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Q949Y0

- UBP6_ARATH

UniProt

Q949Y0 - UBP6_ARATH

Protein

Ubiquitin carboxyl-terminal hydrolase 6

Gene

UBP6

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      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.

    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 sitei113 – 1131Nucleophile
    Active sitei430 – 4301Proton acceptorPROSITE-ProRule annotation

    GO - Molecular functioni

    1. calmodulin binding Source: TAIR
    2. ubiquitin-specific protease activity Source: TAIR

    GO - Biological processi

    1. protein deubiquitination Source: TAIR
    2. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Ubl conjugation pathway

    Keywords - Ligandi

    Calmodulin-binding

    Enzyme and pathway databases

    BioCyciARA:AT1G51710-MONOMER.
    ARA:GQT-1079-MONOMER.

    Protein family/group databases

    MEROPSiC19.094.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 6 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 6
    Short name:
    AtUBP6
    Ubiquitin thioesterase 6
    Ubiquitin-specific-processing protease 6
    Gene namesi
    Name:UBP6
    Ordered Locus Names:At1g51710
    ORF Names:F19C24.8
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 1

    Organism-specific databases

    TAIRiAT1G51710.

    Subcellular locationi

    GO - Cellular componenti

    1. plasmodesma Source: TAIR

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi113 – 1131C → S: Loss of activity. 1 Publication
    Mutagenesisi175 – 1751W → R: Abolishes the calmodulin-binding. 1 Publication
    Mutagenesisi178 – 1781L → K: Abolishes the calmodulin-binding. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 482482Ubiquitin carboxyl-terminal hydrolase 6PRO_0000313033Add
    BLAST

    Proteomic databases

    PaxDbiQ949Y0.
    PRIDEiQ949Y0.

    Expressioni

    Gene expression databases

    ArrayExpressiQ949Y0.
    GenevestigatoriQ949Y0.

    Interactioni

    Subunit structurei

    Interacts with calmodulin (CaM).1 Publication

    Protein-protein interaction databases

    BioGridi26821. 4 interactions.
    MINTiMINT-1351065.

    Structurei

    3D structure databases

    ProteinModelPortaliQ949Y0.
    SMRiQ949Y0. Positions 4-478.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini2 – 7776Ubiquitin-likePROSITE-ProRule annotationAdd
    BLAST
    Domaini104 – 478375USPAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni172 – 19120Calmodulin-bindingAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiNOG286607.
    HOGENOMiHOG000202292.
    InParanoidiQ949Y0.
    KOiK11843.
    OMAiDWGNLKI.
    PhylomeDBiQ949Y0.

    Family and domain databases

    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR000626. Ubiquitin-like.
    IPR029071. Ubiquitin-rel_dom.
    IPR019954. Ubiquitin_CS.
    IPR028889. UCH/PAN2.
    [Graphical view]
    PfamiPF00240. ubiquitin. 1 hit.
    PF00443. UCH. 1 hit.
    [Graphical view]
    SMARTiSM00213. UBQ. 1 hit.
    [Graphical view]
    SUPFAMiSSF54236. SSF54236. 1 hit.
    PROSITEiPS00299. UBIQUITIN_1. 1 hit.
    PS50053. UBIQUITIN_2. 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: Q949Y0-1) [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.

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    MPTVSVKWQK KVLDGIEIDV SLPPYVFKAQ LYDLTGVPPE RQKIMVKGGL    50
    LKDDGDWAAI GVKDGQKLMM MGTADEIVKA PEKAIVFAED LPEEALATNL 100
    GYSAGLVNLG NTCYMNSTVQ CLKSVPELKS ALSNYSLAAR SNDVDQTSHM 150
    LTVATRELFG ELDRSVNAVS PSQFWMVLRK KYPQFSQLQN GMHMQQDAEE 200
    CWTQLLYTLS QSLKAPTSSE GADAVKALFG VNLQSRLHCQ ESGEESSETE 250
    SVYSLKCHIS HEVNHLHEGL KHGLKGELEK TSPALGRTAL YVKESLIDSL 300
    PRYLTVQFVR FFWKRESNQK AKILRKVDYP LVLDIFDLCS EDLRKKLEAP 350
    RQKLREEEGK KLGLQTSAKS GSKDSDVKMT DAEASANGSG ESSTVNPQEG 400
    TSSEKETHMT GIYDLVAVLT HKGRSADSGH YVAWVKQESG KWIQYDDDNP 450
    SMQREEDITK LSGGGDWHMA YITMYKARFV SM 482
    Length:482
    Mass (Da):53,696
    Last modified:December 1, 2001 - v1
    Checksum:iECF357E9C5BEF3F7
    GO

