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P55854 (SUMO3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Small ubiquitin-related modifier 3

Short name=SUMO-3
Alternative name(s):
SMT3 homolog 1
SUMO-2
Ubiquitin-like protein SMT3B
Short name=Smt3B
Gene names
Name:SUMO3
Synonyms:SMT3B, SMT3H1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length103 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Ubiquitin-like protein which can be covalently attached to target lysines either as a monomer or as a lysine-linked polymer. Does not seem to be involved in protein degradation and may function as an antagonist of ubiquitin in the degradation process. Plays a role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Covalent attachment to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by an E3 ligase such as PIAS1-4, RANBP2 or CBX4. Ref.10 Ref.16

Subunit structure

Covalently attached to a number of proteins By similarity. Interacts with ARNTL/BMAL1 By similarity. Interacts with USP25 (via ts SIM domain); the interaction sumoylates USP25 and inhibits its ubiquitin hydrolyzing activity. Interacts with SAE2 and UBE2I. Ref.10 Ref.12 Ref.16

Subcellular location

Cytoplasm. NucleusPML body By similarity Ref.11.

Tissue specificity

Expressed predominantly in liver. Ref.14

Post-translational modification

Polymeric chains can be formed through Lys-11 cross-linking.

Cleavage of precursor form by SENP1, SENP2 or SENP5 is necessary for function.

Sequence similarities

Belongs to the ubiquitin family. SUMO subfamily.

Contains 1 ubiquitin-like domain.

Caution

Frequently wrongly assigned as SMT3A in many databases and publications. However, according to initial nomenclature, SUMO3 corresponds to SMT3B (Ref.9).

Binary interactions

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P55854-1)

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: P55854-2)

The sequence of this isoform differs from the canonical sequence as follows:
     50-50: Q → QVRHLAPPQSLPVCALVLCVPGIPRARASRGWTQMQLPE
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 9292Small ubiquitin-related modifier 3
PRO_0000035957
Propeptide93 – 10311
PRO_0000035958

Regions

Domain15 – 9278Ubiquitin-like

Amino acid modifications

Cross-link11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.10
Cross-link92Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Natural variations

Alternative sequence501Q → QVRHLAPPQSLPVCALVLCV PGIPRARASRGWTQMQLPE in isoform 2.
VSP_054693
Natural variant381P → S. Ref.1
Corresponds to variant rs1051311 [ dbSNP | Ensembl ].
VAR_052692

Experimental info

Mutagenesis111K → R: Abolishes the formation of poly(SUMO) chains. Ref.10
Mutagenesis331I → A: Impaired interaction with USP25; when associated with A-34. Ref.16
Mutagenesis341K → A: Impaired interaction with USP25; when associated with A-33. Ref.16
Sequence conflict321K → E in BAD96311. Ref.5
Sequence conflict761E → R in CAA67896. Ref.1

Secondary structure

................... 103
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified September 19, 2002. Version 2.
Checksum: E337E34CB5B3B187

FASTA10311,637
        10         20         30         40         50         60 
MSEEKPKEGV KTENDHINLK VAGQDGSVVQ FKIKRHTPLS KLMKAYCERQ GLSMRQIRFR 

        70         80         90        100 
FDGQPINETD TPAQLEMEDE DTIDVFQQQT GGVPESSLAG HSF 

« Hide

Isoform 2 [UniParc].

Checksum: B4D3FDFE12CD6B12
Show »

