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O24454

- UBP3_ARATH

UniProt

O24454 - UBP3_ARATH

Protein

Ubiquitin carboxyl-terminal hydrolase 3

Gene

UBP3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      Previous versions | rss
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    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

    1. cysteine-type peptidase activity Source: UniProtKB-KW
    2. ubiquitinyl hydrolase activity Source: InterPro

    GO - Biological processi

    1. ubiquitin-dependent protein catabolic process Source: InterPro

    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: Chromosome 4

    Organism-specific databases

    TAIRiAT4G39910.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    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

    Gene expression databases

    GenevestigatoriO24454.

    Interactioni

    Protein-protein interaction databases

    STRINGi3702.AT4G39910.1-P.

    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.
    OMAiAPKKFIT.
    PhylomeDBiO24454.

    Family and domain databases

    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [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

    MGAAGSKLEK ALGDQFPEGE RYFGFENFGN TCYCNSVLQA LYFCVPFREQ    50
    LLEYYTSNKS VADAEENLMT CLADLFSQIS SQKKKTGVIA PKRFVQRLKK 100
    QNELFRSYMH QDAHEFLNYL LNEVVDILEK EAKATKTEHE TSSSSSPEKI 150
    ANGLKVPQAN GVVHKEPIVT WVHNIFQGIL TNETRCLRCE TVTARDETFL 200
    DLSLDIEQNS SITSCLKNFS STETLHAEDK FFCDKCCSLQ EAQKRMKIKK 250
    PPHILVIHLK RFKYIEQLGR YKKLSYRVVF PLELKLSNTV EPYADVEYSL 300
    FAVVVHVGSG PNHGHYVSLV KSHNHWLFFD DENVEMIEES AVQTFFGSSQ 350
    EYSSNTDHGY ILFYESLGPT K 371
    Length:371
    Mass (Da):42,447
    Last modified:January 1, 1998 - v1
    Checksum:i2C843280BDF24D3B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi T06097.
    RefSeqi NP_568074.1. NM_120154.4.
    UniGenei At.24733.

    3D structure databases

    ProteinModelPortali O24454.
    SMRi O24454. Positions 19-365.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT4G39910.1-P.

    Protein family/group databases

    MEROPSi C19.008.

    Proteomic databases

    PaxDbi O24454.
    PRIDEi O24454.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G39910.1 ; AT4G39910.1 ; AT4G39910 .
    GeneIDi 830150.
    KEGGi ath:AT4G39910.

    Organism-specific databases

    GeneFarmi 4911.
    TAIRi AT4G39910.

    Phylogenomic databases

    eggNOGi COG5533.
    HOGENOMi HOG000231498.
    InParanoidi O24454.
    KOi K11842.
    OMAi APKKFIT.
    PhylomeDBi O24454.

    Enzyme and pathway databases

    BioCyci ARA:AT4G39910-MONOMER.

    Gene expression databases

    Genevestigatori O24454.

    Family and domain databases

    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    [Graphical view ]
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 95 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