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Protein

Ubiquitin-conjugating enzyme E2 D4

Gene

ube2d4

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

Functioni

Catalyzes the covalent attachment of ubiquitin to other proteins. Regulates pronephros development, possibly by promoting ubiquitination and thus inactivation or degradation of map3k10/mlk2.PROSITE-ProRule annotation1 Publication

Catalytic activityi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei85 – 851Glycyl thioester intermediate

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ligase activity Source: UniProtKB-KW
  • mitogen-activated protein kinase kinase kinase binding Source: UniProtKB
  • ubiquitin binding Source: UniProtKB
  • ubiquitin-protein transferase activity Source: UniProtKB

GO - Biological processi

  • pronephric nephron tubule development Source: UniProtKB
  • protein ubiquitination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, 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 D4By similarity (EC:6.3.2.19)
Alternative name(s):
Ubiquitin carrier protein D4By similarity
Ubiquitin-protein ligase D4By similarity
Gene namesi
Name:ube2d4
Synonyms:ube2d3.21 Publication
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-962538. ube2d4.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi85 – 851C → A: Catalytically inactive. No effect on pronephros development. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 147147Ubiquitin-conjugating enzyme E2 D4PRO_0000397918Add
BLAST

Expressioni

Tissue specificityi

At embryonic stages 28 to 35, expressed in the somites, eye primordia, otic vesicle and branchial arches. By stage 35, also weakly expressed in the pronephros.1 Publication

Developmental stagei

Expressed maternally. Present at near constant levels throughout early development.1 Publication

Interactioni

Subunit structurei

Interacts with map3k10/mlk2.1 Publication

Structurei

3D structure databases

ProteinModelPortaliA5PKP9.
SMRiA5PKP9. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

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.

A5PKP9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALKRIQKEL MDLQRDPPAQ CSAGPVGEDL FHWQATIMGP NDSPFQGGVF
60 70 80 90 100
FLTIHFPTDY PFKPPKVAFT TKIYHPNINS NGSICLDILR SQWSPALTVS
110 120 130 140
KVLLSICSLL CDPNPDDPLV PEIAHTYKAD REKYNRLARE WTQKYAM
Length:147
Mass (Da):16,677
Last modified:July 10, 2007 - v1
Checksum:i3832EF718DF47EC2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU124673 mRNA. Translation: ABV25624.1.
BC142569 mRNA. Translation: AAI42570.1.
RefSeqiNP_001093355.1. NM_001099885.1.
UniGeneiXl.13069.

Genome annotation databases

GeneIDi100101299.
KEGGixla:100101299.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU124673 mRNA. Translation: ABV25624.1.
BC142569 mRNA. Translation: AAI42570.1.
RefSeqiNP_001093355.1. NM_001099885.1.
UniGeneiXl.13069.

3D structure databases

ProteinModelPortaliA5PKP9.
SMRiA5PKP9. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100101299.
KEGGixla:100101299.

Organism-specific databases

CTDi51619.
XenbaseiXB-GENE-962538. ube2d4.

Phylogenomic databases

HOVERGENiHBG063308.
KOiK06689.

Enzyme and pathway databases

UniPathwayiUPA00143.

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. "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: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH MAP3K10, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, MUTAGENESIS OF CYS-85.
  2. NIH - Xenopus Gene Collection (XGC) project
    Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: NeurulaImported.

Entry informationi

Entry nameiUB2D4_XENLA
AccessioniPrimary (citable) accession number: A5PKP9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 5, 2010
Last sequence update: July 10, 2007
Last modified: March 4, 2015
This is version 43 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.