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P51668 (UB2D1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 138. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ubiquitin-conjugating enzyme E2 D1

EC=6.3.2.19
Alternative name(s):
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 names
Name:UBE2D1
Synonyms:SFT, UBC5A, UBCH5, UBCH5A
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length147 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.12 Ref.14 Ref.15 Ref.16 Ref.17

Catalytic activity

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

Pathway

Protein modification; protein ubiquitination.

Subunit structure

Component of a E3 ubiquitin ligase complex containing UBE2D1, SIAH1, CACYBP/SIP, SKP1, APC and TBL1X. Interacts with RNF11. Ref.10 Ref.11

Subcellular location

Cytoplasm Ref.13.

Tissue specificity

Ubiquitous. Up-regulated in livers of iron-overloaded patients with hereditary hemochromatosis. Ref.2 Ref.8

Sequence similarities

Belongs to the ubiquitin-conjugating enzyme family.

Caution

Ref.8 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.

Ontologies

Keywords
   Biological processUbl conjugation pathway
   Cellular componentCytoplasm
   LigandATP-binding
Nucleotide-binding
   Molecular functionLigase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processBMP signaling pathway

Traceable author statement. Source: Reactome

MyD88-independent toll-like receptor signaling pathway

Traceable author statement. Source: Reactome

TRIF-dependent toll-like receptor signaling pathway

Traceable author statement. Source: Reactome

anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process

Traceable author statement. Source: Reactome

cellular response to hypoxia

Traceable author statement. Source: Reactome

gene expression

Traceable author statement. Source: Reactome

innate immune response

Traceable author statement. Source: Reactome

mitotic cell cycle

Traceable author statement. Source: Reactome

mitotic spindle assembly checkpoint

Traceable author statement. Source: Reactome

negative regulation of transcription from RNA polymerase II promoter

Traceable author statement. Source: Reactome

negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle

Traceable author statement. Source: Reactome

positive regulation of protein ubiquitination

Inferred from direct assay PubMed 16275645. Source: UniProtKB

positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle

Traceable author statement. Source: Reactome

protein K48-linked ubiquitination

Inferred from direct assay Ref.17. Source: UniProtKB

protein polyubiquitination

Inferred from direct assay PubMed 16275645. Source: UniProtKB

regulation of transcription from RNA polymerase II promoter in response to hypoxia

Traceable author statement. Source: Reactome

regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle

Traceable author statement. Source: Reactome

toll-like receptor 3 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor 4 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor signaling pathway

Traceable author statement. Source: Reactome

transcription initiation from RNA polymerase II promoter

Traceable author statement. Source: Reactome

transcription, DNA-templated

Traceable author statement. Source: Reactome

transforming growth factor beta receptor signaling pathway

Traceable author statement. Source: Reactome

ubiquitin-dependent protein catabolic process

Inferred from direct assay PubMed 16275645. Source: UniProtKB

   Cellular_componentcytoplasm

Inferred from direct assay Ref.13. Source: UniProtKB

cytosol

Traceable author statement. Source: Reactome

nucleoplasm

Traceable author statement. Source: Reactome

ubiquitin ligase complex

Inferred from direct assay PubMed 15247280. Source: BHF-UCL

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

protein binding

Inferred from physical interaction PubMed 16522193. Source: UniProtKB

ubiquitin-protein transferase activity

Inferred from direct assay Ref.14Ref.17. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 147147Ubiquitin-conjugating enzyme E2 D1
PRO_0000082460

Sites

Active site851Glycyl thioester intermediate By similarity

Secondary structure

......................... 147
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P51668 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 2E96FD0179EE119D

FASTA14716,602
        10         20         30         40         50         60 
MALKRIQKEL SDLQRDPPAH CSAGPVGDDL FHWQATIMGP PDSAYQGGVF FLTVHFPTDY 

        70         80         90        100        110        120 
PFKPPKIAFT TKIYHPNINS NGSICLDILR SQWSPALTVS KVLLSICSLL CDPNPDDPLV 

