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Protein

Ubiquitin-conjugating enzyme E2 D1

Gene

UBE2D1

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 catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1. Ubiquitinates STUB1-associated HSP90AB1 in vitro. Lacks inherent specificity for any particular lysine residue of ubiquitin. Essential for viral activation of IRF3. Mediates polyubiquitination of CYP3A4.5 Publications

Catalytic activityi

S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine.PROSITE-ProRule annotation3 Publications
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N(6)-monoubiquitinyl-[acceptor protein]-L-lysine.1 Publication

Pathwayi: protein 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)DescriptionActionsGraphical viewLength
Active sitei85Glycyl thioester intermediatePROSITE-ProRule annotation1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ubiquitin conjugating enzyme activity Source: BHF-UCL
  • ubiquitin-protein transferase activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:HS01066-MONOMER.
BRENDAi2.3.2.B6. 2681.
2.3.2.B8. 2681.
ReactomeiR-HSA-1234176. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
R-HSA-141430. Inactivation of APC/C via direct inhibition of the APC/C complex.
R-HSA-174048. APC/C:Cdc20 mediated degradation of Cyclin B.
R-HSA-174084. Autodegradation of Cdh1 by Cdh1:APC/C.
R-HSA-174154. APC/C:Cdc20 mediated degradation of Securin.
R-HSA-174178. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
R-HSA-174184. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
R-HSA-176407. Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase.
R-HSA-176408. Regulation of APC/C activators between G1/S and early anaphase.
R-HSA-176409. APC/C:Cdc20 mediated degradation of mitotic proteins.
R-HSA-176412. Phosphorylation of the APC/C.
R-HSA-179409. APC-Cdc20 mediated degradation of Nek2A.
R-HSA-201451. Signaling by BMP.
R-HSA-202424. Downstream TCR signaling.
R-HSA-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-HSA-2467813. Separation of Sister Chromatids.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2871837. FCERI mediated NF-kB activation.
R-HSA-5607764. CLEC7A (Dectin-1) signaling.
R-HSA-5689896. Ovarian tumor domain proteases.
R-HSA-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-HSA-936440. Negative regulators of RIG-I/MDA5 signaling.
R-HSA-937041. IKK complex recruitment mediated by RIP1.
R-HSA-983168. Antigen processing: Ubiquitination & Proteasome degradation.
SignaLinkiP51668.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 D1 (EC:2.3.2.233 Publications)
Alternative name(s):
(E3-independent) E2 ubiquitin-conjugating enzyme D1 (EC:2.3.2.241 Publication)
E2 ubiquitin-conjugating enzyme D1
Stimulator of Fe transport
Short name:
SFT
UBC4/5 homolog
UbcH5
Ubiquitin carrier protein D1
Ubiquitin-conjugating enzyme E2(17)KB 1
Ubiquitin-conjugating enzyme E2-17 kDa 1
Ubiquitin-protein ligase D1
Gene namesi
Name:UBE2D1
Synonyms:SFT, UBC5A, UBCH5, UBCH5A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:12474. UBE2D1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: Reactome
  • nucleoplasm Source: Reactome
  • protein complex Source: MGI
  • ubiquitin ligase complex Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi7321.
OpenTargetsiENSG00000072401.
PharmGKBiPA37124.

Polymorphism and mutation databases

BioMutaiUBE2D1.
DMDMi1717848.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000824601 – 147Ubiquitin-conjugating enzyme E2 D1Add BLAST147

Proteomic databases

EPDiP51668.
MaxQBiP51668.
PaxDbiP51668.
PeptideAtlasiP51668.
PRIDEiP51668.

PTM databases

iPTMnetiP51668.
PhosphoSitePlusiP51668.

Expressioni

Tissue specificityi

Ubiquitous. Up-regulated in livers of iron-overloaded patients with hereditary hemochromatosis.2 Publications

Gene expression databases

BgeeiENSG00000072401.
CleanExiHS_UBE2D1.
ExpressionAtlasiP51668. baseline and differential.
GenevisibleiP51668. HS.

Organism-specific databases

HPAiHPA003920.

