ID   UB2D3_RAT               Reviewed;         147 AA.
AC   P61078; P47986;
DT   26-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT   26-APR-2004, sequence version 1.
DT   27-MAR-2024, entry version 143.
DE   RecName: Full=Ubiquitin-conjugating enzyme E2 D3;
DE            EC=2.3.2.23;
DE   AltName: Full=(E3-independent) E2 ubiquitin-conjugating enzyme D3;
DE            EC=2.3.2.24;
DE   AltName: Full=E2 ubiquitin-conjugating enzyme D3;
DE   AltName: Full=Phosphoarginine phosphatase;
DE            Short=PAPase;
DE   AltName: Full=Ubiquitin carrier protein D3;
DE   AltName: Full=Ubiquitin-conjugating enzyme E2(17)KB 3;
DE   AltName: Full=Ubiquitin-conjugating enzyme E2-17 kDa 3;
DE   AltName: Full=Ubiquitin-protein ligase D3;
GN   Name=Ube2d3;
OS   Rattus norvegicus (Rat).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   TISSUE=Testis;
RX   PubMed=7826319; DOI=10.1042/bj3050125;
RA   Wing S.S., Jain P.;
RT   "Molecular cloning, expression and characterization of a ubiquitin
RT   conjugation enzyme (E2(17)kB) highly expressed in rat testis.";
RL   Biochem. J. 305:125-132(1995).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=Sprague-Dawley; TISSUE=Liver;
RA   Yokoi F., Hamato N., Kamei K., Hara S., Miyagi M., Tsunasawa S.,
RA   Hiraishi H., Kumon A.;
RT   "Nomega-phosphoarginine phosphatase activity of ubiquitin-conjugating
RT   enzymes type UBC4A/10A and UBC2E.";
RL   Res. Commun. Biochem. Cell Mol. Biol. 2:331-346(1998).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Heart;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
CC   -!- FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its
CC       covalent attachment to other proteins. In vitro catalyzes 'Lys-11'-, as
CC       well as 'Lys-48'-linked polyubiquitination. Cooperates with the E2
CC       CDC34 and the SCF(FBXW11) E3 ligase complex for the polyubiquitination
CC       of NFKBIA leading to its subsequent proteasomal degradation. Acts as an
CC       initiator E2, priming the phosphorylated NFKBIA target at positions
CC       'Lys-21' and/or 'Lys-22' with a monoubiquitin. Ubiquitin chain
CC       elongation is then performed by CDC34, building ubiquitin chains from
CC       the UBE2D3-primed NFKBIA-linked ubiquitin. Acts also as an initiator
CC       E2, in conjunction with RNF8, for the priming of PCNA.
CC       Monoubiquitination of PCNA, and its subsequent polyubiquitination, are
CC       essential events in the operation of the DNA damage tolerance (DDT)
CC       pathway that is activated after DNA damage caused by UV or chemical
CC       agents during S-phase. Associates with the BRCA1/BARD1 E3 ligase
CC       complex to perform ubiquitination at DNA damage sites following
CC       ionizing radiation leading to DNA repair. Targets DAPK3 for
CC       ubiquitination which influences promyelocytic leukemia protein nuclear
CC       body (PML-NB) formation in the nucleus. In conjunction with the MDM2
CC       and TOPORS E3 ligases, functions ubiquitination of p53/TP53. In
CC       conjunction with the CBL E3 ligase, targets EGFR for polyubiquitination
CC       at the plasma membrane as well as during its internalization and
CC       transport on endosomes. In conjunction with the STUB1 E3 quality
CC       control E3 ligase, ubiquitinates unfolded proteins to catalyze their
CC       immediate destruction. Together with RNF135, catalyzes the viral RNA-
CC       dependent 'Lys-63'-linked polyubiquitination of RIGI to activate the
CC       downstream signaling pathway that leads to interferon beta production.
CC       Together with ZNF598, catalyzes ubiquitination of 40S ribosomal
CC       proteins in response to ribosome collisions. In cooperation with the
CC       GATOR2 complex, catalyzes 'Lys-6'-linked ubiquitination of NPRL2.