    Sequence cautioni

    The sequence AAG50872.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti207 – 2071Y → F in AAG42751. (PubMed:11115897)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF302660 mRNA. Translation: AAG42751.1.
    AC025294 Genomic DNA. Translation: AAG50872.1. Sequence problems.
    CP002684 Genomic DNA. Translation: AEE32705.1.
    AY050817 mRNA. Translation: AAK92752.1.
    AY114081 mRNA. Translation: AAM45129.1.
    BT000658 mRNA. Translation: AAN31805.1.
    AY084730 mRNA. Translation: AAM61304.1.
    AK221019 mRNA. Translation: BAD94710.1.
    PIRiA96556.
    RefSeqiNP_564596.1. NM_104049.3. [Q949Y0-1]
    UniGeneiAt.16941.

    Genome annotation databases

    EnsemblPlantsiAT1G51710.1; AT1G51710.1; AT1G51710. [Q949Y0-1]
    GeneIDi841596.
    KEGGiath:AT1G51710.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF302660 mRNA. Translation: AAG42751.1 .
    AC025294 Genomic DNA. Translation: AAG50872.1 . Sequence problems.
    CP002684 Genomic DNA. Translation: AEE32705.1 .
    AY050817 mRNA. Translation: AAK92752.1 .
    AY114081 mRNA. Translation: AAM45129.1 .
    BT000658 mRNA. Translation: AAN31805.1 .
    AY084730 mRNA. Translation: AAM61304.1 .
    AK221019 mRNA. Translation: BAD94710.1 .
    PIRi A96556.
    RefSeqi NP_564596.1. NM_104049.3. [Q949Y0-1 ]
    UniGenei At.16941.

    3D structure databases

    ProteinModelPortali Q949Y0.
    SMRi Q949Y0. Positions 4-478.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 26821. 4 interactions.
    MINTi MINT-1351065.

    Protein family/group databases

    MEROPSi C19.094.

    Proteomic databases

    PaxDbi Q949Y0.
    PRIDEi Q949Y0.

    Protocols and materials databases

    DNASUi 841596.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G51710.1 ; AT1G51710.1 ; AT1G51710 . [Q949Y0-1 ]
    GeneIDi 841596.
    KEGGi ath:AT1G51710.

    Organism-specific databases

    TAIRi AT1G51710.

    Phylogenomic databases

    eggNOGi NOG286607.
    HOGENOMi HOG000202292.
    InParanoidi Q949Y0.
    KOi K11843.
    OMAi DWGNLKI.
    PhylomeDBi Q949Y0.

    Enzyme and pathway databases

    BioCyci ARA:AT1G51710-MONOMER.
    ARA:GQT-1079-MONOMER.

    Gene expression databases

    ArrayExpressi Q949Y0.
    Genevestigatori Q949Y0.

    Family and domain databases

    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR000626. Ubiquitin-like.
    IPR029071. Ubiquitin-rel_dom.
    IPR019954. Ubiquitin_CS.
    IPR028889. UCH/PAN2.
    [Graphical view ]
    Pfami PF00240. ubiquitin. 1 hit.
    PF00443. UCH. 1 hit.
    [Graphical view ]
    SMARTi SM00213. UBQ. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54236. SSF54236. 1 hit.
    PROSITEi PS00299. UBIQUITIN_1. 1 hit.
    PS50053. UBIQUITIN_2. 1 hit.
    PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "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: NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY ORGANIZATION, NOMENCLATURE.
      Strain: cv. Columbia.
    2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(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. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "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 (MAR-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 336-482.
      Strain: cv. Columbia.
    7. "Arabidopsis ubiquitin-specific protease 6 (AtUBP6) interacts with calmodulin."
      Moon B.C., Choi M.S., Kang Y.H., Kim M.C., Cheong M.S., Park C.Y., Yoo J.H., Koo S.C., Lee S.M., Lim C.O., Cho M.J., Chung W.S.
      FEBS Lett. 579:3885-3890(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CALMODULIN, MUTAGENESIS OF CYS-113; TRP-175 AND LEU-178.

    Entry informationi

    Entry nameiUBP6_ARATH
    AccessioniPrimary (citable) accession number: Q949Y0
    Secondary accession number(s): Q56ZE7, Q9C8H9, Q9FPT4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 91 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