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P35123

- UBP4_MOUSE

UniProt

P35123 - UBP4_MOUSE

Protein

Ubiquitin carboxyl-terminal hydrolase 4

Gene

Usp4

Organism
Mus musculus (Mouse)
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 3 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Hydrolase that deubiquitinates target proteins such as the receptor ADORA2A, PDPK1 and TRIM21. Deubiquitination of ADORA2A increases the amount of functional receptor at the cell surface. Plays a role in the regulation of quality control in the ER 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 sitei311 – 3111NucleophilePROSITE-ProRule annotation
    Metal bindingi461 – 4611ZincBy similarity
    Metal bindingi464 – 4641ZincBy similarity
    Metal bindingi798 – 7981ZincBy similarity
    Metal bindingi801 – 8011ZincBy similarity
    Active sitei880 – 8801Proton acceptorPROSITE-ProRule annotation

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. protein binding Source: UniProtKB
    3. ubiquitin-specific protease activity Source: UniProtKB
    4. ubiquitin thiolesterase activity Source: UniProtKB

    GO - Biological processi

    1. negative regulation of protein ubiquitination Source: UniProtKB
    2. protein deubiquitination Source: UniProtKB
    3. protein localization to cell surface Source: UniProtKB
    4. regulation of protein stability Source: UniProtKB
    5. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Protein family/group databases

    MEROPSiC19.010.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 4 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 4
    Ubiquitin thioesterase 4
    Ubiquitin-specific-processing protease 4
    Ubiquitous nuclear protein
    Gene namesi
    Name:Usp4
    Synonyms:Unp
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 9

    Organism-specific databases

    MGIiMGI:98905. Usp4.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleus 1 Publication
    Note: Shuttles between the nucleus and cytoplasm. Exported to the cytoplasm in a CRM1-dependent manner and recycled back to the nucleus via the importin alpha/beta heterodimeric import receptor.

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB
    2. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi461 – 4611C → Q: Reduces the interaction with RB1. 2 Publications
    Mutagenesisi770 – 7712KK → NS: Reduces nuclear localization. 1 Publication

    Keywords - Diseasei

    Proto-oncogene

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 962962Ubiquitin carboxyl-terminal hydrolase 4PRO_0000080622Add
    BLAST

    Post-translational modificationi

    Monoubiquitinated by TRIM21. Ubiquitination does not lead to its proteasomal degradation. Autodeubiquitinated By similarity.By similarity

    Keywords - PTMi

    Ubl conjugation

    Proteomic databases

    MaxQBiP35123.
    PaxDbiP35123.
    PRIDEiP35123.

    PTM databases

    PhosphoSiteiP35123.

    Expressioni

    Tissue specificityi

    Expressed in brain, kidney, liver and spleen (at protein level).1 Publication

    Developmental stagei

    Overexpression leads to oncogenic transformation of NIH 3T3 cells.

    Gene expression databases

    ArrayExpressiP35123.
    BgeeiP35123.
    CleanExiMM_USP4.
    GenevestigatoriP35123.

    Interactioni

    Subunit structurei

    Interacts with RB1 (both dephosphorylated and hypophosphorylated forms). Interacts with ADORA2A (via cytoplasmic C-terminus); the interaction is direct By similarity. Interacts with RB1, RBL1 and RBL2.By similarity1 Publication

    Protein-protein interaction databases

    IntActiP35123. 1 interaction.
    MINTiMINT-4139272.

    Structurei

    Secondary structure

    1
    962
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi13 – 219
    Turni22 – 254
    Beta strandi33 – 386
    Helixi39 – 4911
    Beta strandi51 – 533
    Turni56 – 605
    Helixi62 – 643
    Helixi72 – 743
    Beta strandi75 – 773
    Turni78 – 814
    Turni89 – 913
    Beta strandi92 – 976
    Helixi98 – 10811
    Beta strandi118 – 1247
    Beta strandi126 – 1283
    Beta strandi130 – 1334
    Beta strandi138 – 1447
    Beta strandi147 – 15610
    Helixi162 – 17211
    Beta strandi181 – 1855
    Beta strandi187 – 1915
    Turni202 – 2065
    Beta strandi211 – 2177

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3JYUX-ray2.37A/B1-229[»]
    ProteinModelPortaliP35123.
    SMRiP35123. Positions 7-226, 297-483, 775-924.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP35123.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini11 – 122112DUSPPROSITE-ProRule annotationAdd
    BLAST
    Domaini142 – 22685Ubiquitin-like 1Add
    BLAST
    Domaini302 – 922621USPAdd
    BLAST
    Domaini483 – 57189Ubiquitin-like 2Add
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni405 – 4073Necessary for interaction with RBL2
    Regioni459 – 4635Necessary for interaction with RB1 and RBL2

