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Q9Y6I4

- UBP3_HUMAN

UniProt

Q9Y6I4 - UBP3_HUMAN

Protein

Ubiquitin carboxyl-terminal hydrolase 3

Gene

USP3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 2 (02 Sep 2008)
      Previous versions | rss
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    Functioni

    Hydrolase that deubiquitinates monoubiquitinated target proteins such as histone H2A and H2B. Required for proper progression through S phase and subsequent mitotic entry. May regulate the DNA damage response (DDR) checkpoint through deubiquitination of H2A at DNA damage sites. Associates with the chromatin.1 Publication

    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 sitei168 – 1681NucleophilePROSITE-ProRule annotation
    Active sitei471 – 4711Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri27 – 10478UBP-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. histone binding Source: UniProtKB
    2. ubiquitin-specific protease activity Source: ProtInc
    3. ubiquitin thiolesterase activity Source: UniProtKB
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. DNA repair Source: UniProtKB
    2. histone deubiquitination Source: UniProtKB
    3. mitotic cell cycle Source: UniProtKB
    4. regulation of protein stability Source: UniProtKB
    5. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Chromatin regulator, Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Cell cycle, DNA damage, Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Protein family/group databases

    MEROPSiC19.026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 3 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 3
    Ubiquitin thioesterase 3
    Ubiquitin-specific-processing protease 3
    Gene namesi
    Name:USP3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 15

    Organism-specific databases

    HGNCiHGNC:12626. USP3.

    Subcellular locationi

    Nucleus 1 Publication
    Note: Localizes preferentially with monoubiquitinated H2A to chromatin.

    GO - Cellular componenti

    1. nuclear chromatin Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi56 – 561H → A: Does not reduce monoubiquitinated H2A and H2B stability. Interaction with monoubiquitinated H2A is strongly inhibited. 1 Publication
    Mutagenesisi168 – 1681C → S: Does not reduce H2A stability. Interacts more strongly with monoubiquitinated H2A than with nonubiquitinated H2A. Its nuclear localization to chromatin is enhanced. 1 Publication

    Organism-specific databases

    PharmGKBiPA37251.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 520520Ubiquitin carboxyl-terminal hydrolase 3PRO_0000080619Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiQ9Y6I4.
    PaxDbiQ9Y6I4.
    PRIDEiQ9Y6I4.

    PTM databases

    PhosphoSiteiQ9Y6I4.

    Expressioni

    Tissue specificityi

    Expressed in all tissues examined, with strongest expression in pancreas.

    Gene expression databases

    ArrayExpressiQ9Y6I4.
    BgeeiQ9Y6I4.
    CleanExiHS_USP3.
    GenevestigatoriQ9Y6I4.

    Interactioni

    Subunit structurei

    Interacts (via UBP-type domain) with H2A; the interaction is less efficient than with monoubiquitinated H2A.1 Publication

    Protein-protein interaction databases

    BioGridi115285. 28 interactions.
    DIPiDIP-53585N.
    IntActiQ9Y6I4. 20 interactions.
    STRINGi9606.ENSP00000369681.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Y6I4.
    SMRiQ9Y6I4. Positions 3-512.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini159 – 511353USPAdd
    BLAST

    Domaini

    Both protease activity and an intact zinc finger are required for H2A monodeubiquitination.

    Sequence similaritiesi

    Belongs to the peptidase C19 family. USP3 subfamily.Curated
    Contains 1 UBP-type zinc finger.PROSITE-ProRule annotation
    Contains 1 USP domain.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri27 – 10478UBP-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5533.
    HOGENOMiHOG000231498.
    HOVERGENiHBG103589.
    InParanoidiQ9Y6I4.
    KOiK11986.
    OMAiESCLYDL.
    PhylomeDBiQ9Y6I4.
    TreeFamiTF315281.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    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: Q9Y6I4-1) [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

    MECPHLSSSV CIAPDSAKFP NGSPSSWCCS VCRSNKSPWV CLTCSSVHCG    50
    RYVNGHAKKH YEDAQVPLTN HKKSEKQDKV QHTVCMDCSS YSTYCYRCDD 100
    FVVNDTKLGL VQKVREHLQN LENSAFTADR HKKRKLLENS TLNSKLLKVN 150
    GSTTAICATG LRNLGNTCFM NAILQSLSNI EQFCCYFKEL PAVELRNGKT 200
    AGRRTYHTRS QGDNNVSLVE EFRKTLCALW QGSQTAFSPE SLFYVVWKIM 250
    PNFRGYQQQD AHEFMRYLLD HLHLELQGGF NGVSRSAILQ ENSTLSASNK 300
    CCINGASTVV TAIFGGILQN EVNCLICGTE SRKFDPFLDL SLDIPSQFRS 350
    KRSKNQENGP VCSLRDCLRS FTDLEELDET ELYMCHKCKK KQKSTKKFWI 400
    QKLPKVLCLH LKRFHWTAYL RNKVDTYVEF PLRGLDMKCY LLEPENSGPE 450
    SCLYDLAAVV VHHGSGVGSG HYTAYATHEG RWFHFNDSTV TLTDEETVVK 500
    AKAYILFYVE HQAKAGSDKL 520
    Length:520
    Mass (Da):58,897
    Last modified:September 2, 2008 - v2
    Checksum:iAC27FE9BD0438893
    GO
    Isoform 2 (identifier: Q9Y6I4-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         51-95: RYVNGHAKKHYEDAQVPLTNHKKSEKQDKVQHTVCMDCSSYSTYC → S

    Note: No experimental confirmation available.

