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Protein

Ubiquitin-conjugating enzyme E2 D4

Gene

UBE2D4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11' and 'Lys-48'-linked polyubiquitination.1 Publication

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. ATP binding Source: UniProtKB-KW
  2. ligase activity Source: UniProtKB-KW
  3. ubiquitin conjugating enzyme activity Source: MGI
  4. ubiquitin-protein transferase activity Source: UniProtKB

GO - Biological processi

  1. protein K11-linked ubiquitination Source: UniProtKB
  2. protein K27-linked ubiquitination Source: UniProtKB
  3. protein K29-linked ubiquitination Source: UniProtKB
  4. protein K48-linked ubiquitination Source: UniProtKB
  5. protein K63-linked ubiquitination Source: UniProtKB
  6. protein K6-linked ubiquitination Source: UniProtKB
  7. protein ubiquitination Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi2.3.2.B6. 2681.
ReactomeiREACT_75842. Antigen processing: Ubiquitination & Proteasome degradation.
SignaLinkiQ9Y2X8.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 D4 (EC:6.3.2.19)
Alternative name(s):
HBUCE1
Ubiquitin carrier protein D4
Ubiquitin-protein ligase D4
Gene namesi
Name:UBE2D4
Synonyms:UBCH5D
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:21647. UBE2D4.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134954568.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 147147Ubiquitin-conjugating enzyme E2 D4PRO_0000270202Add
BLAST

Proteomic databases

MaxQBiQ9Y2X8.
PaxDbiQ9Y2X8.
PRIDEiQ9Y2X8.

PTM databases

PhosphoSiteiQ9Y2X8.

Expressioni

Gene expression databases

BgeeiQ9Y2X8.
CleanExiHS_UBE2D4.
ExpressionAtlasiQ9Y2X8. baseline and differential.
GenevestigatoriQ9Y2X8.

Organism-specific databases

HPAiHPA003920.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
DTX2Q86UW93EBI-745527,EBI-740376
RNF11Q9Y3C54EBI-745527,EBI-396669
RNF126Q9BV683EBI-745527,EBI-357322
ZNRF1Q8ND253EBI-745527,EBI-2129250

Protein-protein interaction databases

BioGridi119641. 92 interactions.
IntActiQ9Y2X8. 84 interactions.
MINTiMINT-1192345.
STRINGi9606.ENSP00000222402.

Structurei

3D structure databases

ProteinModelPortaliQ9Y2X8.
SMRiQ9Y2X8. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG5078.
GeneTreeiENSGT00760000119012.
HOGENOMiHOG000233455.
HOVERGENiHBG063308.
InParanoidiQ9Y2X8.
KOiK06689.
OMAiMIAREWT.
PhylomeDBiQ9Y2X8.
TreeFamiTF101108.

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.

Q9Y2X8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALKRIQKEL TDLQRDPPAQ CSAGPVGDDL FHWQATIMGP NDSPYQGGVF
60 70 80 90 100
FLTIHFPTDY PFKPPKVAFT TKIYHPNINS NGSICLDILR SQWSPALTVS
110 120 130 140
KVLLSICSLL CDPNPDDPLV PEIAHTYKAD REKYNRLARE WTQKYAM
Length:147
Mass (Da):16,649
Last modified:October 31, 1999 - v1
Checksum:i5F91A2C6BC667254
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF125044 mRNA. Translation: AAD31180.1.
AK001446 mRNA. Translation: BAA91697.1.
CH236951 Genomic DNA. Translation: EAL24010.1.
CH471073 Genomic DNA. Translation: EAW94182.1.
BC004104 mRNA. Translation: AAH04104.1.
CCDSiCCDS5474.1.
RefSeqiNP_057067.1. NM_015983.3.
UniGeneiHs.19196.

Genome annotation databases

EnsembliENST00000222402; ENSP00000222402; ENSG00000078967.
GeneIDi51619.
KEGGihsa:51619.
UCSCiuc003tja.2. human.

Polymorphism databases

DMDMi74753478.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF125044 mRNA. Translation: AAD31180.1.
AK001446 mRNA. Translation: BAA91697.1.
CH236951 Genomic DNA. Translation: EAL24010.1.
CH471073 Genomic DNA. Translation: EAW94182.1.
BC004104 mRNA. Translation: AAH04104.1.
CCDSiCCDS5474.1.
RefSeqiNP_057067.1. NM_015983.3.
UniGeneiHs.19196.

3D structure databases

ProteinModelPortaliQ9Y2X8.
SMRiQ9Y2X8. Positions 1-147.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119641. 92 interactions.
IntActiQ9Y2X8. 84 interactions.
MINTiMINT-1192345.
STRINGi9606.ENSP00000222402.

PTM databases

PhosphoSiteiQ9Y2X8.

Polymorphism databases

DMDMi74753478.

Proteomic databases

MaxQBiQ9Y2X8.
PaxDbiQ9Y2X8.
PRIDEiQ9Y2X8.

Protocols and materials databases

DNASUi51619.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000222402; ENSP00000222402; ENSG00000078967.
GeneIDi51619.
KEGGihsa:51619.
UCSCiuc003tja.2. human.

Organism-specific databases

CTDi51619.
GeneCardsiGC07P043966.
HGNCiHGNC:21647. UBE2D4.
HPAiHPA003920.
neXtProtiNX_Q9Y2X8.
PharmGKBiPA134954568.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5078.
GeneTreeiENSGT00760000119012.
HOGENOMiHOG000233455.
HOVERGENiHBG063308.
InParanoidiQ9Y2X8.
KOiK06689.
OMAiMIAREWT.
PhylomeDBiQ9Y2X8.
TreeFamiTF101108.

Enzyme and pathway databases

UniPathwayiUPA00143.
BRENDAi2.3.2.B6. 2681.
ReactomeiREACT_75842. Antigen processing: Ubiquitination & Proteasome degradation.
SignaLinkiQ9Y2X8.

Miscellaneous databases

GenomeRNAii51619.
NextBioi55531.
PROiQ9Y2X8.

Gene expression databases

BgeeiQ9Y2X8.
CleanExiHS_UBE2D4.
ExpressionAtlasiQ9Y2X8. baseline and differential.
GenevestigatoriQ9Y2X8.

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 and screening of two ubiquitin conjugation enzymes."
    Li G., Jin J., Hu S., Li W., Yuan J., Qiang B.
    Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Brain.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. "Human chromosome 7: DNA sequence and biology."
    Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S.
    , Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.
    Science 300:767-772(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Ovary.
  6. "The E2 ubiquitin-conjugating enzymes direct polyubiquitination to preferred lysines."
    David Y., Ziv T., Admon A., Navon A.
    J. Biol. Chem. 285:8595-8604(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiUB2D4_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2X8
Secondary accession number(s): A4D1V0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 8, 2007
Last sequence update: October 31, 1999
Last modified: March 31, 2015
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.