Reviewed, UniProtKB/Swiss-Prot Q92890 (UFD1_HUMAN)

Names and origin

Protein names

Recommended name:
Ubiquitin fusion degradation protein 1 homolog
Short name=UB fusion protein 1

Gene names

Name:

UFD1L

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	307 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. It may be involved in the development of some ectoderm-derived structures.
Pathway	Protein degradation; proteasomal ubiquitin-dependent pathway.
Subunit structure	Heterodimer with NPLOC4, this heterodimer binds VCP and inhibits Golgi membrane fusion.
Subcellular location	Nucleus By similarity. Cytoplasm › cytosol By similarity.
Tissue specificity	Found in adult heart, skeletal muscle and pancreas, and in fetal liver and kidney.
Sequence similarities	Belongs to the UFD1 family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	skeletal system development Traceable author statement. Source: ProtInc ubiquitin-dependent protein catabolic process Ref.1 Traceable author statement. Source: ProtInc
Cellular component	cytosol Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	protein binding Inferred from physical interaction. Source: UniProtKB ubiquitin-specific protease activity Ref.1 Traceable author statement. Source: ProtInc
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform Short (identifier: Q92890-2)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: Major isoform.

Isoform Long (identifier: Q92890-1)

The sequence of this isoform differs from the canonical sequence as follows:
     106-106: E → EDGLVQLETVNLQVATYSKSKFCYLPHWMMQNLLLEE

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 307

307

Ubiquitin fusion degradation protein 1 homolog

PRO_0000194984

Amino acid modifications

Modified residue

1

1

N-acetylmethionine Ref.11

Modified residue

245

1

Phosphoserine Ref.9

Modified residue

247

1

Phosphoserine Ref.9 Ref.6

Modified residue

299

1

Phosphoserine Ref.9 Ref.7 Ref.8 Ref.12

Natural variations

Alternative sequence

106

1

E → EDGLVQLETVNLQVATYSKS KFCYLPHWMMQNLLLEE in isoform Long.

VSP_006707

Natural variant

130

1

P → A: dbSNP rs17744624. Ref.1

VAR_052436

Experimental info

Sequence conflict

33

1

G → W in AAD08720. Ref.1

Sequence conflict

183

1

I → H in AAD08720. Ref.1

Secondary structure

1

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307

Helix Strand Turn

Details...

