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Protein

Ubiquitin-fold modifier 1

Gene

UFM1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 (PubMed:15071506, PubMed:20018847). 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 (PubMed:15071506, PubMed:20018847). 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 (Probable).1 Publication3 Publications

GO - Biological processi

Keywordsi

Biological processUbl 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
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

EuPathDBiHostDB:ENSG00000120686.11
HGNCiHGNC:20597 UFM1
MIMi610553 gene
neXtProtiNX_P61960

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Leukodystrophy, hypomyelinating, 14 (HLD14)1 Publication
The disease is caused by mutations affecting the gene represented in this entry. The disease-causing variant may be a homozygous 3-bp deletion in the promoter region of the UFM1 gene, which segregates with the disorder in affected families. In vitro expression studies in different cell lines showed that the mutation significantly reduces transcriptional activity in certain neuronal cell lines (SY5Y and U373), but not in other cell lines, including HeLa and HOF-F2.1 Publication
Disease descriptionAn autosomal recessive, severe disorder characterized by atrophy of the basal ganglia and cerebellum, hypomyelination, severe developmental delay, typically without intentional movements and language development, and microcephaly. Almost all patients exhibit spasticity, extrapyramidal movement abnormalities, and severe drug-resistant epilepsy. Disease onset is early in infancy, and most patients die in the first years of life.
See also OMIM:617899

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi83G → A: Confers resistance to cleavage. 1 Publication1

Keywords - Diseasei

Leukodystrophy

Organism-specific databases

DisGeNETi51569
MalaCardsiUFM1
MIMi617899 phenotype
OpenTargetsiENSG00000120686
Orphaneti139441 Hypomyelination with atrophy of basal ganglia and cerebellum
PharmGKBiPA134863405

Polymorphism and mutation databases

DMDMi48428799

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000421221 – 83Ubiquitin-fold modifier 1Add BLAST83
PropeptideiPRO_000004212384 – 85Removed in mature form1 Publication2

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki69Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1)1 Publication
Cross-linki83Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)2 Publications

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiP61960
MaxQBiP61960
PaxDbiP61960
PeptideAtlasiP61960
PRIDEiP61960
ProteomicsDBi57344
57345 [P61960-2]
TopDownProteomicsiP61960-1 [P61960-1]
P61960-2 [P61960-2]

PTM databases

iPTMnetiP61960
PhosphoSitePlusiP61960

Expressioni

Inductioni

Up-regulated by thapsigargin.1 Publication

Gene expression databases

BgeeiENSG00000120686 Expressed in 235 organ(s), highest expression level in amniotic fluid
CleanExiHS_UFM1
ExpressionAtlasiP61960 baseline and differential
GenevisibleiP61960 HS

Organism-specific databases

HPAiHPA039758

Interactioni

Subunit structurei

Interacts with UBA5.1 Publication

Protein-protein interaction databases

BioGridi119616, 84 interactors
IntActiP61960, 12 interactors
MINTiP61960
STRINGi9606.ENSP00000239878

Structurei

Secondary structure

185
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP61960
SMRiP61960
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61960

Family & Domainsi

Sequence similaritiesi

Belongs to the UFM1 family.Curated

Phylogenomic databases

eggNOGiKOG3483 Eukaryota
ENOG4111TVI LUCA
GeneTreeiENSGT00390000010391
HOGENOMiHOG000238677
HOVERGENiHBG094129
InParanoidiP61960
KOiK12162
OMAiPWQTSAI
OrthoDBiEOG091G0DO7
PhylomeDBiP61960
TreeFamiTF312934

Family and domain databases

CDDicd01766 Ufm1, 1 hit
InterProiView protein in InterPro
IPR029071 Ubiquitin-like_domsf
IPR005375 UFM1
PANTHERiPTHR15825 PTHR15825, 1 hit
PfamiView protein in Pfam
PF03671 Ufm1, 1 hit
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

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y614H0Y614_HUMAN
Ubiquitin-fold modifier 1
UFM1
81Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti12S → W in CAA94181 (Ref. 7) Curated1
Sequence conflicti78 – 80PRD → LEI in CAA94181 (Ref. 7) Curated3

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0411861 – 20MSKVS…LPYKV → MIRAFPTTTPRSLHLFTSST FLARALPGAFPTGACEER in isoform 2. 1 PublicationAdd BLAST20

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 No translation available.
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.5 human [P61960-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

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 No translation available.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WXSNMR-A1-85[»]
5HKHX-ray2.55A/C2-83[»]
5IA7X-ray2.00A/B1-83[»]
5IA8X-ray2.00A/B2-83[»]
5IAAX-ray1.85C/D1-83[»]
5L95X-ray2.10C/D4-83[»]
ProteinModelPortaliP61960
SMRiP61960
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119616, 84 interactors
IntActiP61960, 12 interactors
MINTiP61960
STRINGi9606.ENSP00000239878

PTM databases

iPTMnetiP61960
PhosphoSitePlusiP61960

Polymorphism and mutation databases

DMDMi48428799

Proteomic databases

EPDiP61960
MaxQBiP61960
PaxDbiP61960
PeptideAtlasiP61960
PRIDEiP61960
ProteomicsDBi57344
57345 [P61960-2]
TopDownProteomicsiP61960-1 [P61960-1]
P61960-2 [P61960-2]

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.5 human [P61960-1]

Organism-specific databases

CTDi51569
DisGeNETi51569
EuPathDBiHostDB:ENSG00000120686.11
GeneCardsiUFM1
HGNCiHGNC:20597 UFM1
HPAiHPA039758
MalaCardsiUFM1
MIMi610553 gene
617899 phenotype
neXtProtiNX_P61960
OpenTargetsiENSG00000120686
Orphaneti139441 Hypomyelination with atrophy of basal ganglia and cerebellum
PharmGKBiPA134863405
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3483 Eukaryota
ENOG4111TVI LUCA
GeneTreeiENSGT00390000010391
HOGENOMiHOG000238677
HOVERGENiHBG094129
InParanoidiP61960
KOiK12162
OMAiPWQTSAI
OrthoDBiEOG091G0DO7
PhylomeDBiP61960
TreeFamiTF312934

Miscellaneous databases

ChiTaRSiUFM1 human
EvolutionaryTraceiP61960
GeneWikiiUFM1
GenomeRNAii51569
PROiPR:P61960
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000120686 Expressed in 235 organ(s), highest expression level in amniotic fluid
CleanExiHS_UFM1
ExpressionAtlasiP61960 baseline and differential
GenevisibleiP61960 HS

Family and domain databases

CDDicd01766 Ufm1, 1 hit
InterProiView protein in InterPro
IPR029071 Ubiquitin-like_domsf
IPR005375 UFM1
PANTHERiPTHR15825 PTHR15825, 1 hit
PfamiView protein in Pfam
PF03671 Ufm1, 1 hit
PIRSFiPIRSF038027 Ubiquitin-like_Ufm1, 1 hit
SUPFAMiSSF54236 SSF54236, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiUFM1_HUMAN
AccessioniPrimary (citable) accession number: P61960
Secondary accession number(s): Q14346
, Q5VXS0, Q6IAG6, Q9CPX2, Q9NZF2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2004
Last sequence update: June 7, 2004
Last modified: November 7, 2018
This is version 142 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human chromosome 13
    Human chromosome 13: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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