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Q2KJ09

- UBP16_RAT

UniProt

Q2KJ09 - UBP16_RAT

Protein

Ubiquitin carboxyl-terminal hydrolase 16

Gene

Usp16

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 70 (01 Oct 2014)
      Sequence version 2 (24 Mar 2009)
      Previous versions | rss
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    Functioni

    Specifically deubiquitinates 'Lys-120' of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Deubiquitination of histone H2A is a prerequisite for subsequent phosphorylation at 'Ser-11' of histone H3 (H3S10ph), and is required for chromosome segregation when cells enter into mitosis. In resting B- and T-lymphocytes, phosphorylation by AURKB leads to enhance its activity, thereby maintaining transcription in resting lymphocytes. Regulates Hox gene expression via histone H2A deubiquitination. Prefers nucleosomal substrates. Does not deubiquitinate histone H2B.UniRule annotation

    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).UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi24 – 241Zinc 1UniRule annotation
    Metal bindingi26 – 261Zinc 1UniRule annotation
    Metal bindingi48 – 481Zinc 2UniRule annotation
    Metal bindingi51 – 511Zinc 2UniRule annotation
    Metal bindingi73 – 731Zinc 3UniRule annotation
    Metal bindingi76 – 761Zinc 3UniRule annotation
    Metal bindingi81 – 811Zinc 2UniRule annotation
    Metal bindingi89 – 891Zinc 2UniRule annotation
    Metal bindingi93 – 931Zinc 3UniRule annotation
    Metal bindingi102 – 1021Zinc 3UniRule annotation
    Metal bindingi115 – 1151Zinc 1UniRule annotation
    Metal bindingi118 – 1181Zinc 1UniRule annotation
    Active sitei204 – 2041NucleophileUniRule annotation
    Active sitei760 – 7601Proton acceptorUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri46 – 12479UBP-typeUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. cysteine-type endopeptidase activity Source: UniProtKB
    2. histone binding Source: UniProtKB
    3. transcription coactivator activity Source: UniProtKB
    4. ubiquitin binding Source: UniProtKB
    5. ubiquitin-specific protease activity Source: UniProtKB
    6. ubiquitin thiolesterase activity Source: UniProtKB
    7. zinc ion binding Source: UniProtKB

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: UniProtKB
    2. histone deubiquitination Source: UniProtKB
    3. histone H2A K63-linked deubiquitination Source: UniProtKB
    4. mitotic nuclear division Source: UniProtKB
    5. monoubiquitinated histone H2A deubiquitination Source: UniProtKB
    6. positive regulation of transcription, DNA-templated Source: UniProtKB
    7. positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
    8. positive regulation of translational elongation Source: UniProtKB
    9. protein homotetramerization Source: UniProtKB
    10. regulation of transcription from RNA polymerase II promoter Source: UniProtKB
    11. transcription, DNA-templated Source: UniProtKB-KW
    12. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Activator, Chromatin regulator, Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Cell cycle, Cell division, Mitosis, Transcription, Transcription regulation, Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Protein family/group databases

    MEROPSiC19.050.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 16UniRule annotation (EC:3.4.19.12UniRule annotation)
    Alternative name(s):
    Deubiquitinating enzyme 16UniRule annotation
    Ubiquitin thioesterase 16UniRule annotation
    Ubiquitin-specific-processing protease 16UniRule annotation
    Gene namesi
    Name:Usp16
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 11

    Organism-specific databases

    RGDi1307192. Usp16.

    Subcellular locationi

    Nucleus UniRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 826826Ubiquitin carboxyl-terminal hydrolase 16PRO_0000367504Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei414 – 4141PhosphoserineBy similarity

    Post-translational modificationi

    Phosphorylated at the onset of mitosis and dephosphorylated during the metaphase/anaphase transition. Phosphorylation by AURKB enhances the deubiquitinase activity.UniRule annotation

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ2KJ09.
    PRIDEiQ2KJ09.

    Expressioni

    Gene expression databases

    GenevestigatoriQ2KJ09.

    Interactioni

    Subunit structurei

    Homotetramer.UniRule annotation

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000002173.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini195 – 825631USPAdd
    BLAST

    Domaini

    The UBP-type zinc finger binds 3 zinc ions that form a pair of cross-braced ring fingers encapsulated within a third zinc finger in the primary structure. It recognizes the C-terminal tail of free ubiquitin.UniRule annotation

    Sequence similaritiesi

    Belongs to the peptidase C19 family. USP16 subfamily.UniRule annotation
    Contains 1 UBP-type zinc finger.UniRule annotation
    Contains 1 USP domain.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri46 – 12479UBP-typeUniRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5207.
    GeneTreeiENSGT00750000117419.
    HOGENOMiHOG000154755.
    HOVERGENiHBG062704.
    InParanoidiQ2KJ09.
    KOiK11844.
    OMAiECSIQHC.
    OrthoDBiEOG7J9VNZ.
    PhylomeDBiQ2KJ09.
    TreeFamiTF326075.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    HAMAPiMF_03062. UBP16.
    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view]
    PfamiPF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view]
    PROSITEiPS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q2KJ09-1) [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