Interactioni

Subunit structurei

Component of a E3 ubiquitin ligase complex containing UBE2D1, SIAH1, CACYBP/SIP, SKP1, APC and TBL1X. Interacts with RNF11.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DTX2Q4ZH493EBI-743540,EBI-10192429
DTX2Q86UW93EBI-743540,EBI-740376
MID1O153446EBI-743540,EBI-2340316
MID2Q9UJV3-25EBI-743540,EBI-10172526
MKRN2Q9H0005EBI-743540,EBI-2341005
MKRN3Q130644EBI-743540,EBI-2340269
OTUB1Q96FW18EBI-743540,EBI-1058491
RNF11Q9Y3C56EBI-743540,EBI-396669
RNF111Q6ZNA45EBI-743540,EBI-2129175
RNF115Q9Y4L56EBI-743540,EBI-2129242
RNF126Q9BV688EBI-743540,EBI-357322
RNF14Q9UBS84EBI-743540,EBI-2130308
RNF185Q96GF13EBI-743540,EBI-2340249
RNF5Q999427EBI-743540,EBI-348482
TRAF6Q9Y4K32EBI-743540,EBI-359276
TRIM39Q9HCM96EBI-743540,EBI-739510
TRIM8Q9BZR93EBI-743540,EBI-2340370
XIAPP981703EBI-743540,EBI-517127
ZNRF1Q8ND256EBI-743540,EBI-2129250

Protein-protein interaction databases

BioGridi113169. 265 interactors.
DIPiDIP-44088N.
IntActiP51668. 111 interactors.
MINTiMINT-1433717.
STRINGi9606.ENSP00000363019.

Structurei

Secondary structure

1147
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1 – 15Combined sources15
Beta strandi21 – 26Combined sources6
Beta strandi29 – 38Combined sources10
Beta strandi41 – 43Combined sources3
Turni44 – 47Combined sources4
Beta strandi49 – 55Combined sources7
Turni58 – 61Combined sources4
Beta strandi66 – 69Combined sources4
Helixi87 – 89Combined sources3
Turni90 – 92Combined sources3
Helixi99 – 111Combined sources13
Beta strandi115 – 117Combined sources3
Helixi121 – 129Combined sources9
Helixi131 – 146Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2C4PX-ray2.35A/B1-147[»]
2YHOX-ray2.10B/D/F/H1-147[»]
3OJ4X-ray3.40A/D1-147[»]
3PTFX-ray2.70A/B1-147[»]
4AP4X-ray2.21B/E1-147[»]
4QPLX-ray1.90B/D1-147[»]
5FERX-ray2.34B/E1-147[»]
ProteinModelPortaliP51668.
SMRiP51668.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP51668.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG0417. Eukaryota.
COG5078. LUCA.
GeneTreeiENSGT00760000119012.
HOGENOMiHOG000233455.
HOVERGENiHBG063308.
InParanoidiP51668.
KOiK06689.
OMAiQEIAREW.
OrthoDBiEOG091G0GF8.
PhylomeDBiP51668.
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.

P51668-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALKRIQKEL SDLQRDPPAH CSAGPVGDDL FHWQATIMGP PDSAYQGGVF
60 70 80 90 100
FLTVHFPTDY PFKPPKIAFT TKIYHPNINS NGSICLDILR SQWSPALTVS
110 120 130 140
KVLLSICSLL CDPNPDDPLV PDIAQIYKSD KEKYNRHARE WTQKYAM
Length:147
Mass (Da):16,602
Last modified:October 1, 1996 - v1
Checksum:i2E96FD0179EE119D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X78140 mRNA. Translation: CAA55019.1.
AF257220 mRNA. Translation: AAM81086.1.
AJ272367 mRNA. Translation: CAC82177.1.
AK291901 mRNA. Translation: BAF84590.1.
AJ293565 Genomic DNA. Translation: CAC82097.1.
BT007041 mRNA. Translation: AAP35690.1.
AC016396 Genomic DNA. No translation available.
AC023170 Genomic DNA. No translation available.
CH471083 Genomic DNA. Translation: EAW54169.1.
BC005980 mRNA. Translation: AAH05980.1.
BC015997 mRNA. Translation: AAH15997.1.
AF020761 mRNA. No translation available.
CCDSiCCDS7252.1.
PIRiI39202.
RefSeqiNP_003329.1. NM_003338.4.
UniGeneiHs.129683.

