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A8HAL1

- UBP16_DANRE

UniProt

A8HAL1 - UBP16_DANRE

Protein

Ubiquitin carboxyl-terminal hydrolase 16

Gene

usp16

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 59 (01 Oct 2014)
      Sequence version 1 (13 Nov 2007)
      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. 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 bindingi76 – 761Zinc 3UniRule annotation
    Metal bindingi79 – 791Zinc 3UniRule annotation
    Metal bindingi84 – 841Zinc 2UniRule annotation
    Metal bindingi91 – 911Zinc 2UniRule annotation
    Metal bindingi95 – 951Zinc 3UniRule annotation
    Metal bindingi104 – 1041Zinc 3UniRule annotation
    Metal bindingi117 – 1171Zinc 1UniRule annotation
    Metal bindingi120 – 1201Zinc 1UniRule annotation
    Active sitei217 – 2171NucleophileUniRule annotation
    Active sitei752 – 7521Proton acceptorUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri46 – 12681UBP-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. positive regulation of transcription, DNA-templated Source: UniProtKB
    6. positive regulation of translational elongation Source: UniProtKB
    7. protein homotetramerization Source: UniProtKB
    8. transcription, DNA-templated Source: UniProtKB-KW
    9. 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

    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
    ORF Names:si:dkey-121n8.2
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Chromosome 15

    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 – 815815Ubiquitin carboxyl-terminal hydrolase 16PRO_0000367505Add
    BLAST

    Expressioni

    Gene expression databases

    BgeeiA8HAL1.

    Interactioni

    Subunit structurei

    Homotetramer.UniRule annotation

    Structurei

    3D structure databases

    ProteinModelPortaliA8HAL1.
    SMRiA8HAL1. Positions 22-142.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini208 – 814607USPAdd
    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 – 12681UBP-typeUniRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5560.
    GeneTreeiENSGT00750000117419.
    HOGENOMiHOG000154755.
    HOVERGENiHBG062704.
    KOiK11844.
    OMAiECSIQHC.
    OrthoDBiEOG7J9VNZ.
    PhylomeDBiA8HAL1.
    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]

    Sequencei

    Sequence statusi: Complete.

    A8HAL1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGKKKVKDRS AGTDSSSETA GPSCTHIRKG TENSVLKKAC LNEHWSSCQD    50
    CEQDKPEEKQ ILEDQTDGES PAVWMCLKCG HRGCGRSGNQ HAIKHYETPR 100
    SEPHCLVLSL DVWSVWCYIC DDEVQYSSTG QLAQLITNIR KQVLTAPDKR 150
    NASKKSWKED ISVMNSAEQT QDEEKGKKGK QKSSSKQEDS PKSHQSAAAG 200
    SSAVVSVRGL SNLGNTCFFN AVVQSLSQTQ YLRELLKQIA EEKSSFSITP 250
    ALSSELDPLQ IQLERPGSLT LAMCQLMNEI QETKKGVVTP KELFTQVCKK 300
    APRFKGFQQQ DSQELLRYLL DGMRAEEAKR VNSGILEALK SSGKNFEAEQ 350
    TKKIVKEYEK DGAPKNFVDR VFGGAMSSTV MCKECKTVSL VTEMFLDLSL 400
    PVADEAYRKK NQKKAVQHRH SVSDDGDQDT SSLANGNEDM PTGTGSKYQQ 450
    KKAKKQAKKQ AKNQRRQQKQ GGKVTLDAIT NQSSTDPADS SMQTQTVSVN 500
    GSADAQPADT NQEDLSLEKH NEDQDDEEPE QEQAASVNNR FTALSEDQTT 550
    EDIAEQVNED EDEIEQNCAE EEELVEELNT MSLTTPSEGD VENGEDTLED 600
    VKEYTVVNRD PELAFRALAS RTAPVKQECS VESCLYQFTE VEHLTENNRL 650
    MCVTCTKQQP GYKDGCKKAV YRDALKQMLI SDPPVVLTLH LKRFQQVAYS 700
    VCKVNRHVQF PQILDLAPFC SLNCTGVKEG ETQVLYSLYG IVEHSGTMRS 750
    GHYTAYVKSR PSTHNCVQNG TAAASGDAEA SKGSWFHISD SSVHPVPEAK 800
    VQSSQAYLLF YEKIS 815
    Length:815
    Mass (Da):90,450
    Last modified:November 13, 2007 - v1
    Checksum:i50CF71DC500EE191
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CR854897 Genomic DNA. Translation: CAP09451.1.
    RefSeqiNP_001139569.1. NM_001146097.1.
    UniGeneiDr.24329.
    Dr.99665.

    Genome annotation databases

    EnsembliENSDART00000085645; ENSDARP00000080080; ENSDARG00000060633.
    GeneIDi569700.
    KEGGidre:569700.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CR854897 Genomic DNA. Translation: CAP09451.1 .
    RefSeqi NP_001139569.1. NM_001146097.1.
    UniGenei Dr.24329.
    Dr.99665.

    3D structure databases

    ProteinModelPortali A8HAL1.
    SMRi A8HAL1. Positions 22-142.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSDART00000085645 ; ENSDARP00000080080 ; ENSDARG00000060633 .
    GeneIDi 569700.
    KEGGi dre:569700.

    Organism-specific databases

    CTDi 10600.

    Phylogenomic databases

    eggNOGi COG5560.
    GeneTreei ENSGT00750000117419.
    HOGENOMi HOG000154755.
    HOVERGENi HBG062704.
    KOi K11844.
    OMAi ECSIQHC.
    OrthoDBi EOG7J9VNZ.
    PhylomeDBi A8HAL1.
    TreeFami TF326075.

    Miscellaneous databases

    NextBioi 20889807.
    PROi A8HAL1.

    Gene expression databases

    Bgeei A8HAL1.

    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. "The zebrafish reference genome sequence and its relationship to the human genome."
      Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
      , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
      Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Tuebingen.

    Entry informationi

    Entry nameiUBP16_DANRE
    AccessioniPrimary (citable) accession number: A8HAL1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: November 13, 2007
    Last modified: October 1, 2014
    This is version 59 of the entry and version 1 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