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Protein

Ubiquitin-conjugating enzyme E2 D2

Gene

ube2d2

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the covalent attachment of ubiquitin to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53 (By similarity).PROSITE-ProRule annotation

Catalytic activityi

ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.PROSITE-ProRule annotation

Pathway:iprotein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.PROSITE-ProRule annotation
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei85 – 851Glycyl thioester intermediatePROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 D2 (EC:6.3.2.19)
Alternative name(s):
Ubiquitin carrier protein 4
Short name:
xUBC4
Ubiquitin carrier protein D2
Ubiquitin-protein ligase D2
Gene namesi
Name:ube2d2
Synonyms:ubc4, ube2d3.1
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-972284. ube2d3.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 147147Ubiquitin-conjugating enzyme E2 D2PRO_0000082465Add
BLAST

Proteomic databases

PRIDEiP62840.

Interactioni

Subunit structurei

Interacts with SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex.By similarity

Protein-protein interaction databases

BioGridi100827. 2 interactions.

Structurei

Secondary structure

1
147
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1514Combined sources
Beta strandi21 – 288Combined sources
Beta strandi32 – 376Combined sources
Beta strandi50 – 556Combined sources
Turni58 – 625Combined sources
Beta strandi66 – 716Combined sources
Turni87 – 926Combined sources
Helixi99 – 11113Combined sources
Helixi121 – 1299Combined sources
Helixi131 – 14515Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EB6X-ray3.40B1-147[»]
ProteinModelPortaliP62840.
SMRiP62840. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62840.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

HOVERGENiHBG063308.
KOiK06689.

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.

P62840-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALKRIHKEL NDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF
60 70 80 90 100
FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDILR SQWSPALTIS
110 120 130 140
KVLLSICSLL CDPNPDDPLV PEIARIYKTD REKYNRIARE WTQKYAM
Length:147
Mass (Da):16,735
Last modified:August 16, 2004 - v1
Checksum:iC942BE7853CBC355
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB105546 mRNA. Translation: BAD06215.1.
BC084359 mRNA. Translation: AAH84359.1.
RefSeqiNP_001084434.1. NM_001090965.1.
UniGeneiXl.45490.

Genome annotation databases

GeneIDi403384.
KEGGixla:403384.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB105546 mRNA. Translation: BAD06215.1.
BC084359 mRNA. Translation: AAH84359.1.
RefSeqiNP_001084434.1. NM_001090965.1.
UniGeneiXl.45490.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EB6X-ray3.40B1-147[»]
ProteinModelPortaliP62840.
SMRiP62840. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi100827. 2 interactions.

Proteomic databases

PRIDEiP62840.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi403384.
KEGGixla:403384.

Organism-specific databases

CTDi7323.
XenbaseiXB-GENE-972284. ube2d3.

Phylogenomic databases

HOVERGENiHBG063308.
KOiK06689.

Enzyme and pathway databases

UniPathwayiUPA00143.

Miscellaneous databases

EvolutionaryTraceiP62840.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning of cDNAs encoding Xenopus ubiquitin-conjugating enzyme(E2) and their expression in various Xenopus tissues."
    Karasawa A., Matushita H., Yagura T.
    Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Oocyte.
  2. NIH - Xenopus Gene Collection (XGC) project
    Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Eye.
  3. "A ubiquitin-conjugating enzyme, ube2d3.2, regulates xMLK2 and pronephros formation in Xenopus."
    Jean S., Moss T.
    Differentiation 76:431-441(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.

Entry informationi

Entry nameiUB2D2_XENLA
AccessioniPrimary (citable) accession number: P62840
Secondary accession number(s): P51669, Q5XGS3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 16, 2004
Last sequence update: August 16, 2004
Last modified: July 22, 2015
This is version 71 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

3D-structure

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.