FASTA14115,768

References

« Hide 'large scale' references
[1]"SMT3A, a human homologue of the S. cerevisiae SMT3 gene, maps to chromosome 21qter and defines a novel gene family."
Lapenta V., Chiurazzi P., van der Spek P.J., Pizzuti A., Hanaoka F., Brahe C.
Genomics 40:362-367(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT SER-38.
Tissue: Brain.
[2]"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 (OCT-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[3]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S., Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W., Korn B., Zuo D., Hu Y., LaBaer J.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[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] (ISOFORMS 1 AND 2).
Tissue: Brain cortex.
[5]Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Coronary artery.
[6]"The DNA sequence of human chromosome 21."
Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.-S., Toyoda A., Ishii K., Totoki Y., Choi D.-K., Groner Y., Soeda E., Ohki M., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., Polley A. expand/collapse author list , Menzel U., Delabar J., Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M., Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K., Asakawa S., Shintani A., Sasaki T., Nagamine K., Mitsuyama S., Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K., Brandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G., Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L., Dagand E., Wehrmeyer S., Borzym K., Gardiner K., Nizetic D., Francis F., Lehrach H., Reinhardt R., Yaspo M.-L.
Nature 405:311-319(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]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 (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]"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: Bone marrow and Kidney.
[9]"Functional heterogeneity of small ubiquitin-related protein modifiers SUMO-1 versus SUMO-2/3."
Saitoh H., Hinchey J.
J. Biol. Chem. 275:6252-6258(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION.
[10]"Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9."
Tatham M.H., Jaffray E., Vaughan O.A., Desterro J.M.P., Botting C.H., Naismith J.H., Hay R.T.
J. Biol. Chem. 276:35368-35374(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SUMOYLATION OF PML, POLYSUMOYLATION, INTERACTION WITH SAE1 AND UBE2I, SUMOYLATION AT LYS-11, IDENTIFICATION BY MASS SPECTROMETRY, MUTAGENESIS OF LYS-11.
[11]"Molecular features of human ubiquitin-like SUMO genes and their encoded proteins."
Su H.-L., Li S.S.-L.
Gene 296:65-73(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[12]"Role of an N-terminal site of Ubc9 in SUMO-1, -2, and -3 binding and conjugation."
Tatham M.H., Kim S., Yu B., Jaffray E., Song J., Zheng J., Rodriguez M.S., Hay R.T., Chen Y.
Biochemistry 42:9959-9969(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH UBE2I.
[13]"A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex."
Reverter D., Lima C.D.
Structure 12:1519-1531(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: CLEAVAGE.
[14]"Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1."
Xu Z., Au S.W.N.
Biochem. J. 386:325-330(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: CLEAVAGE, TISSUE SPECIFICITY.
[15]"Characterization of a family of nucleolar SUMO-specific proteases with preference for SUMO-2 or SUMO-3."
Gong L., Yeh E.T.H.
J. Biol. Chem. 281:15869-15877(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: CLEAVAGE.
[16]"Mechanism and consequences for paralog-specific sumoylation of ubiquitin-specific protease 25."
Meulmeester E., Kunze M., Hsiao H.H., Urlaub H., Melchior F.
Mol. Cell 30:610-619(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SUMOYLATION OF USP25, INTERACTION WITH USP25, MUTAGENESIS OF ILE-33 AND LYS-34.
[17]"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].
[18]"Solution structure of human SUMO-3 C47S and its binding surface for Ubc9."
Ding H., Xu Y., Chen Q., Dai H., Tang Y., Wu J., Shi Y.
Biochemistry 44:2790-2799(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 14-92.
[19]"The structure of SENP1-SUMO-2 complex suggests a structural basis for discrimination between SUMO paralogues during processing."
Shen L.N., Dong C., Liu H., Naismith J.H., Hay R.T.
Biochem. J. 397:279-288(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) IN COMPLEX WITH SENP1, CLEAVAGE.
+Additional computationally mapped references.

Web resources

Wikipedia

SUMO protein entry

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X99584 mRNA. Translation: CAA67896.1.
BT007008 mRNA. Translation: AAP35654.1.
CR542173 mRNA. Translation: CAG46970.1.
CR542188 mRNA. Translation: CAG46985.1.
AK222591 mRNA. Translation: BAD96311.1.
AK300822 mRNA. Translation: BAG62476.1.
AK312350 mRNA. Translation: BAG35271.1.
AL773603 Genomic DNA. No translation available.
CH471079 Genomic DNA. Translation: EAX09392.1.
BC000036 mRNA. Translation: AAH00036.1.
BC008420 mRNA. Translation: AAH08420.1.
CCDSCCDS33587.1.
RefSeqNP_001273345.1. NM_001286416.1. [P55854-2]
NP_008867.2. NM_006936.2. [P55854-1]
UniGeneHs.474005.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1U4ANMR-A14-92[»]
2IO1X-ray2.60B/D/F14-103[»]
ProteinModelPortalP55854.
SMRP55854. Positions 14-88.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112496. 138 interactions.
DIPDIP-29255N.
IntActP55854. 49 interactions.
MINTMINT-1398263.
STRING9606.ENSP00000330343.

PTM databases

PhosphoSiteP55854.

Polymorphism databases

DMDM23503102.

Proteomic databases

MaxQBP55854.
PaxDbP55854.
PRIDEP55854.

Protocols and materials databases

DNASU6612.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000332859; ENSP00000330343; ENSG00000184900.
ENST00000411651; ENSP00000409666; ENSG00000184900.
GeneID6612.
KEGGhsa:6612.
UCSCuc002zfz.1. human. [P55854-1]

Organism-specific databases

CTD6612.
GeneCardsGC21M046548.
HGNCHGNC:11124. SUMO3.
HPACAB012180.
HPA042123.
HPA048064.
MIM602231. gene.
neXtProtNX_P55854.
PharmGKBPA35973.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5227.
HOGENOMHOG000207495.
HOVERGENHBG053025.
KOK12160.
PhylomeDBP55854.
TreeFamTF315116.

Enzyme and pathway databases

ReactomeREACT_17015. Metabolism of proteins.

Gene expression databases

ArrayExpressP55854.
BgeeP55854.
CleanExHS_SUMO3.
GenevestigatorP55854.

Family and domain databases

InterProIPR022617. Rad60/SUMO_like.
IPR027218. SUMO_chordates.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PANTHERPTHR10562:SF10. PTHR10562:SF10. 1 hit.
PfamPF11976. Rad60-SLD. 1 hit.
[Graphical view]
SMARTSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMSSF54236. SSF54236. 1 hit.
PROSITEPS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSUMO3. human.
EvolutionaryTraceP55854.
GeneWikiSUMO3.
GenomeRNAi6612.
NextBio25743.
PROP55854.
SOURCESearch...

Entry information

Entry nameSUMO3_HUMAN
AccessionPrimary (citable) accession number: P55854
Secondary accession number(s): B2R5X4 expand/collapse secondary AC list , B4DUW4, Q53HI9, Q6FGD4, Q9BWR4
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: September 19, 2002
Last modified: July 9, 2014
This is version 129 of the entry and version 2 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

MIM cross-references

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

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 21

Human chromosome 21: entries, gene names and cross-references to MIM