O24454 (UBP3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin carboxyl-terminal hydrolase 3
EC=3.4.19.12

Alternative name(s):
Deubiquitinating enzyme 3
Short name=AtUBP3
Ubiquitin thioesterase 3
Ubiquitin-specific-processing protease 3

Gene names

Name:	UBP3
Ordered Locus Names:	At4g39910
ORF Names:	T5J17.80

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	371 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	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Required for the correct development of pollen. Ref.5 Ref.8
Catalytic activity	Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Subcellular location	Nucleus Ref.1.
Tissue specificity	Constitutively and ubiquitously expressed. Ref.1
Sequence similarities	Belongs to the peptidase C19 family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Nucleus
Molecular function	Hydrolase Protease Thiol protease
PTM	Lipoprotein Myristate
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	cysteine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Potential
	Chain	2 – 371	370	Ubiquitin carboxyl-terminal hydrolase 3		PRO_0000080694
Regions
	Motif	83 – 100	18	Bipartite nuclear localization signal Potential
Sites
	Active site	32	1	Nucleophile
	Active site	315	1	Proton acceptor By similarity
Amino acid modifications
	Lipidation	2	1	N-myristoyl glycine Ref.7
Experimental info
	Mutagenesis	32	1	C → S: Loss of activity. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	O24454 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: 2C843280BDF24D3B	FASTA	371	42,447
	10 20 30 40 50 60 MGAAGSKLEK ALGDQFPEGE RYFGFENFGN TCYCNSVLQA LYFCVPFREQ LLEYYTSNKS 70 80 90 100 110 120 VADAEENLMT CLADLFSQIS SQKKKTGVIA PKRFVQRLKK QNELFRSYMH QDAHEFLNYL 130 140 150 160 170 180 LNEVVDILEK EAKATKTEHE TSSSSSPEKI ANGLKVPQAN GVVHKEPIVT WVHNIFQGIL 190 200 210 220 230 240 TNETRCLRCE TVTARDETFL DLSLDIEQNS SITSCLKNFS STETLHAEDK FFCDKCCSLQ 250 260 270 280 290 300 EAQKRMKIKK PPHILVIHLK RFKYIEQLGR YKKLSYRVVF PLELKLSNTV EPYADVEYSL 310 320 330 340 350 360 FAVVVHVGSG PNHGHYVSLV KSHNHWLFFD DENVEMIEES AVQTFFGSSQ EYSSNTDHGY 370 ILFYESLGPT K

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"AtUBP3 and AtUBP4 are two closely related Arabidopsis thaliana ubiquitin-specific proteases present in the nucleus." Chandler J.S., McArdle B., Callis J. Mol. Gen. Genet. 255:302-310(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-32, TISSUE SPECIFICITY. Strain: cv. Landsberg erecta.
[2]	"Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana." Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B. , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R. Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5 and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using Escherichia coli in vivo and in vitro assays." Rao-Naik C., Chandler J.S., McArdle B., Callis J. Arch. Biochem. Biophys. 379:198-208(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are required for the resistance to the amino acid analog canavanine." Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D. Plant Physiol. 124:1828-1843(2000) [PubMed] [Europe PMC] [Abstract] Cited for: GENE FAMILY ORGANIZATION, NOMENCLATURE.
[7]	"Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote." Boisson B., Giglione C., Meinnel T. J. Biol. Chem. 278:43418-43429(2003) [PubMed] [Europe PMC] [Abstract] Cited for: N-MYRISTOYLATION.
[8]	"The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for pollen development and transmission in Arabidopsis." Doelling J.H., Phillips A.R., Soyler-Ogretim G., Wise J., Chandler J.S., Callis J., Otegui M.S., Vierstra R.D. Plant Physiol. 145:801-813(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U76845 mRNA. Translation: AAB67966.1. AL035708 Genomic DNA. Translation: CAB38904.1. AL161596 Genomic DNA. Translation: CAB80654.1. CP002687 Genomic DNA. Translation: AEE87136.1. AY058889 mRNA. Translation: AAL24275.1. AY079044 mRNA. Translation: AAL79594.1.
IPI	IPI00529126.
PIR	T06097.
RefSeq	NP_568074.1. NM_120154.4.
UniGene	At.24733.
3D structure databases
ProteinModelPortal	O24454.
SMR	O24454. Positions 19-365.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT4G39910.1-P.
Protein family/group databases
MEROPS	C19.008.
Proteomic databases
PaxDb	O24454.
PRIDE	O24454.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT4G39910.1; AT4G39910.1; AT4G39910.
GeneID	830150.
KEGG	ath:AT4G39910.
Organism-specific databases
GeneFarm	4911.
TAIR	At4g39910.
Phylogenomic databases
eggNOG	COG5533.
HOGENOM	HOG000231498.
InParanoid	O24454.
KO	K11842.
OMA	TEPTWVH.
PhylomeDB	O24454.
ProtClustDB	CLSN2688340.
Gene expression databases
Genevestigator	O24454.
GermOnline	AT4G39910. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. [Graphical view]
Pfam	PF00443. UCH. 1 hit. [Graphical view]
PROSITE	PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

UBP3_ARATH

Accession

Primary (citable) accession number: O24454

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2005
Last sequence update:	January 1, 1998
Last modified:	May 1, 2013
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program