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P61078

- UB2D3_RAT

UniProt

P61078 - UB2D3_RAT

Protein

Ubiquitin-conjugating enzyme E2 D3

Gene

Ube2d3

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript 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. 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 polyubiquitination Source: UniProtKB
    7. ubiquitin-dependent protein catabolic process Source: RGD

    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

    UniPathwayiUPA00143.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin-conjugating enzyme E2 D3 (EC:6.3.2.19)
    Alternative name(s):
    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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Unplaced

    Organism-specific databases

    RGDi619912. 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_0000082468Add
    BLAST

    Amino acid modifications

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

    Post-translational modificationi

    Phosphorylated by AURKB.By similarity

    Keywords - PTMi

    Disulfide bond, Phosphoprotein

    Proteomic databases

    PRIDEiP61078.

    PTM databases

    PhosphoSiteiP61078.

    Expressioni

    Gene expression databases

    GenevestigatoriP61078.

    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 By similarity.By similarity

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000045087.

    Structurei

    3D structure databases

    ProteinModelPortaliP61078.
    SMRiP61078. Positions 1-147.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    HOGENOMiHOG000233455.
    HOVERGENiHBG063308.
    InParanoidiP61078.
    KOiK06689.
    PhylomeDBiP61078.

    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.

    P61078-1 [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
    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_006233336.1.
    XP_006233399.1. XM_006233337.1.
    XP_006233400.1. XM_006233338.1.
    UniGeneiRn.2778.

    Genome annotation databases

    GeneIDi81920.
    KEGGirno:81920.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U13177 mRNA. Translation: AAA85102.1 .
    U13175 mRNA. Translation: AAA85100.1 .
    AB006852 mRNA. Translation: BAA87330.1 .
    BC072696 mRNA. Translation: AAH72696.1 .
    PIRi S53358.
    RefSeqi NP_112516.1. NM_031237.1.
    XP_006233398.1. XM_006233336.1.
    XP_006233399.1. XM_006233337.1.
    XP_006233400.1. XM_006233338.1.
    UniGenei Rn.2778.

    3D structure databases

    ProteinModelPortali P61078.
    SMRi P61078. Positions 1-147.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10116.ENSRNOP00000045087.

    PTM databases

    PhosphoSitei P61078.

    Proteomic databases

    PRIDEi P61078.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 81920.
    KEGGi rno:81920.

    Organism-specific databases

    CTDi 7323.
    RGDi 619912. Ube2d3.

    Phylogenomic databases

    HOGENOMi HOG000233455.
    HOVERGENi HBG063308.
    InParanoidi P61078.
    KOi K06689.
    PhylomeDBi P61078.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .

    Miscellaneous databases

    NextBioi 28636.

    Gene expression databases

    Genevestigatori P61078.

    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. "Molecular cloning, expression and characterization of a ubiquitin conjugation enzyme (E2(17)kB) highly expressed in rat testis."
      Wing S.S., Jain P.
      Biochem. J. 305:125-132(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Tissue: Testis.
    2. "Nomega-phosphoarginine phosphatase activity of ubiquitin-conjugating enzymes type UBC4A/10A and UBC2E."
      Yokoi F., Hamato N., Kamei K., Hara S., Miyagi M., Tsunasawa S., Hiraishi H., Kumon A.
      Res. Commun. Biochem. Cell Mol. Biol. 2:331-346(1998)
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: Sprague-Dawley.
      Tissue: Liver.
    3. "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].
      Tissue: Heart.

    Entry informationi

    Entry nameiUB2D3_RAT
    AccessioniPrimary (citable) accession number: P61078
    Secondary accession number(s): P47986
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 26, 2004
    Last sequence update: April 26, 2004
    Last modified: October 1, 2014
    This is version 86 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3