       130        140 
PDIAQIYKSD KEKYNRHARE WTQKYAM 

« Hide

References

« Hide 'large scale' references
[1]"Identification of a human ubiquitin-conjugating enzyme that mediates the E6-AP-dependent ubiquitination of p53."
Scheffner M., Huibregtse J.M., Howley P.M.
Proc. Natl. Acad. Sci. U.S.A. 91:8797-8801(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"UbcH5A, a member of human E2 ubiquitin-conjugating enzymes, is closely related to SFT, a stimulator of iron transport, and is up-regulated in hereditary hemochromatosis."
Gehrke S.G., Riedel H.-D., Herrmann T., Hadaschik B., Bents K., Veltkamp C., Stremmel W.
Blood 101:3288-3293(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY.
[3]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]"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. expand/collapse author list , 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(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Skeletal muscle.
[5]"The DNA sequence and comparative analysis of human chromosome 10."
Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. expand/collapse author list , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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: Bone marrow and Skin.
[8]"Functional expression cloning and characterization of SFT, a stimulator of Fe transport."
Gutierrez J.A., Yu J., Rivera S., Wessling-Resnick M.
J. Cell Biol. 139:895-905(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 134-147, TISSUE SPECIFICITY.
[9]Erratum
Gutierrez J.A., Yu J., Rivera S., Wessling-Resnick M.
J. Cell Biol. 147:205-205(1999)
[10]"Siah-1, SIP, and Ebi collaborate in a novel pathway for beta-catenin degradation linked to p53 responses."
Matsuzawa S., Reed J.C.
Mol. Cell 7:915-926(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT OF A COMPLEX WITH SIAH1; CACYBP; SKP1; APC AND TBL1X.
[11]"The RING-H2 protein RNF11 is overexpressed in breast cancer and is a target of Smurf2 E3 ligase."
Subramaniam V., Li H., Wong M.J., Kitching R., Attisano L., Wrana J., Zubovits J., Burger A.M., Seth A.K.
Br. J. Cancer 89:1538-1544(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RNF11.
[12]"Two different classes of E2 ubiquitin-conjugating enzymes are required for the mono-ubiquitination of proteins and elongation by polyubiquitin chains with a specific topology."
Windheim M., Peggie M., Cohen P.
Biochem. J. 409:723-729(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[13]"The autoantigen Ro52 is an E3 ligase resident in the cytoplasm but enters the nucleus upon cellular exposure to nitric oxide."
Espinosa A., Oke V., Elfving A., Nyberg F., Covacu R., Wahren-Herlenius M.
Exp. Cell Res. 314:3605-3613(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[14]"Members of the E2D (UbcH5) family mediate the ubiquitination of the conserved cysteine of Pex5p, the peroxisomal import receptor."
Grou C.P., Carvalho A.F., Pinto M.P., Wiese S., Piechura H., Meyer H.E., Warscheid B., Sa-Miranda C., Azevedo J.E.
J. Biol. Chem. 283:14190-14197(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[15]"CYP3A4 ubiquitination by gp78 (the tumor autocrine motility factor receptor, AMFR) and CHIP E3 ligases."
Pabarcus M.K., Hoe N., Sadeghi S., Patterson C., Wiertz E., Correia M.A.
Arch. Biochem. Biophys. 483:66-74(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[16]"Key role of Ubc5 and lysine-63 polyubiquitination in viral activation of IRF3."
Zeng W., Xu M., Liu S., Sun L., Chen Z.J.
Mol. Cell 36:315-325(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[17]"The E2 ubiquitin-conjugating enzymes direct polyubiquitination to preferred lysines."
David Y., Ziv T., Admon A., Navon A.
J. Biol. Chem. 285:8595-8604(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[18]"The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor."
Zhang L., Fairall L., Goult B.T., Calkin A.C., Hong C., Millard C.J., Tontonoz P., Schwabe J.W.
Genes Dev. 25:1262-1274(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH MYLIP.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS7252.1.
PIRI39202.
RefSeqNP_003329.1. NM_003338.4.
UniGeneHs.129683.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP51668.
SMRP51668. Positions 1-147.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid113169. 243 interactions.
DIPDIP-44088N.
IntActP51668. 98 interactions.
MINTMINT-1433717.
STRING9606.ENSP00000363019.

PTM databases

PhosphoSiteP51668.

Polymorphism databases

DMDM1717848.

Proteomic databases

MaxQBP51668.
PaxDbP51668.
PRIDEP51668.

Protocols and materials databases

DNASU7321.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000373910; ENSP00000363019; ENSG00000072401.
GeneID7321.
KEGGhsa:7321.
UCSCuc001jke.2. human.

Organism-specific databases

CTD7321.
GeneCardsGC10P060094.
HGNCHGNC:12474. UBE2D1.
HPAHPA003920.
MIM602961. gene.
neXtProtNX_P51668.
PharmGKBPA37124.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5078.
HOGENOMHOG000233455.
HOVERGENHBG063308.
InParanoidP51668.
KOK06689.
OMAWQATISG.
OrthoDBEOG7PCJGX.
PhylomeDBP51668.
TreeFamTF101108.

Enzyme and pathway databases

ReactomeREACT_111102. Signal Transduction.
REACT_115566. Cell Cycle.
REACT_116125. Disease.
REACT_120956. Cellular responses to stress.
REACT_21300. Mitotic M-M/G1 phases.
REACT_6850. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
REACT_6900. Immune System.
REACT_71. Gene Expression.
REACT_8017. APC-Cdc20 mediated degradation of Nek2A.
SignaLinkP51668.
UniPathwayUPA00143.

Gene expression databases

BgeeP51668.
CleanExHS_UBE2D1.
GenevestigatorP51668.

Family and domain databases

Gene3D3.10.110.10. 1 hit.
InterProIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMSSF54495. SSF54495. 1 hit.
PROSITEPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP51668.
GeneWikiUBE2D1.
GenomeRNAi7321.
NextBio28626.
PROP51668.
SOURCESearch...

Entry information

Entry nameUB2D1_HUMAN
AccessionPrimary (citable) accession number: P51668
Secondary accession number(s): A6NLF6, A8K786
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 9, 2014
This is version 138 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 10

Human chromosome 10: entries, gene names and cross-references to MIM