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Q84WU2

- UBP13_ARATH

UniProt

Q84WU2 - UBP13_ARATH

Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

UBP13

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 80 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      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 By similarity.By similarity

    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 sitei207 – 2071NucleophilePROSITE-ProRule annotation
    Active sitei454 – 4541Proton 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:AT3G11910-MONOMER.
    ARA:GQT-2250-MONOMER.

    Protein family/group databases

    MEROPSiC19.A53.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 13 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 13
    Short name:
    AtUBP13
    Ubiquitin thioesterase 13
    Ubiquitin-specific-processing protease 13
    Gene namesi
    Name:UBP13
    Ordered Locus Names:At3g11910
    ORF Names:F26K24.20, MEC18.1
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G11910.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: TAIR
    2. plasmodesma Source: TAIR

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 11151115Ubiquitin carboxyl-terminal hydrolase 13PRO_0000313040Add
    BLAST

    Post-translational modificationi

    Ubiquitinated.1 Publication

    Keywords - PTMi

    Ubl conjugation

    Proteomic databases

    PaxDbiQ84WU2.
    PRIDEiQ84WU2.

    Expressioni

    Gene expression databases

    ArrayExpressiQ84WU2.
    GenevestigatoriQ84WU2.

    Interactioni

    Protein-protein interaction databases

    BioGridi5698. 3 interactions.

    Structurei

    3D structure databases

    ProteinModelPortaliQ84WU2.
    SMRiQ84WU2. Positions 56-638.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini53 – 178126MATHPROSITE-ProRule annotationAdd
    BLAST
    Domaini198 – 522325USPAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase C19 family.Curated
    Contains 1 MATH domain.PROSITE-ProRule annotation
    Contains 1 USP domain.Curated

    Phylogenomic databases

    eggNOGiCOG5077.
    HOGENOMiHOG000160240.
    InParanoidiQ84WU2.
    KOiK11838.
    OMAiEGERTIN.
    PhylomeDBiQ84WU2.

    Family and domain databases

    InterProiIPR002083. MATH.
    IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR008974. TRAF-like.
    IPR028889. UCH/PAN2.
    IPR024729. USP7_ICP0-binding_dom.
    IPR029346. USP_C.
    [Graphical view]
    PfamiPF00917. MATH. 1 hit.
    PF00443. UCH. 1 hit.
    PF14533. USP7_C2. 1 hit.
    PF12436. USP7_ICP0_bdg. 1 hit.
    [Graphical view]
    SMARTiSM00061. MATH. 1 hit.
    [Graphical view]
    SUPFAMiSSF49599. SSF49599. 1 hit.
    PROSITEiPS50144. MATH. 1 hit.
    PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    This entry describes 1 isoform i produced by alternative splicing. Align

    Note: A number of isoforms are produced. According to EST sequences.

    Isoform 1 (identifier: Q84WU2-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MTMMTPPPLD QQEDEEMLVP NPDLVEGPQP MEVAQTDPAA TAVENPPPED     50
    PPSLKFTWTI PMFTRLNTRK HYSDVFVVGG YKWRILIFPK GNNVDHLSMY 100
    LDVADAANLP YGWSRYSQFS LAVVNQVNNR YSIRKETQHQ FNARESDWGF 150
    TSFMPLSELY EPTRGYLVND TVLIEAEVAV RKVLDYWSYD SKKETGFVGL 200
    KNQGATCYMN SLLQTLYHIP YFRKAVYHMP TTENDAPTAS IPLALQSLFY 250
    KLQYNDTSVA TKELTKSFGW DTYDSFMQHD VQELNRVLCE KLEDKMKGTV 300
    VEGTIQKLFE GHHMNYIECI NVDYKSTRKE SFYDLQLDVK GCKDVYASFD 350
    KYVEVERLEG DNKYHAEGHD LQDAKKGVLF IDFPPVLQLQ LKRFEYDFMR 400
    DTMVKINDRY EFPLQLDLDR EDGRYLSPDA DKSVRNLYTL HSVLVHSGGV 450
    HGGHYYAFIR PTLSDQWYKF DDERVTKEDV KRALEEQYGG EEELPQNNPG 500
    FNNPPFKFTK YSNAYMLVYI RESDKDKIIC NVDEKDIAEH LRVRLKKEQE 550
    EKEDKRKYKA QAHLFTTIKV ARDDDITEQI GKNIYFDLVD HEKVRSFRIQ 600
    KQTPFQQFKE EVAKEFGVPV QLQRFWIWAK RQNHTYRPNR PLSPNEELQT 650
    VGQIREASNK ANNAELKLFL EIERGPDDLP IPPPEKTSED ILLFFKLYDP 700
    ENAVLRYVGR LMVKSSSKPM DIVGQLNKMA GFAPDEEIEL FEEIKFEPCV 750
    MCEQIDKKTS FRLCQIEDGD IICYQKPLSI EESEFRYPDV PSFLEYVQNR 800
    ELVRFRTLEK PKEDEFTMEL SKLHTYDDVV ERVAEKLGLD DPSKLRLTSH 850
    NCYSQQPKPQ PIKYRGVDHL SDMLVHYNQT SDILYYEVLD IPLPELQGLK 900
    TLKVAFHSAT KDEVIIHNIR LPKQSTVGDV INELKTKVEL SHQDAELRLL 950
    EVFFHKIYKI FPSTERIENI NDQYWTLRAE EIPEEEKNIG PNDRLIHVYH 1000
    FTKEAGQNQQ VQNFGEPFFL VIHEGETLEE IKTRIQKKLH VPDEDFAKWK 1050
    FASFSMGRPD YLLDTDVVYN RFQRRDVYGA WEQYLGLEHI DNAPKRAYAA 1100
    NQNRHAYEKP VKIYN 1115
    Length:1,115
    Mass (Da):130,649
    Last modified:June 1, 2003 - v1
    Checksum:i29D3A53A60CCDFF1
    GO