Beta strand

16 – 18

3

Beta strand

20 – 26

7

Beta strand

31 – 35

5

Turn

39 – 44

6

Beta strand

45 – 47

3

Helix

50 – 58

9

Beta strand

66 – 71

6

Turn

72 – 75

4

Beta strand

76 – 84

9

Beta strand

91 – 93

3

Helix

97 – 102

6

Beta strand

108 – 115

8

Beta strand

121 – 129

9

Helix

130 – 134

5

Helix

138 – 146

9

Beta strand

157 – 164

8

Beta strand

166 – 181

16

Beta strand

188 – 191

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform Short [UniParc]. Last modified November 13, 2007. Version 3. Checksum: FC69860002C042C6	FASTA	307	34,500
	10 20 30 40 50 60 MFSFNMFDHP IPRVFQNRFS TQYRCFSVSM LAGPNDRSDV EKGGKIIMPP SALDQLSRLN 70 80 90 100 110 120 ITYPMLFKLT NKNSDRMTHC GVLEFVADEG ICYLPHWMMQ NLLLEEGGLV QVESVNLQVA 130 140 150 160 170 180 TYSKFQPQSP DFLDITNPKA VLENALRNFA CLTTGDVIAI NYNEKIYELR VMETKPDKAV 190 200 210 220 230 240 SIIECDMNVD FDAPLGYKEP ERQVQHEEST EGEADHSGYA GELGFRAFSG SGNRLDGKKK 250 260 270 280 290 300 GVEPSPSPIK PGDIKRGIPN YEFKLGKITF IRNSRPLVKK VEEDEAGGRF VAFSGEGQSL RKKGRKP
	Isoform Long. Checksum: 94D55B70E7F5A27F	FASTA	343	38,725
	10 20 30 40 50 60 MFSFNMFDHP IPRVFQNRFS TQYRCFSVSM LAGPNDRSDV EKGGKIIMPP SALDQLSRLN 70 80 90 100 110 120 ITYPMLFKLT NKNSDRMTHC GVLEFVADEG ICYLPHWMMQ NLLLEEDGLV QLETVNLQVA 130 140 150 160 170 180 TYSKSKFCYL PHWMMQNLLL EEGGLVQVES VNLQVATYSK FQPQSPDFLD ITNPKAVLEN 190 200 210 220 230 240 ALRNFACLTT GDVIAINYNE KIYELRVMET KPDKAVSIIE CDMNVDFDAP LGYKEPERQV 250 260 270 280 290 300 QHEESTEGEA DHSGYAGELG FRAFSGSGNR LDGKKKGVEP SPSPIKPGDI KRGIPNYEFK 310 320 330 340 LGKITFIRNS RPLVKKVEED EAGGRFVAFS GEGQSLRKKG RKP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"UFD1L, a developmentally expressed ubiquitination gene, is deleted in CATCH 22 syndrome." Pizzuti A., Novelli G., Ratti A., Amati F., Mari A., Calabrese G., Nicolis S., Silani V., Marino B., Scarlato G., Ottolenghi S., Dallapiccola B. Hum. Mol. Genet. 6:259-265(1997) [PubMed: 9063746] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS LONG AND SHORT), VARIANT ALA-130. Tissue: Brain.
[2]	"Characterization of human UFD1, a ubiquitin fusion-degradation protein." Gong L., Yeh E.T.H. Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM SHORT). Tissue: Heart.
[3]	"A genome annotation-driven approach to cloning the human ORFeome." Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I. Genome Biol. 5:R84.1-R84.11(2004) [PubMed: 15461802] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM SHORT).
[4]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM SHORT). Tissue: Brain and Skin.
[5]	"Cloning and characterization of the gene encoding human NPL4, a protein interacting with the ubiquitin fusion-degradation protein (UFD1L)." Botta A., Tandoi C., Fini G., Calabrese G., Dallapiccola B., Novelli G. Gene 275:39-46(2001) [PubMed: 11574150] [Abstract] Cited for: INTERACTION WITH NPLOC4.
[6]	"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra." Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D. J. Proteome Res. 6:4150-4162(2007) [PubMed: 17924679] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-247, MASS SPECTROMETRY. Tissue: Epithelium.
[7]	"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry." Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A. Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-299, MASS SPECTROMETRY.
[8]	"Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment." Carrascal M., Ovelleiro D., Casas V., Gay M., Abian J. J. Proteome Res. 7:5167-5176(2008) [PubMed: 19367720] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-299, MASS SPECTROMETRY. Tissue: T-cell.
[9]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-245; SER-247 AND SER-299, MASS SPECTROMETRY.
[10]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[11]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, MASS SPECTROMETRY.
[12]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-299, MASS SPECTROMETRY. Tissue: T-cell.
[13]	"Solution structure of human ubiquitin fusion degradation protein 1 homolog UFD1." RIKEN structural genomics initiative (RSGI) Submitted (APR-2008) to the PDB data bank Cited for: STRUCTURE BY NMR OF 11-193.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U64444 mRNA. Translation: AAD08720.1.
AF141201 mRNA. Translation: AAD28788.1.
CR456607 mRNA. Translation: CAG30493.1.
BC001049 mRNA. Translation: AAH01049.1.
BC005087 mRNA. Translation: AAH05087.1.

IPI

IPI00218292.
IPI00655754.

RefSeq

NP_005650.2.

UniGene

Hs.474213

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2YUJ	NMR	-	A	11-193	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q92890. 14 interactions.

STRING

Q92890.

PTM databases

PhosphoSite

Q92890.

2-D gel databases

OGP

Q92890.

Proteomic databases

PRIDE

Q92890.

Genome annotation databases

Ensembl

ENST00000263202; ENSP00000263202; ENSG00000070010; Homo sapiens. [Genome view]

GeneID

7353.

UCSC

uc002zpm.1. human.

Organism-specific databases

CTD

7353.

GeneCards

GC22M017812.

H-InvDB

HIX0016237.

HGNC

HGNC:12520. UFD1L.

MIM

601754. gene.

Orphanet

567. Monosomy 22q11.

PharmGKB

PA37167.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

HBG001266.

OrthoDB

EOG9B5RQW.

Gene expression databases

ArrayExpress

Q92890.

Bgee

Q92890.

CleanEx

HS_UFD1L.

Genevestigator

Q92890.

Family and domain databases

InterPro

IPR004854. UFD1.
[Graphical view]

Pfam

PF03152. UFD1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

28788.

SOURCE

Search...

Entry information

Entry name

UFD1_HUMAN

Accession

Primary (citable) accession number: Q92890
Secondary accession number(s): Q9Y5N0

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 13, 2007
Last modified:	March 2, 2010
This is version 82 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any 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.