CC       {ECO:0000250|UniProtKB:P61077}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine +
CC         [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-
CC         activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-
CC         conjugating enzyme]-L-cysteine.; EC=2.3.2.23;
CC         Evidence={ECO:0000250|UniProtKB:P61077, ECO:0000255|PROSITE-
CC         ProRule:PRU00388, ECO:0000255|PROSITE-ProRule:PRU10133};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine +
CC         [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-
CC         cysteine + N(6)-monoubiquitinyl-[acceptor protein]-L-lysine.;
CC         EC=2.3.2.24; Evidence={ECO:0000250|UniProtKB:P61077};
CC   -!- PATHWAY: Protein modification; protein ubiquitination.
CC       {ECO:0000255|PROSITE-ProRule:PRU00388}.
CC   -!- SUBUNIT: Interacts with SCF (SKP1-CUL1-F-box protein) E3 ubiquitin
CC       ligase complex; when Cullin is neddylated, the interaction between the
CC       E2 and the SCF complex is strengthened. Interacts with DAPK3. Interacts
CC       with BRCA1; the DNA damage checkpoint promotes the association with
CC       BRCA1 after ionizing radiation. Interacts non-covalently with
CC       ubiquitin. Interacts with E3 ubiquitin-protein ligase CBLC. Interacts
CC       with UBTD1 (By similarity). Interacts with RIGI and RNF135; involved in
CC       RIGI ubiquitination and activation (By similarity).
CC       {ECO:0000250|UniProtKB:P61077}.
CC   -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000250|UniProtKB:P61077};
CC       Peripheral membrane protein {ECO:0000250|UniProtKB:P61077}. Endosome
CC       membrane {ECO:0000250|UniProtKB:P61077}; Peripheral membrane protein
CC       {ECO:0000250|UniProtKB:P61077}.
CC   -!- PTM: Phosphorylated by AURKB. {ECO:0000250|UniProtKB:P61079}.
CC   -!- SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.
CC       {ECO:0000255|PROSITE-ProRule:PRU00388}.
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DR   EMBL; U13177; AAA85102.1; -; mRNA.
DR   EMBL; U13175; AAA85100.1; -; mRNA.
DR   EMBL; AB006852; BAA87330.1; -; mRNA.
DR   EMBL; BC072696; AAH72696.1; -; mRNA.
DR   PIR; S53358; S53358.
DR   RefSeq; NP_112516.1; NM_031237.1.
DR   RefSeq; XP_006233398.1; XM_006233336.3.
DR   RefSeq; XP_006233399.1; XM_006233337.2.
DR   RefSeq; XP_006233400.1; XM_006233338.2.
DR   AlphaFoldDB; P61078; -.
DR   BMRB; P61078; -.
DR   SMR; P61078; -.
DR   STRING; 10116.ENSRNOP00000060962; -.
DR   iPTMnet; P61078; -.
DR   PhosphoSitePlus; P61078; -.
DR   SwissPalm; P61078; -.
DR   jPOST; P61078; -.
DR   PaxDb; 10116-ENSRNOP00000060962; -.
DR   PeptideAtlas; P61078; -.
DR   Ensembl; ENSRNOT00000066204.4; ENSRNOP00000060962.3; ENSRNOG00000013741.8.
DR   Ensembl; ENSRNOT00055019116; ENSRNOP00055015402; ENSRNOG00055011277.
DR   Ensembl; ENSRNOT00060037241; ENSRNOP00060030728; ENSRNOG00060021415.
DR   Ensembl; ENSRNOT00065043315; ENSRNOP00065035511; ENSRNOG00065025147.
DR   GeneID; 81920; -.
DR   KEGG; rno:81920; -.
DR   AGR; RGD:619912; -.
DR   CTD; 7323; -.
DR   RGD; 619912; Ube2d3.
DR   eggNOG; KOG0417; Eukaryota.
DR   GeneTree; ENSGT00940000153169; -.
DR   HOGENOM; CLU_030988_13_3_1; -.
DR   InParanoid; P61078; -.
DR   OrthoDB; 5478564at2759; -.
DR   PhylomeDB; P61078; -.
DR   Reactome; R-RNO-1234176; Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
DR   Reactome; R-RNO-201451; Signaling by BMP.
DR   Reactome; R-RNO-2173795; Downregulation of SMAD2/3:SMAD4 transcriptional activity.
