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P61078

- UB2D3_RAT

UniProt

P61078 - UB2D3_RAT

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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

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
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

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 Source: UniProtKB-KW
  2. plasma membrane Source: UniProtKB-KW
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_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

        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_006233336.2.
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:
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 .
PIRi S53358.
RefSeqi NP_112516.1. NM_031237.1.
XP_006233398.1. XM_006233336.2.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 87 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