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Protein

Ubiquitin-fold modifier 1

Gene

UFM1

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

Functioni

Ubiquitin-like modifier which can be covalently attached via an isopeptide bond to substrate proteins as a monomer or a lysine-linked polymer. The so-called ufmylation, requires the UFM1-activating E1 enzyme UBA5, the UFM1-conjugating E2 enzyme UFC1, and the UFM1-ligase E3 enzyme UFL1 (PubMed:15071506, PubMed:20018847). This post-translational modification on lysine residues of proteins may play a crucial role in a number of cellular processes. TRIP4 ufmylation may for instance play a role in nuclear receptors-mediated transcription (PubMed:25219498). Other substrates may include DDRGK1 with which it may play a role in the cellular response to endoplasmic reticulum stress (By similarity).By similarity3 Publications

GO - Biological processi

  1. protein polyufmylation Source: UniProtKB
  2. protein ufmylation Source: UniProtKB
  3. regulation of intracellular estrogen receptor signaling pathway Source: UniProtKB
  4. response to endoplasmic reticulum stress Source: MGI
Complete GO annotation...

Keywords - Biological processi

Ubl conjugation pathway

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-fold modifier 1
Gene namesi
Name:UFM1
Synonyms:C13orf20
ORF Names:BM-002
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 13

Organism-specific databases

HGNCiHGNC:20597. UFM1.

Subcellular locationi

Nucleus 1 Publication. Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. extracellular vesicular exosome Source: UniProtKB
  3. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi83 – 831G → A: Confers resistance to cleavage. 1 Publication

Organism-specific databases

PharmGKBiPA134863405.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8383Ubiquitin-fold modifier 1PRO_0000042122Add
BLAST
Propeptidei84 – 852Removed in mature form1 PublicationPRO_0000042123

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki69 – 69Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1)1 Publication
Cross-linki83 – 83Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)2 Publications

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP61960.
PaxDbiP61960.
PRIDEiP61960.

PTM databases

PhosphoSiteiP61960.

Expressioni

Gene expression databases

BgeeiP61960.
CleanExiHS_UFM1.
GenevestigatoriP61960.

Organism-specific databases

HPAiHPA039758.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
CDK5RAP3Q96JB51EBI-1045061,EBI-718818

Protein-protein interaction databases

BioGridi119616. 48 interactions.
IntActiP61960. 6 interactions.
MINTiMINT-7005139.
STRINGi9606.ENSP00000239878.

Structurei

Secondary structure

1
85
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118Combined sources
Beta strandi14 – 163Combined sources
Beta strandi20 – 234Combined sources
Beta strandi25 – 284Combined sources
Helixi29 – 3911Combined sources
Beta strandi44 – 5310Combined sources
Helixi63 – 697Combined sources
Beta strandi72 – 798Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WXSNMR-A1-85[»]
ProteinModelPortaliP61960.
SMRiP61960. Positions 1-85.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61960.

Family & Domainsi

Sequence similaritiesi

Belongs to the UFM1 family.Curated

Phylogenomic databases

eggNOGiNOG249065.
GeneTreeiENSGT00390000010391.
HOGENOMiHOG000238677.
HOVERGENiHBG094129.
InParanoidiP61960.
KOiK12162.
OMAiVTFKIIL.
OrthoDBiEOG7Q8CQW.
PhylomeDBiP61960.
TreeFamiTF312934.

Family and domain databases

InterProiIPR029071. Ubiquitin-rel_dom.
IPR005375. UFM1.
[Graphical view]
PfamiPF03671. Ufm1. 1 hit.
[Graphical view]
PIRSFiPIRSF038027. Ubiquitin-like_Ufm1. 1 hit.
SUPFAMiSSF54236. SSF54236. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P61960-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MSKVSFKITL TSDPRLPYKV LSVPESTPFT AVLKFAAEEF KVPAATSAII
60 70 80
TNDGIGINPA QTAGNVFLKH GSELRIIPRD RVGSC
Length:85
Mass (Da):9,118
Last modified:June 7, 2004 - v1
Checksum:iEDB2412E5E5836D8
GO
Isoform 2 (identifier: P61960-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-20: MSKVSFKITLTSDPRLPYKV → MIRAFPTTTPRSLHLFTSSTFLARALPGAFPTGACEER

Show »
Length:103
Mass (Da):10,960
Checksum:iBA4D1DE2215D5ACC
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti12 – 121S → W in CAA94181 (Ref. 7) Curated
Sequence conflicti78 – 803PRD → LEI in CAA94181 (Ref. 7) Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2020MSKVS…LPYKV → MIRAFPTTTPRSLHLFTSST FLARALPGAFPTGACEER in isoform 2. 1 PublicationVSP_041186Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB154404 mRNA. Translation: BAD15373.1.
AF208844 mRNA. Translation: AAF64258.1.
CR457189 mRNA. Translation: CAG33470.1.
DA664581 mRNA. No translation available.
AL356863 Genomic DNA. Translation: CAH70411.1.
AL356863 Genomic DNA. Translation: CAH70414.1.
BC005193 mRNA. Translation: AAH05193.1.
Z70222 mRNA. Translation: CAA94181.1.
CCDSiCCDS66533.1. [P61960-2]
CCDS9366.1. [P61960-1]
RefSeqiNP_001273632.1. NM_001286703.1.
NP_001273633.1. NM_001286704.1. [P61960-2]
NP_001273634.1. NM_001286705.1.
NP_001273635.1. NM_001286706.1.
NP_057701.1. NM_016617.3. [P61960-1]
UniGeneiHs.643655.