DR   Reactome; R-RNO-5357905; Regulation of TNFR1 signaling.
DR   Reactome; R-RNO-8866654; E3 ubiquitin ligases ubiquitinate target proteins.
DR   Reactome; R-RNO-8951664; Neddylation.
DR   Reactome; R-RNO-9033241; Peroxisomal protein import.
DR   Reactome; R-RNO-9705462; Inactivation of CSF3 (G-CSF) signaling.
DR   Reactome; R-RNO-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR   UniPathway; UPA00143; -.
DR   PRO; PR:P61078; -.
DR   Proteomes; UP000002494; Chromosome 2.
DR   Bgee; ENSRNOG00000013741; Expressed in thymus and 20 other cell types or tissues.
DR   ExpressionAtlas; P61078; baseline and differential.
DR   GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0000151; C:ubiquitin ligase complex; IBA:GO_Central.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0061631; F:ubiquitin conjugating enzyme activity; ISS:UniProtKB.
DR   GO; GO:0061630; F:ubiquitin protein ligase activity; ISO:RGD.
DR   GO; GO:0031625; F:ubiquitin protein ligase binding; IBA:GO_Central.
DR   GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:RGD.
DR   GO; GO:0006915; P:apoptotic process; IEA:UniProtKB-KW.
DR   GO; GO:0071276; P:cellular response to cadmium ion; IEP:RGD.
DR   GO; GO:0071288; P:cellular response to mercury ion; IEP:RGD.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
DR   GO; GO:0051865; P:protein autoubiquitination; ISO:RGD.
DR   GO; GO:0070979; P:protein K11-linked ubiquitination; ISS:UniProtKB.
DR   GO; GO:0070936; P:protein K48-linked ubiquitination; ISS:UniProtKB.
DR   GO; GO:0085020; P:protein K6-linked ubiquitination; ISS:UniProtKB.
DR   GO; GO:0006513; P:protein monoubiquitination; ISO:RGD.
DR   GO; GO:0000209; P:protein polyubiquitination; ISS:UniProtKB.
DR   GO; GO:0016567; P:protein ubiquitination; ISO:RGD.
DR   GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IDA:RGD.
DR   CDD; cd00195; UBCc; 1.
DR   Gene3D; 3.10.110.10; Ubiquitin Conjugating Enzyme; 1.
DR   InterPro; IPR000608; UBQ-conjugat_E2.
DR   InterPro; IPR023313; UBQ-conjugating_AS.
DR   InterPro; IPR016135; UBQ-conjugating_enzyme/RWD.
DR   PANTHER; PTHR24068; UBIQUITIN-CONJUGATING ENZYME E2; 1.
DR   PANTHER; PTHR24068:SF415; UBIQUITIN-CONJUGATING ENZYME E2 D3; 1.
DR   Pfam; PF00179; UQ_con; 1.
DR   SMART; SM00212; UBCc; 1.
DR   SUPFAM; SSF54495; UBC-like; 1.
DR   PROSITE; PS00183; UBC_1; 1.
DR   PROSITE; PS50127; UBC_2; 1.
DR   Genevisible; P61078; RN.
PE   2: Evidence at transcript level;
KW   Apoptosis; ATP-binding; Cell membrane; Disulfide bond; DNA damage;
KW   DNA repair; Endosome; Membrane; Nucleotide-binding; Phosphoprotein;
KW   Reference proteome; Transferase; Ubl conjugation pathway.
FT   CHAIN           1..147
FT                   /note="Ubiquitin-conjugating enzyme E2 D3"
FT                   /id="PRO_0000082468"
FT   DOMAIN          1..147
FT                   /note="UBC core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT   ACT_SITE        85
FT                   /note="Glycyl thioester intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00388,
FT                   ECO:0000255|PROSITE-ProRule:PRU10133"
FT   DISULFID        21..107
FT                   /evidence="ECO:0000250|UniProtKB:P61077"
SQ   SEQUENCE   147 AA;  16687 MW;  ADD74A8A708EFEE3 CRC64;
     MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY
     PFKPPKVAFT TRIYHPNINS NGSICLDILR SQWSPALTIS KVLLSICSLL CDPNPDDPLV
     PEIARIYKTD RDKYNRISRE WTQKYAM
//