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O24454 (UBP3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 92. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length371 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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.

Contains 1 USP domain.

Ontologies

Keywords
   Biological processUbl conjugation pathway
   Cellular componentNucleus
   Molecular functionHydrolase
Protease
Thiol protease
   PTMLipoprotein
Myristate
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processubiquitin-dependent protein catabolic process

Inferred from electronic annotation. Source: InterPro

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioncysteine-type peptidase activity

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Potential
Chain2 – 371370Ubiquitin carboxyl-terminal hydrolase 3
PRO_0000080694

Regions

Domain23 – 367345USP
Motif83 – 10018Bipartite nuclear localization signal Potential

Sites

Active site321Nucleophile
Active site3151Proton acceptor By similarity

Amino acid modifications

Lipidation21N-myristoyl glycine Ref.7

Experimental info

Mutagenesis321C → S: Loss of activity. Ref.1

Sequences

Sequence LengthMass (Da)Tools
O24454 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: 2C843280BDF24D3B

FASTA37142,447
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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. expand/collapse author list , 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: MYRISTOYLATION AT GLY-2.
[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.

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.
PIRT06097.
RefSeqNP_568074.1. NM_120154.4.
UniGeneAt.24733.

3D structure databases

ProteinModelPortalO24454.
SMRO24454. Positions 19-365.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING3702.AT4G39910.1-P.

Protein family/group databases

MEROPSC19.008.

Proteomic databases

PaxDbO24454.
PRIDEO24454.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT4G39910.1; AT4G39910.1; AT4G39910.
GeneID830150.
KEGGath:AT4G39910.

Organism-specific databases

GeneFarm4911.
TAIRAT4G39910.

Phylogenomic databases

eggNOGCOG5533.
HOGENOMHOG000231498.
InParanoidO24454.
KOK11842.
OMAQFNRHIK.
PhylomeDBO24454.
ProtClustDBCLSN2688340.

Enzyme and pathway databases

BioCycARA:AT4G39910-MONOMER.

Gene expression databases

GenevestigatorO24454.

Family and domain databases

InterProIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
[Graphical view]
PfamPF00443. UCH. 1 hit.
[Graphical view]
PROSITEPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameUBP3_ARATH
AccessionPrimary (citable) accession number: O24454
Entry history
Integrated into UniProtKB/Swiss-Prot: April 26, 2005
Last sequence update: January 1, 1998
Last modified: April 16, 2014
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names