P61960 (UFM1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-fold modifier 1

Gene names

Name:	UFM1
Synonyms:	C13orf20
ORF Names:	BM-002

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	85 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ubiquitin-like modifier protein which binds to a number of target proteins, such as DDRGK1. Ref.1 Ref.8
Subcellular location	Nucleus. Cytoplasm. Note: Predominantly nuclear. Also expressed diffusely in the cytoplasm. Ref.1
Sequence similarities	Belongs to the UFM1 family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing
PTM	Isopeptide bond
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein ufmylation Inferred from direct assay Ref.1. Source: UniProtKB
Cellular_component	cytoplasm Inferred from direct assay Ref.1. Source: UniProtKB nucleus Inferred from direct assay Ref.1. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CDK5RAP3	Q96JB5	1	EBI-1045061,EBI-718818

Alternative products

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

Isoform 1 (identifier: P61960-1)

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.

Isoform 2 (identifier: P61960-2)

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

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 83

83

Ubiquitin-fold modifier 1

PRO_0000042122

Propeptide

84 – 85

2

Removed in mature form

PRO_0000042123

Amino acid modifications

Cross-link

83

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) Potential

Natural variations

Alternative sequence

1 – 20

20

MSKVS…LPYKV → MIRAFPTTTPRSLHLFTSST FLARALPGAFPTGACEER in isoform 2.

VSP_041186

Experimental info

Mutagenesis

83

1

G → A: Confers resistance to cleavage. Ref.1

Sequence conflict

12

1

S → W in CAA94181. Ref.7

Sequence conflict

78 – 80

3

PRD → LEI in CAA94181. Ref.7

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

85

Helix Strand Turn

Details...

Beta strand

4 – 11

8

Beta strand

14 – 16

3

Beta strand

20 – 23

4

Beta strand

25 – 28

4

Helix

29 – 39

11

Beta strand

44 – 53

10

Helix

63 – 69

7

Beta strand

72 – 79

8

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 7, 2004. Version 1. Checksum: EDB2412E5E5836D8	FASTA	85	9,118
	10 20 30 40 50 60 MSKVSFKITL TSDPRLPYKV LSVPESTPFT AVLKFAAEEF KVPAATSAII TNDGIGINPA 70 80 QTAGNVFLKH GSELRIIPRD RVGSC
	Isoform 2 [UniParc]. Checksum: BA4D1DE2215D5ACC	FASTA	103	10,960
	10 20 30 40 50 60 MIRAFPTTTP RSLHLFTSST FLARALPGAF PTGACEERLS VPESTPFTAV LKFAAEEFKV 70 80 90 100 PAATSAIITN DGIGINPAQT AGNVFLKHGS ELRIIPRDRV GSC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes." Kimura K., Wakamatsu A., Suzuki Y., Ota T., Nishikawa T., Yamashita R., Yamamoto J., Sekine M., Tsuritani K., Wakaguri H., Ishii S., Sugiyama T., Saito K., Isono Y., Irie R., Kushida N., Yoneyama T., Otsuka R. , Kanda K., Yokoi T., Kondo H., Wagatsuma M., Murakawa K., Ishida S., Ishibashi T., Takahashi-Fujii A., Tanase T., Nagai K., Kikuchi H., Nakai K., Isogai T., Sugano S. Genome Res. 16:55-65(2006) [PubMed] [Europe PMC] [Abstract] 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]	"A novel type of E3 ligase for the Ufm1 conjugation system." Tatsumi K., Sou Y.S., Tada N., Nakamura E., Iemura S., Natsume T., Kang S.H., Chung C.H., Kasahara M., Kominami E., Yamamoto M., Tanaka K., Komatsu M. J. Biol. Chem. 285:5417-5427(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]	"Solution structure and dynamics of Ufm1, a ubiquitin-fold modifier 1." Sasakawa H., Sakata E., Yamaguchi Y., Komatsu M., Tatsumi K., Kominami E., Tanaka K., Kato K. Biochem. Biophys. Res. Commun. 343:21-26(2006) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00010207.
IPI00477342.

RefSeq

NP_057701.1. NM_016617.2.

UniGene

Hs.643655.
Hs.741337.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WXS	NMR	-	A	1-85	[»]

ProteinModelPortal

P61960.

ModBase

Search...

Protein-protein interaction databases

IntAct

P61960. 1 interaction.

STRING

9606.ENSP00000239878.

PTM databases

PhosphoSite

P61960.

Polymorphism databases

DMDM

48428799.

Proteomic databases

PaxDb

P61960.

PRIDE

P61960.

Protocols and materials databases

DNASU

51569.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000239878; ENSP00000239878; ENSG00000120686.
ENST00000379641; ENSP00000368962; ENSG00000120686.
ENST00000379649; ENSP00000368970; ENSG00000120686.

GeneID

51569.

KEGG

hsa:51569.

UCSC

uc001uwu.3. human.

Organism-specific databases

CTD

51569.

GeneCards

GC13P038923.

HGNC

HGNC:20597. UFM1.

HPA

HPA039758.

MIM

610553. gene.

neXtProt

NX_P61960.

PharmGKB

PA134863405.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG249065.

HOGENOM

HOG000238677.

HOVERGEN

HBG094129.

KO

K12162.

OMA

DPKLPYK.

OrthoDB

EOG46MBM3.

PhylomeDB

P61960.

Gene expression databases

ArrayExpress

P61960.

Bgee

P61960.

CleanEx

HS_UFM1.

Genevestigator

P61960.

GermOnline

ENSG00000120686. Homo sapiens.

Family and domain databases

InterPro

IPR005375. UFM1.
[Graphical view]

Pfam

PF03671. Ufm1. 1 hit.
[Graphical view]

PIRSF

PIRSF038027. Ubiquitin-like_Ufm1. 1 hit.

ProtoNet

Search...

Other

ChiTaRS

UFM1. human.

EvolutionaryTrace

P61960.

GenomeRNAi

51569.

NextBio

55392.

SOURCE

Search...

Entry information

Entry name

UFM1_HUMAN

Accession

Primary (citable) accession number: P61960
Secondary accession number(s): Q14346 , Q5VXS0, Q6IAG6, Q9CPX2, Q9NZF2

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2004
Last sequence update:	June 7, 2004
Last modified:	May 1, 2013
This is version 94 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

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.