    Show »
    Length:476
    Mass (Da):53,743
    Checksum:i5F201F63795E938A
    GO

    Sequence cautioni

    The sequence AAD42992.1 differs from that shown. Reason: Frameshift at positions 265, 274 and 299.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti439 – 4391C → W in AAD42992. (PubMed:10480896)Curated
    Sequence conflicti473 – 4731T → I in BAG62807. (PubMed:14702039)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti360 – 3601P → T.
    Corresponds to variant rs34776764 [ dbSNP | Ensembl ].
    VAR_051521

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei51 – 9545RYVNG…YSTYC → S in isoform 2. 1 PublicationVSP_044712Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF073344 mRNA. Translation: AAD42992.1. Frameshift.
    BT007269 mRNA. Translation: AAP35933.1.
    AK301236 mRNA. Translation: BAG62807.1.
    AC007950 Genomic DNA. No translation available.
    AC118274 Genomic DNA. No translation available.
    CH471082 Genomic DNA. Translation: EAW77651.1.
    BC018113 mRNA. Translation: AAH18113.1.
    BC065300 mRNA. Translation: AAH65300.1.
    BC107137 mRNA. Translation: AAI07138.1.
    BC107138 mRNA. Translation: AAI07139.1.
    CCDSiCCDS32265.1. [Q9Y6I4-1]
    CCDS58370.1. [Q9Y6I4-2]
    RefSeqiNP_001243631.1. NM_001256702.1. [Q9Y6I4-2]
    NP_006528.2. NM_006537.3. [Q9Y6I4-1]
    UniGeneiHs.458499.

    Genome annotation databases

    EnsembliENST00000380324; ENSP00000369681; ENSG00000140455. [Q9Y6I4-1]
    ENST00000540797; ENSP00000445828; ENSG00000140455. [Q9Y6I4-2]
    GeneIDi9960.
    KEGGihsa:9960.
    UCSCiuc002amf.4. human. [Q9Y6I4-1]

    Polymorphism databases

    DMDMi205371844.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF073344 mRNA. Translation: AAD42992.1 . Frameshift.
    BT007269 mRNA. Translation: AAP35933.1 .
    AK301236 mRNA. Translation: BAG62807.1 .
    AC007950 Genomic DNA. No translation available.
    AC118274 Genomic DNA. No translation available.
    CH471082 Genomic DNA. Translation: EAW77651.1 .
    BC018113 mRNA. Translation: AAH18113.1 .
    BC065300 mRNA. Translation: AAH65300.1 .
    BC107137 mRNA. Translation: AAI07138.1 .
    BC107138 mRNA. Translation: AAI07139.1 .
    CCDSi CCDS32265.1. [Q9Y6I4-1 ]
    CCDS58370.1. [Q9Y6I4-2 ]
    RefSeqi NP_001243631.1. NM_001256702.1. [Q9Y6I4-2 ]
    NP_006528.2. NM_006537.3. [Q9Y6I4-1 ]
    UniGenei Hs.458499.

    3D structure databases

    ProteinModelPortali Q9Y6I4.
    SMRi Q9Y6I4. Positions 3-512.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 115285. 28 interactions.
    DIPi DIP-53585N.
    IntActi Q9Y6I4. 20 interactions.
    STRINGi 9606.ENSP00000369681.

    Protein family/group databases

    MEROPSi C19.026.

    PTM databases

    PhosphoSitei Q9Y6I4.

    Polymorphism databases

    DMDMi 205371844.

    Proteomic databases

    MaxQBi Q9Y6I4.
    PaxDbi Q9Y6I4.
    PRIDEi Q9Y6I4.

    Protocols and materials databases

    DNASUi 9960.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000380324 ; ENSP00000369681 ; ENSG00000140455 . [Q9Y6I4-1 ]
    ENST00000540797 ; ENSP00000445828 ; ENSG00000140455 . [Q9Y6I4-2 ]
    GeneIDi 9960.
    KEGGi hsa:9960.
    UCSCi uc002amf.4. human. [Q9Y6I4-1 ]

    Organism-specific databases

    CTDi 9960.
    GeneCardsi GC15P063796.
    H-InvDB HIX0012328.
    HGNCi HGNC:12626. USP3.
    MIMi 604728. gene.
    neXtProti NX_Q9Y6I4.
    PharmGKBi PA37251.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5533.
    HOGENOMi HOG000231498.
    HOVERGENi HBG103589.
    InParanoidi Q9Y6I4.
    KOi K11986.
    OMAi ESCLYDL.
    PhylomeDBi Q9Y6I4.
    TreeFami TF315281.

    Miscellaneous databases

    ChiTaRSi USP3. human.
    GenomeRNAii 9960.
    NextBioi 37582.
    PROi Q9Y6I4.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9Y6I4.
    Bgeei Q9Y6I4.
    CleanExi HS_USP3.
    Genevestigatori Q9Y6I4.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    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. "Characterization and chromosomal localization of USP3, a novel human ubiquitin-specific protease."
      Sloper-Mould K.E., Eyre H.J., Wang X.-W., Sutherland G.R., Baker R.T.
      J. Biol. Chem. 274:26878-26884(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
      Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
      Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Spleen.
    4. "Analysis of the DNA sequence and duplication history of human chromosome 15."
      Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A.
      , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
      Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "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] (ISOFORM 1).
      Tissue: Eye and Skin.
    7. Cited for: FUNCTION, INTERACTION WITH H2A, SUBCELLULAR LOCATION, MUTAGENESIS OF HIS-56 AND CYS-168, IDENTIFICATION BY MASS SPECTROMETRY.
    8. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiUBP3_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y6I4
    Secondary accession number(s): B4DVU5, F5H1A6, Q8WVD0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: September 2, 2008
    Last modified: October 1, 2014
    This is version 122 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 15
      Human chromosome 15: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. Peptidase families
      Classification of peptidase families and list of entries
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3