d3

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. 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. acid-amino acid ligase activity Source: InterPro
    2. ATP binding Source: UniProtKB-KW
    3. protein binding Source: UniProtKB
    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: Ensembl
    7. protein polyubiquitination Source: UniProtKB

    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_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. plasma membrane Source: UniProtKB-SubCell

    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

    PRIDEiP61079.

    PTM databases

    PhosphoSiteiP61079.

    Expressioni

    Gene expression databases

    ArrayExpressiP61079.
    BgeeiP61079.
    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. 5 interactions.

    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.
    OMAiSAGPCED.
    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

    MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF    50
    FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDILR SQWSPALTIS 100
    KVLLSICSLL CDPNPDDPLV PEIARIYKTD RDKYNRISRE WTQKYAM 147
    Length:147
    Mass (Da):16,687
    Last modified:April 26, 2004 - v1
    Checksum:iADD74A8A708EFEE3
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    CCDSi CCDS38644.1.
    RefSeqi NP_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.
    UniGenei Mm.391601.
    Mm.471976.
    Mm.49884.

    3D structure databases

    ProteinModelPortali P61079.
    SMRi P61079. Positions 1-147.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 211216. 5 interactions.

    PTM databases

    PhosphoSitei P61079.

    Proteomic databases

    PRIDEi P61079.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000106291 ; ENSMUSP00000101898 ; ENSMUSG00000078578 .
    ENSMUST00000166033 ; ENSMUSP00000130096 ; ENSMUSG00000078578 .
    GeneIDi 66105.
    KEGGi mmu:66105.
    UCSCi uc008rln.1. mouse.

    Organism-specific databases

    CTDi 7323.
    MGIi MGI:1913355. Ube2d3.

    Phylogenomic databases

    HOGENOMi HOG000233455.
    HOVERGENi HBG063308.
    InParanoidi P61079.
    KOi K06689.
    OMAi SAGPCED.
    OrthoDBi EOG7PCJGX.
    PhylomeDBi P61079.
    TreeFami TF101108.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .
    Reactomei 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

    ChiTaRSi UBE2D3. mouse.
    NextBioi 320638.
    PROi P61079.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P61079.
    Bgeei P61079.
    Genevestigatori P61079.

    Family and domain databases

    Gene3Di 3.10.110.10. 1 hit.
    InterProi IPR000608. UBQ-conjugat_E2.
    IPR023313. UBQ-conjugating_AS.
    IPR016135. UBQ-conjugating_enzyme/RWD.
    [Graphical view ]
    Pfami PF00179. UQ_con. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54495. SSF54495. 1 hit.
    PROSITEi PS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
    PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 105 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