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Protein

Ubiquitin carboxyl-terminal hydrolase 3

Gene

UBP3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei32 – 321Nucleophile
Active sitei315 – 3151Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciARA:AT4G39910-MONOMER.

Protein family/group databases

MEROPSiC19.008.

Names & Taxonomyi

Protein namesi
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 namesi
Name:UBP3
Ordered Locus Names:At4g39910
ORF Names:T5J17.80
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G39910.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi32 – 321C → S: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedSequence Analysis
Chaini2 – 371370Ubiquitin carboxyl-terminal hydrolase 3PRO_0000080694Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi2 – 21N-myristoyl glycine1 Publication

Keywords - PTMi

Lipoprotein, Myristate

Proteomic databases

PaxDbiO24454.
PRIDEiO24454.

Expressioni

Tissue specificityi

Constitutively and ubiquitously expressed.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi3702.AT4G39910.1.

Structurei

3D structure databases

ProteinModelPortaliO24454.
SMRiO24454. Positions 19-365.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini23 – 367345USPAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi83 – 10018Bipartite nuclear localization signalSequence AnalysisAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated
Contains 1 USP domain.Curated

Phylogenomic databases

eggNOGiCOG5533.
HOGENOMiHOG000231498.
InParanoidiO24454.
KOiK11842.
OMAiLEYYTSN.
PhylomeDBiO24454.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O24454-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGAAGSKLEK ALGDQFPEGE RYFGFENFGN TCYCNSVLQA LYFCVPFREQ
60 70 80 90 100
LLEYYTSNKS VADAEENLMT CLADLFSQIS SQKKKTGVIA PKRFVQRLKK
110 120 130 140 150
QNELFRSYMH QDAHEFLNYL LNEVVDILEK EAKATKTEHE TSSSSSPEKI
160 170 180 190 200
ANGLKVPQAN GVVHKEPIVT WVHNIFQGIL TNETRCLRCE TVTARDETFL
210 220 230 240 250
DLSLDIEQNS SITSCLKNFS STETLHAEDK FFCDKCCSLQ EAQKRMKIKK
260 270 280 290 300
PPHILVIHLK RFKYIEQLGR YKKLSYRVVF PLELKLSNTV EPYADVEYSL
310 320 330 340 350
FAVVVHVGSG PNHGHYVSLV KSHNHWLFFD DENVEMIEES AVQTFFGSSQ
360 370
EYSSNTDHGY ILFYESLGPT K
Length:371
Mass (Da):42,447
Last modified:January 1, 1998 - v1
Checksum:i2C843280BDF24D3B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiT06097.
RefSeqiNP_568074.1. NM_120154.4.
UniGeneiAt.24733.

Genome annotation databases

EnsemblPlantsiAT4G39910.1; AT4G39910.1; AT4G39910.
GeneIDi830150.
KEGGiath:AT4G39910.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiT06097.
RefSeqiNP_568074.1. NM_120154.4.
UniGeneiAt.24733.

3D structure databases

ProteinModelPortaliO24454.
SMRiO24454. Positions 19-365.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G39910.1.

Protein family/group databases

MEROPSiC19.008.

Proteomic databases

PaxDbiO24454.
PRIDEiO24454.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G39910.1; AT4G39910.1; AT4G39910.
GeneIDi830150.
KEGGiath:AT4G39910.

Organism-specific databases

GeneFarmi4911.
TAIRiAT4G39910.

Phylogenomic databases

eggNOGiCOG5533.
HOGENOMiHOG000231498.
InParanoidiO24454.
KOiK11842.
OMAiLEYYTSN.
PhylomeDBiO24454.

Enzyme and pathway databases

BioCyciARA:AT4G39910-MONOMER.

Miscellaneous databases

PROiO24454.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: 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.

Entry informationi

Entry nameiUBP3_ARATH
AccessioniPrimary (citable) accession number: O24454
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2005
Last sequence update: January 1, 1998
Last modified: July 22, 2015
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.