P61078 (UB2D3_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:

Ube2d3

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	147 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	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.
Catalytic activity	ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
Pathway	Protein modification; protein ubiquitination.
Subunit structure	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 By similarity. Interacts with DAPK3 By similarity. Interacts with BRCA1; the DNA damage checkpoint promotes the association with BRCA1 after ionizing radiation By similarity. Interacts non-covalently with ubiquitin By similarity.
Subcellular location	Cell membrane; Peripheral membrane protein By similarity. Endosome membrane; Peripheral membrane protein By similarity.
Sequence similarities	Belongs to the ubiquitin-conjugating enzyme family.

Ontologies

Keywords
Biological process	Apoptosis DNA damage DNA repair Ubl conjugation pathway
Cellular component	Cell membrane Endosome Membrane
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
PTM	Disulfide bond
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW apoptotic process Inferred from electronic annotation. Source: UniProtKB-KW proteasomal ubiquitin-dependent protein catabolic process Inferred from sequence or structural similarity. Source: UniProtKB protein K11-linked ubiquitination Inferred from sequence or structural similarity. Source: UniProtKB protein K48-linked ubiquitination Inferred from sequence or structural similarity. Source: UniProtKB
Cellular_component	endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin-protein ligase activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 147	147	Ubiquitin-conjugating enzyme E2 D3		PRO_0000082468
Sites
	Active site	85	1	Glycyl thioester intermediate By similarity
Amino acid modifications
	Disulfide bond	21 ↔ 107		By similarity

Sequences

	Sequence		Length	Mass (Da)
	P61078 [UniParc]. Last modified April 26, 2004. Version 1. Checksum: ADD74A8A708EFEE3	FASTA	147	16,687
	10 20 30 40 50 60 MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY 70 80 90 100 110 120 PFKPPKVAFT TRIYHPNINS NGSICLDILR SQWSPALTIS KVLLSICSLL CDPNPDDPLV 130 140 PEIARIYKTD RDKYNRISRE WTQKYAM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U13177 mRNA. Translation: AAA85102.1. U13175 mRNA. Translation: AAA85100.1. AB006852 mRNA. Translation: BAA87330.1. BC072696 mRNA. Translation: AAH72696.1.
IPI	IPI00192159.
PIR	S53358.
RefSeq	NP_112516.1. NM_031237.1.
UniGene	Rn.2778.
3D structure databases
ProteinModelPortal	P61078.
ModBase	Search...
Protein-protein interaction databases
STRING	10116.ENSRNOP00000045087.
PTM databases
PhosphoSite	P61078.
Proteomic databases
PRIDE	P61078.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	81920.
KEGG	rno:81920.
Organism-specific databases
CTD	7323.
RGD	619912. Ube2d3.
Phylogenomic databases
HOGENOM	HOG000233455.
HOVERGEN	HBG063308.
InParanoid	P61078.
KO	K06689.
OrthoDB	EOG4RR6JK.
Enzyme and pathway databases
UniPathway	UPA00143.
Gene expression databases
ArrayExpress	P61078.
Genevestigator	P61078.
GermOnline	ENSRNOG00000013741. Rattus norvegicus.
Family and domain databases
Gene3D	3.10.110.10. 1 hit.
InterPro	IPR000608. UBQ-conjugat_E2. IPR023313. UBQ-conjugating_AS. IPR016135. UBQ-conjugating_enzyme/RWD. [Graphical view]
Pfam	PF00179. UQ_con. 1 hit. [Graphical view]
SUPFAM	SSF54495. UBQ-conjugat/RWD-like. 1 hit.
PROSITE	PS00183. UBIQUITIN_CONJUGAT_1. 1 hit. PS50127. UBIQUITIN_CONJUGAT_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	28636.

Entry information

Entry name

UB2D3_RAT

Accession

Primary (citable) accession number: P61078
Secondary accession number(s): P47986

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2004
Last sequence update:	April 26, 2004
Last modified:	May 1, 2013
This is version 76 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program