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi133 – 1419Nuclear export signal
    Motifi766 – 7716Nuclear localization signal

    Domaini

    The Ubiquitin-like domain 2 inserts into the catalytic domain and competes with the ubiquitin substrate, partially inhibiting DUB activity.By similarity

    Sequence similaritiesi

    Belongs to the peptidase C19 family. USP4 subfamily.Curated
    Contains 1 DUSP domain.PROSITE-ProRule annotation
    Contains 2 ubiquitin-like domains.Curated
    Contains 1 USP domain.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG5560.
    GeneTreeiENSGT00670000097750.
    HOGENOMiHOG000264375.
    HOVERGENiHBG000864.
    InParanoidiQ8BTL9.
    KOiK11835.
    OMAiCHSEGCM.
    OrthoDBiEOG77Q4VW.
    TreeFamiTF106276.

    Family and domain databases

    Gene3Di3.30.2230.10. 1 hit.
    InterProiIPR006615. Pept_C19_DUSP.
    IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028135. Ub_USP-typ.
    IPR028889. UCH/PAN2.
    IPR028134. USP.
    [Graphical view]
    PANTHERiPTHR24006:SF360. PTHR24006:SF360. 1 hit.
    PfamiPF06337. DUSP. 1 hit.
    PF14836. Ubiquitin_3. 1 hit.
    PF00443. UCH. 1 hit.
    [Graphical view]
    SMARTiSM00695. DUSP. 1 hit.
    [Graphical view]
    SUPFAMiSSF143791. SSF143791. 1 hit.
    PROSITEiPS51283. DUSP. 1 hit.
    PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P35123-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAEGRGSRER PDVETQKTEL GALMGTTLQR GAQWYLIDSR WFKQWKKYVG    50
    FDSWDMYNVG EHNLFPGPID NSGLFSDPES QTLKEHLIDE LDYVLVPAEA 100
    WNKLLNWYGC VEGQQPIVRK VVEHGLFVKH CKVEVYLLEL KLCENSDPTN 150
    VLSCHFSKAD TIATIEKEMR KLFNIPAERE TRLWNKYMSN TYEQLSKLDN 200
    TIQDAGLYQG QVLVIEPQNE DGTWPRQSLQ SKSSTAPSRN FTTSSKPSAS 250
    PYCSVSASLI ANGDSTNSSG MHSSGVSRGG SGFSASYNCQ EPPSPHIQPG 300
    LCGLGNLGNT CFMNSALQCL SNTAPLTEYF LKDEYEAEIN RDNPLGMKGE 350
    IAEAYAELIK QMWSGRDTHV APRMFKTQVG RFAPQFSGYQ QQDSQELLAF 400
    ILDGLHEDLN RVKKKPYLEP KDANGRPDAV VAKEAWENHR LRNDSVIVDT 450
    FHGLFKSTLV CPECAKVSVT FDPFCYLTLP LPLKKDRIME VFLVPADPQC 500
    RPIQYRVTVP LMGAISDLCE ALSKLSGIAA ENMVVTDVYN HRFHKIFQMD 550
    EGLSHITPRD DIFVYEVCNT SMDGSECITL PVYFREKKSR PSSASSGAVL 600
    YGQPLLVSVP KHKLTLESLY QAVCDRISRY IKQPLPDEFL SSPLEPGACN 650
    GSRSSYEGDE EEEMDHQEEG KEQLSEVEGS GEDDQGDDHS ESAQKVKGQP 700
    RHKRLFTFSL VNSCGTADIN SLATDGKLLK LNSRSTLAID WDSETRSLYF 750
    DEQESEACEK HLSMSQPQKK KKAAVALREC IELFTTMETL GEHDPWYCPT 800
    CKKHQQATKK FDLWSLPKIL VVHLKRFSYN RYWRDKLDTV VEFPVRALNM 850
    SEFVCDRSAR PYVYDLIAVS NHYGAMGVGH YTAYAKNRLN GKWYYFDDSS 900
    VSLASEDQIV TKAAYVLFYQ RRDDECSSTS SLGSFPGSDG GVKLSSSHQG 950
    MGDEEAYNMD TN 962
    Length:962
    Mass (Da):108,343
    Last modified:July 27, 2011 - v3
    Checksum:i95F95BE86186DA52
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti123 – 1242EH → DD in AAB82339. (PubMed:8336951)Curated
    Sequence conflicti123 – 1242EH → DD in AAC53587. (PubMed:9602026)Curated
    Sequence conflicti292 – 2921P → A in AAB82339. (PubMed:8336951)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L00681 mRNA. Translation: AAB82339.1.
    AF026469 Genomic DNA. Translation: AAC53587.1.
    AK089425 mRNA. Translation: BAC40877.1.
    AK143582 mRNA. Translation: BAE25450.1.
    AK149964 mRNA. Translation: BAE29198.1.
    AK169933 mRNA. Translation: BAE41468.1.
    AK171271 mRNA. Translation: BAE42357.1.
    CH466560 Genomic DNA. Translation: EDL21282.1.
    CCDSiCCDS23523.1.
    PIRiI58376.
    RefSeqiNP_035808.2. NM_011678.2.
    UniGeneiMm.3974.