    MGKKRTKGKS VPEKASSEST EPMCRHLRKG LEQGNLKKAL VNVEWNICQD    50
    CKTDNKVKDK SEEEAEDPSV WLCLKCGHQG CGRDSQEQHA LKHYTTPRSE 100
    PHYLVLSLDN WSVWCYKCDE EIKYCSSNRL GQVVDYVRKQ AGRITSKPAE 150
    KNNGHIELEN KKLEKESKNE QEREKSESMA KENIPLDSAS QITVKGLSNL 200
    GNTCFFNAVM QNLSQTPVLR ELLKEVKMSG TIVKIEPPDL ALTEPLEVNL 250
    EPPGPLTLAM SQFLNEMQEN KKRIVTPKEL FSQVCKKATR FKGYQQQDSQ 300
    ELLRYLLDGM RAEEHQRVSK GILKAFGNST EKLDEEVKNK VKDYEKKKAI 350
    PSFVDRIFGG ELTSTIMCDD CRTVSLVHES FLDLSLPVLD DQSGKKNIND 400
    KNVKKTMEEE DKDSEEEKDD SYMKTRSDVP SGTSKHTQKK AKKQAKKQAK 450
    NQRRQQKIQE RFLHFNEICT TNYTEDNDHE AETALPGEGE VDTEFNRGSQ 500
    EELTQTELCA NQKDVNGQEE MIESAADERK CPEHPEVKSV STESDLGSLT 550
    SAPECPRDLN GAFLEERTSG ELDITNGLKN LTLNAAVDPD EISIEILNDS 600
    HSPALKVYEV MNEDPETAFC TLANREAFST DECSIQHCLY QFTRNEKLQD 650
    ANKLLCEVCT RRQCNGPKAN IKGERKHVYT NAKKQMLVSL APPVLTLHLK 700
    RFQQAGFNLR KVNKHIKFPE ILDLAPFCTL KCKNVAEEST RVLYSLYGVV 750
    EHSGTMRSGH YTAYAKERTA SCHLSNLVLH GDIPQDCEME STKGQWFHIS 800
    DTHVQAVPIT KVLNSQAYLL FYERIL 826
    Length:826
    Mass (Da):93,762
    Last modified:March 24, 2009 - v2
    Checksum:i2DCC40B25676BA5E
    GO
    Isoform 2 (identifier: Q2KJ09-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         149-149: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:825
    Mass (Da):93,691
    Checksum:i9F57C2952CF266B6
    GO

    Sequence cautioni

    The sequence AAI12387.1 differs from that shown. Reason: Contaminating sequence. Potential poly-A sequence.

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei149 – 1491Missing in isoform 2. 1 PublicationVSP_036725

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CH473989 Genomic DNA. Translation: EDM10641.1.
    BC112386 mRNA. Translation: AAI12387.1. Sequence problems.
    RefSeqiNP_001093971.1. NM_001100501.1. [Q2KJ09-2]
    XP_006248077.1. XM_006248015.1. [Q2KJ09-1]
    UniGeneiRn.55800.

    Genome annotation databases

    EnsembliENSRNOT00000002173; ENSRNOP00000002173; ENSRNOG00000001598. [Q2KJ09-1]
    GeneIDi288306.
    KEGGirno:288306.
    UCSCiRGD:1307192. rat. [Q2KJ09-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CH473989 Genomic DNA. Translation: EDM10641.1 .
    BC112386 mRNA. Translation: AAI12387.1 . Sequence problems.
    RefSeqi NP_001093971.1. NM_001100501.1. [Q2KJ09-2 ]
    XP_006248077.1. XM_006248015.1. [Q2KJ09-1 ]
    UniGenei Rn.55800.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10116.ENSRNOP00000002173.

    Protein family/group databases

    MEROPSi C19.050.

    Proteomic databases

    PaxDbi Q2KJ09.
    PRIDEi Q2KJ09.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000002173 ; ENSRNOP00000002173 ; ENSRNOG00000001598 . [Q2KJ09-1 ]
    GeneIDi 288306.
    KEGGi rno:288306.
    UCSCi RGD:1307192. rat. [Q2KJ09-1 ]

    Organism-specific databases

    CTDi 10600.
    RGDi 1307192. Usp16.

    Phylogenomic databases

    eggNOGi COG5207.
    GeneTreei ENSGT00750000117419.
    HOGENOMi HOG000154755.
    HOVERGENi HBG062704.
    InParanoidi Q2KJ09.
    KOi K11844.
    OMAi ECSIQHC.
    OrthoDBi EOG7J9VNZ.
    PhylomeDBi Q2KJ09.
    TreeFami TF326075.

    Miscellaneous databases

    NextBioi 627930.
    PROi Q2KJ09.

    Gene expression databases

    Genevestigatori Q2KJ09.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    HAMAPi MF_03062. UBP16.
    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view ]
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
      Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-659 (ISOFORM 2).
      Tissue: Prostate.

    Entry informationi

    Entry nameiUBP16_RAT
    AccessioniPrimary (citable) accession number: Q2KJ09
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: March 24, 2009
    Last modified: October 1, 2014
    This is version 70 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3