    Sequence cautioni

    The sequence AAF23207.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence BAB17021.1 differs from that shown. Reason: Erroneous gene model prediction.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC016795 Genomic DNA. Translation: AAF23207.1. Sequence problems.
    AP002040 Genomic DNA. Translation: BAB17021.1. Sequence problems.
    CP002686 Genomic DNA. Translation: AEE75116.1.
    BT002760 mRNA. Translation: AAO22588.1.
    AK226819 mRNA. Translation: BAE98915.1.
    RefSeqiNP_187797.3. NM_112024.5. [Q84WU2-1]
    UniGeneiAt.25337.

    Genome annotation databases

    EnsemblPlantsiAT3G11910.1; AT3G11910.1; AT3G11910. [Q84WU2-1]
    GeneIDi820364.
    KEGGiath:AT3G11910.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC016795 Genomic DNA. Translation: AAF23207.1 . Sequence problems.
    AP002040 Genomic DNA. Translation: BAB17021.1 . Sequence problems.
    CP002686 Genomic DNA. Translation: AEE75116.1 .
    BT002760 mRNA. Translation: AAO22588.1 .
    AK226819 mRNA. Translation: BAE98915.1 .
    RefSeqi NP_187797.3. NM_112024.5. [Q84WU2-1 ]
    UniGenei At.25337.

    3D structure databases

    ProteinModelPortali Q84WU2.
    SMRi Q84WU2. Positions 56-638.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 5698. 3 interactions.

    Protein family/group databases

    MEROPSi C19.A53.

    Proteomic databases

    PaxDbi Q84WU2.
    PRIDEi Q84WU2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G11910.1 ; AT3G11910.1 ; AT3G11910 . [Q84WU2-1 ]
    GeneIDi 820364.
    KEGGi ath:AT3G11910.

    Organism-specific databases

    TAIRi AT3G11910.

    Phylogenomic databases

    eggNOGi COG5077.
    HOGENOMi HOG000160240.
    InParanoidi Q84WU2.
    KOi K11838.
    OMAi EGERTIN.
    PhylomeDBi Q84WU2.

    Enzyme and pathway databases

    BioCyci ARA:AT3G11910-MONOMER.
    ARA:GQT-2250-MONOMER.

    Gene expression databases

    ArrayExpressi Q84WU2.
    Genevestigatori Q84WU2.

    Family and domain databases

    InterProi IPR002083. MATH.
    IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR008974. TRAF-like.
    IPR028889. UCH/PAN2.
    IPR024729. USP7_ICP0-binding_dom.
    IPR029346. USP_C.
    [Graphical view ]
    Pfami PF00917. MATH. 1 hit.
    PF00443. UCH. 1 hit.
    PF14533. USP7_C2. 1 hit.
    PF12436. USP7_ICP0_bdg. 1 hit.
    [Graphical view ]
    SMARTi SM00061. MATH. 1 hit.
    [Graphical view ]
    SUPFAMi SSF49599. SSF49599. 1 hit.
    PROSITEi PS50144. MATH. 1 hit.
    PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
      Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
      , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
      Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones."
      Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.
      DNA Res. 7:217-221(2000) [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. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-545.
      Strain: cv. Columbia.
    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. "Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis."
      Saracco S.A., Hansson M., Scalf M., Walker J.M., Smith L.M., Vierstra R.D.
      Plant J. 59:344-358(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiUBP13_ARATH
    AccessioniPrimary (citable) accession number: Q84WU2
    Secondary accession number(s): Q0WVD3, Q9FU99, Q9SF08
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 80 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