Genome annotation databases

EnsembliENST00000373910; ENSP00000363019; ENSG00000072401.
GeneIDi7321.
KEGGihsa:7321.
UCSCiuc001jke.3. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X78140 mRNA. Translation: CAA55019.1.
AF257220 mRNA. Translation: AAM81086.1.
AJ272367 mRNA. Translation: CAC82177.1.
AK291901 mRNA. Translation: BAF84590.1.
AJ293565 Genomic DNA. Translation: CAC82097.1.
BT007041 mRNA. Translation: AAP35690.1.
AC016396 Genomic DNA. No translation available.
AC023170 Genomic DNA. No translation available.
CH471083 Genomic DNA. Translation: EAW54169.1.
BC005980 mRNA. Translation: AAH05980.1.
BC015997 mRNA. Translation: AAH15997.1.
AF020761 mRNA. No translation available.
CCDSiCCDS7252.1.
PIRiI39202.
RefSeqiNP_003329.1. NM_003338.4.
UniGeneiHs.129683.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2C4PX-ray2.35A/B1-147[»]
2YHOX-ray2.10B/D/F/H1-147[»]
3OJ4X-ray3.40A/D1-147[»]
3PTFX-ray2.70A/B1-147[»]
4AP4X-ray2.21B/E1-147[»]
4QPLX-ray1.90B/D1-147[»]
5FERX-ray2.34B/E1-147[»]
ProteinModelPortaliP51668.
SMRiP51668.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113169. 265 interactors.
DIPiDIP-44088N.
IntActiP51668. 111 interactors.
MINTiMINT-1433717.
STRINGi9606.ENSP00000363019.

PTM databases

iPTMnetiP51668.
PhosphoSitePlusiP51668.

Polymorphism and mutation databases

BioMutaiUBE2D1.
DMDMi1717848.

Proteomic databases

EPDiP51668.
MaxQBiP51668.
PaxDbiP51668.
PeptideAtlasiP51668.
PRIDEiP51668.

Protocols and materials databases

DNASUi7321.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000373910; ENSP00000363019; ENSG00000072401.
GeneIDi7321.
KEGGihsa:7321.
UCSCiuc001jke.3. human.

Organism-specific databases

CTDi7321.
DisGeNETi7321.
GeneCardsiUBE2D1.
HGNCiHGNC:12474. UBE2D1.
HPAiHPA003920.
MIMi602961. gene.
neXtProtiNX_P51668.
OpenTargetsiENSG00000072401.
PharmGKBiPA37124.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0417. Eukaryota.
COG5078. LUCA.
GeneTreeiENSGT00760000119012.
HOGENOMiHOG000233455.
HOVERGENiHBG063308.
InParanoidiP51668.
KOiK06689.
OMAiQEIAREW.
OrthoDBiEOG091G0GF8.
PhylomeDBiP51668.
TreeFamiTF101108.

Enzyme and pathway databases

UniPathwayiUPA00143.
BioCyciZFISH:HS01066-MONOMER.
BRENDAi2.3.2.B6. 2681.
2.3.2.B8. 2681.
ReactomeiR-HSA-1234176. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
R-HSA-141430. Inactivation of APC/C via direct inhibition of the APC/C complex.
R-HSA-174048. APC/C:Cdc20 mediated degradation of Cyclin B.
R-HSA-174084. Autodegradation of Cdh1 by Cdh1:APC/C.
R-HSA-174154. APC/C:Cdc20 mediated degradation of Securin.
R-HSA-174178. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
R-HSA-174184. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
R-HSA-176407. Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase.
R-HSA-176408. Regulation of APC/C activators between G1/S and early anaphase.
R-HSA-176409. APC/C:Cdc20 mediated degradation of mitotic proteins.
R-HSA-176412. Phosphorylation of the APC/C.
R-HSA-179409. APC-Cdc20 mediated degradation of Nek2A.
R-HSA-201451. Signaling by BMP.
R-HSA-202424. Downstream TCR signaling.
R-HSA-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-HSA-2467813. Separation of Sister Chromatids.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2871837. FCERI mediated NF-kB activation.
R-HSA-5607764. CLEC7A (Dectin-1) signaling.
R-HSA-5689896. Ovarian tumor domain proteases.
R-HSA-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-HSA-936440. Negative regulators of RIG-I/MDA5 signaling.
R-HSA-937041. IKK complex recruitment mediated by RIP1.
R-HSA-983168. Antigen processing: Ubiquitination & Proteasome degradation.
SignaLinkiP51668.

Miscellaneous databases

ChiTaRSiUBE2D1. human.
EvolutionaryTraceiP51668.
GeneWikiiUBE2D1.
GenomeRNAii7321.
PROiP51668.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000072401.
CleanExiHS_UBE2D1.
ExpressionAtlasiP51668. baseline and differential.
GenevisibleiP51668. HS.

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...

Entry informationi

Entry nameiUB2D1_HUMAN
AccessioniPrimary (citable) accession number: P51668
Secondary accession number(s): A6NLF6, A8K786
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: November 30, 2016
This is version 164 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

Caution

PubMed:9362508 cloned and sequenced SFT which consisted of UBE2D1 last coding exon along with intronic sequences on the 5'-end of this exon. A function in iron transport has been described.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. SIMILARITY comments
    Index of protein domains and families

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 one 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.