P55854 (SUMO3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

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	103 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 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.9 Ref.15
Subunit structure	Covalently attached to a number of proteins 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.9 Ref.11 Ref.15
Subcellular location	Cytoplasm Ref.10.
Tissue specificity	Expressed predominantly in liver. Ref.13
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.8).

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cytoplasm
Coding sequence diversity	Polymorphism
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: Compara protein localization to nucleus Inferred from electronic annotation. Source: Compara protein sumoylation Inferred from direct assay PubMed 17696781. Source: UniProtKB
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell kinetochore Traceable author statement Ref.1. Source: ProtInc nuclear body Inferred from electronic annotation. Source: Compara
Molecular_function	SUMO ligase activity Inferred from electronic annotation. Source: Compara
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SART1	O43290	2	EBI-474067,EBI-607761
SP100	P23497	2	EBI-474067,EBI-751145

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 92

92

Small ubiquitin-related modifier 3

PRO_0000035957

Propeptide

93 – 103

11

PRO_0000035958

Regions

Domain

15 – 92

78

Ubiquitin-like

Amino acid modifications

Cross-link

11

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.9

Cross-link

92

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

Natural variations

Natural variant

38

1

P → S. Ref.1
Corresponds to variant rs1051311 [ dbSNP | Ensembl ].

VAR_052692

Experimental info

Mutagenesis

11

1

K → R: Abolishes the formation of poly(SUMO) chains. Ref.9

Mutagenesis

33

1

I → A: Impaired interaction with USP25; when associated with A-34. Ref.15

Mutagenesis

34

1

K → A: Impaired interaction with USP25; when associated with A-33. Ref.15

Sequence conflict

32

1

K → E in BAD96311. Ref.5

Sequence conflict

76

1

E → R in CAA67896. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

103

Helix Strand Turn

Details...

Beta strand

16 – 22

7

Turn

24 – 26

3

Beta strand

28 – 34

7

Beta strand

35 – 37

3

Helix

40 – 50

11

Helix

54 – 56

3

Beta strand

57 – 61

5

Turn

72 – 76

5

Beta strand

82 – 87

6

Beta strand

90 – 92

3

Sequences

	Sequence		Length	Mass (Da)
	P55854 [UniParc]. Last modified September 19, 2002. Version 2. Checksum: E337E34CB5B3B187	FASTA	103	11,637
	10 20 30 40 50 60 MSEEKPKEGV KTENDHINLK VAGQDGSVVQ FKIKRHTPLS KLMKAYCERQ GLSMRQIRFR 70 80 90 100 FDGQPINETD TPAQLEMEDE DTIDVFQQQT GGVPESSLAG HSF

References

	« Hide 'large scale' referencesShow '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], 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].
[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].
[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. , 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]. 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]. Tissue: Coronary artery.
[6]	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. , 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].
[7]	"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]. Tissue: Bone marrow and Kidney.
[8]	"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.
[9]	"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, MASS SPECTROMETRY, MUTAGENESIS OF LYS-11.
[10]	"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.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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.
[15]	"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.
[16]	"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].
[17]	"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.
[18]	"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.
AK312350 mRNA. Translation: BAG35271.1.
CH471079 Genomic DNA. Translation: EAX09392.1.
BC000036 mRNA. Translation: AAH00036.1.
BC008420 mRNA. Translation: AAH08420.1.

IPI

IPI00299147.

RefSeq

NP_008867.2. NM_006936.2.

UniGene

Hs.474005.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1U4A	NMR	-	A	14-92	[»]
2IO1	X-ray	2.60	B/D/F	14-103	[»]

ProteinModelPortal

P55854.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-29255N.

IntAct

P55854. 32 interactions.

MINT

MINT-1398263.

STRING

9606.ENSP00000330343.

PTM databases

PhosphoSite

P55854.

Polymorphism databases

DMDM

23503102.

Proteomic databases

PaxDb

P55854.

PRIDE

P55854.

Protocols and materials databases

DNASU

6612.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000332859; ENSP00000330343; ENSG00000184900.

GeneID

6612.

KEGG

hsa:6612.

UCSC

uc002zfz.1. human.

Organism-specific databases

CTD

6612.

GeneCards

GC21M046191.

HGNC

HGNC:11124. SUMO3.

HPA

CAB012180.

MIM

602231. gene.

neXtProt

NX_P55854.

PharmGKB

PA35973.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5227.

HOGENOM

HOG000207495.

HOVERGEN

HBG053025.

KO

K12160.

PhylomeDB

P55854.

Gene expression databases

ArrayExpress

P55854.

Bgee

P55854.

CleanEx

HS_SUMO3.

Genevestigator

P55854.

GermOnline

ENSG00000184900. Homo sapiens.

Family and domain databases

InterPro

IPR022617. SUMO.
IPR027218. SUMO_chordates.
IPR000626. Ubiquitin.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

PANTHER

PTHR10562:SF10. PTHR10562:SF10. 1 hit.

Pfam

PF11976. Rad60-SLD. 1 hit.
[Graphical view]

SMART

SM00213. UBQ. 1 hit.
[Graphical view]

PROSITE

PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

SUMO3. human.

EvolutionaryTrace

P55854.

GenomeRNAi

6612.

NextBio

25743.

SOURCE

Search...

Entry information

Entry name

SUMO3_HUMAN

Accession

Primary (citable) accession number: P55854
Secondary accession number(s): B2R5X4 , Q53HI9, Q6FGD4, Q9BWR4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	September 19, 2002
Last modified:	May 1, 2013
This is version 116 of the entry and version 2 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.