Genome annotation databases

EnsembliENST00000239878; ENSP00000239878; ENSG00000120686. [P61960-1]
ENST00000379649; ENSP00000368970; ENSG00000120686. [P61960-2]
GeneIDi51569.
KEGGihsa:51569.
UCSCiuc001uwu.3. human. [P61960-1]

Polymorphism databases

DMDMi48428799.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB154404 mRNA. Translation: BAD15373.1.
AF208844 mRNA. Translation: AAF64258.1.
CR457189 mRNA. Translation: CAG33470.1.
DA664581 mRNA. No translation available.
AL356863 Genomic DNA. Translation: CAH70411.1.
AL356863 Genomic DNA. Translation: CAH70414.1.
BC005193 mRNA. Translation: AAH05193.1.
Z70222 mRNA. Translation: CAA94181.1.
CCDSiCCDS66533.1. [P61960-2]
CCDS9366.1. [P61960-1]
RefSeqiNP_001273632.1. NM_001286703.1.
NP_001273633.1. NM_001286704.1. [P61960-2]
NP_001273634.1. NM_001286705.1.
NP_001273635.1. NM_001286706.1.
NP_057701.1. NM_016617.3. [P61960-1]
UniGeneiHs.643655.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WXSNMR-A1-85[»]
ProteinModelPortaliP61960.
SMRiP61960. Positions 1-85.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119616. 48 interactions.
IntActiP61960. 6 interactions.
MINTiMINT-7005139.
STRINGi9606.ENSP00000239878.

PTM databases

PhosphoSiteiP61960.

Polymorphism databases

DMDMi48428799.

Proteomic databases

MaxQBiP61960.
PaxDbiP61960.
PRIDEiP61960.

Protocols and materials databases

DNASUi51569.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000239878; ENSP00000239878; ENSG00000120686. [P61960-1]
ENST00000379649; ENSP00000368970; ENSG00000120686. [P61960-2]
GeneIDi51569.
KEGGihsa:51569.
UCSCiuc001uwu.3. human. [P61960-1]

Organism-specific databases

CTDi51569.
GeneCardsiGC13P038923.
HGNCiHGNC:20597. UFM1.
HPAiHPA039758.
MIMi610553. gene.
neXtProtiNX_P61960.
PharmGKBiPA134863405.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG249065.
GeneTreeiENSGT00390000010391.
HOGENOMiHOG000238677.
HOVERGENiHBG094129.
InParanoidiP61960.
KOiK12162.
OMAiVTFKIIL.
OrthoDBiEOG7Q8CQW.
PhylomeDBiP61960.
TreeFamiTF312934.

Miscellaneous databases

ChiTaRSiUFM1. human.
EvolutionaryTraceiP61960.
GeneWikiiUFM1.
GenomeRNAii51569.
NextBioi55392.
PROiP61960.
SOURCEiSearch...

Gene expression databases

BgeeiP61960.
CleanExiHS_UFM1.
GenevestigatoriP61960.

Family and domain databases

InterProiIPR029071. Ubiquitin-rel_dom.
IPR005375. UFM1.
[Graphical view]
PfamiPF03671. Ufm1. 1 hit.
[Graphical view]
PIRSFiPIRSF038027. Ubiquitin-like_Ufm1. 1 hit.
SUPFAMiSSF54236. SSF54236. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier."
    Komatsu M., Chiba T., Tatsumi K., Iemura S., Tanida I., Okazaki N., Ueno T., Kominami E., Natsume T., Tanaka K.
    EMBO J. 23:1977-1986(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF GLY-83.
  2. "Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells."
    Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G., Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W., Tao J., Huang Q.-H., Zhou J., Hu G.-X.
    , Gu J., Chen S.-J., Chen Z.
    Genome Res. 10:1546-1560(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Bone marrow.
  3. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
    Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
    Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Neuroblastoma.
  5. "The DNA sequence and analysis of human chromosome 13."
    Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
    Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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] (ISOFORM 1).
    Tissue: Kidney.
  7. "Characterization of different mRNA types expressed in human brain."
    Dmitrenko V.V., Garifulin O.M., Kavsan V.M.
    Submitted (MAR-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-80 (ISOFORM 1).
    Tissue: Brain.
  8. Cited for: FUNCTION.
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "Modification of ASC1 by UFM1 is crucial for ERalpha transactivation and breast cancer development."
    Yoo H.M., Kang S.H., Kim J.Y., Lee J.E., Seong M.W., Lee S.W., Ka S.H., Sou Y.S., Komatsu M., Tanaka K., Lee S.T., Noh D.Y., Baek S.H., Jeon Y.J., Chung C.H.
    Mol. Cell 56:261-274(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, UFMYLATION AT LYS-69.
  11. Cited for: STRUCTURE BY NMR.

Entry informationi

Entry nameiUFM1_HUMAN
AccessioniPrimary (citable) accession number: P61960
Secondary accession number(s): Q14346
, Q5VXS0, Q6IAG6, Q9CPX2, Q9NZF2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: June 7, 2004
Last modified: March 4, 2015
This is version 110 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 13
    Human chromosome 13: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
  5. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.