    Genome annotation databases

    EnsembliENSMUST00000035237; ENSMUSP00000035237; ENSMUSG00000032612.
    GeneIDi22258.
    KEGGimmu:22258.
    UCSCiuc009rph.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L00681 mRNA. Translation: AAB82339.1 .
    AF026469 Genomic DNA. Translation: AAC53587.1 .
    AK089425 mRNA. Translation: BAC40877.1 .
    AK143582 mRNA. Translation: BAE25450.1 .
    AK149964 mRNA. Translation: BAE29198.1 .
    AK169933 mRNA. Translation: BAE41468.1 .
    AK171271 mRNA. Translation: BAE42357.1 .
    CH466560 Genomic DNA. Translation: EDL21282.1 .
    CCDSi CCDS23523.1.
    PIRi I58376.
    RefSeqi NP_035808.2. NM_011678.2.
    UniGenei Mm.3974.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3JYU X-ray 2.37 A/B 1-229 [» ]
    ProteinModelPortali P35123.
    SMRi P35123. Positions 7-226, 297-483, 775-924.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P35123. 1 interaction.
    MINTi MINT-4139272.

    Protein family/group databases

    MEROPSi C19.010.

    PTM databases

    PhosphoSitei P35123.

    Proteomic databases

    MaxQBi P35123.
    PaxDbi P35123.
    PRIDEi P35123.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000035237 ; ENSMUSP00000035237 ; ENSMUSG00000032612 .
    GeneIDi 22258.
    KEGGi mmu:22258.
    UCSCi uc009rph.2. mouse.

    Organism-specific databases

    CTDi 7375.
    MGIi MGI:98905. Usp4.

    Phylogenomic databases

    eggNOGi COG5560.
    GeneTreei ENSGT00670000097750.
    HOGENOMi HOG000264375.
    HOVERGENi HBG000864.
    InParanoidi Q8BTL9.
    KOi K11835.
    OMAi CHSEGCM.
    OrthoDBi EOG77Q4VW.
    TreeFami TF106276.

    Miscellaneous databases

    EvolutionaryTracei P35123.
    NextBioi 302345.
    PROi P35123.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P35123.
    Bgeei P35123.
    CleanExi MM_USP4.
    Genevestigatori P35123.

    Family and domain databases

    Gene3Di 3.30.2230.10. 1 hit.
    InterProi IPR006615. Pept_C19_DUSP.
    IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028135. Ub_USP-typ.
    IPR028889. UCH/PAN2.
    IPR028134. USP.
    [Graphical view ]
    PANTHERi PTHR24006:SF360. PTHR24006:SF360. 1 hit.
    Pfami PF06337. DUSP. 1 hit.
    PF14836. Ubiquitin_3. 1 hit.
    PF00443. UCH. 1 hit.
    [Graphical view ]
    SMARTi SM00695. DUSP. 1 hit.
    [Graphical view ]
    SUPFAMi SSF143791. SSF143791. 1 hit.
    PROSITEi PS51283. DUSP. 1 hit.
    PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Unp, a mouse gene related to the tre oncogene."
      Gupta K., Copeland N.G., Gilbert D.J., Jenkins N.A., Gray D.A.
      Oncogene 8:2307-2310(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [MRNA].
    2. "Genomic structure of Unp, a murine gene encoding a ubiquitin-specific protease."
      di Fruscio M., Gilchrist C.A., Baker R.T., Gray D.A.
      Biochim. Biophys. Acta 1398:9-17(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 129.
      Tissue: Testis.
    3. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6J and NOD.
      Tissue: Bone marrow and Spleen.
    4. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
      Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "Association of UNP, a ubiquitin-specific protease, with the pocket proteins pRb, p107 and p130."
      Blanchette P., Gilchrist C.A., Baker R.T., Gray D.A.
      Oncogene 20:5533-5537(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RB1; RBL1 AND RBL2, MUTAGENESIS OF CYS-461.
    6. "Nuclear-cytoplasmic shuttling of the oncogenic mouse UNP/USP4 deubiquitylating enzyme."
      Soboleva T.A., Jans D.A., Johnson-Saliba M., Baker R.T.
      J. Biol. Chem. 280:745-752(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF 770-GLN--LYS-771, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
    7. "Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)."
      Structural genomics consortium (SGC)
      Submitted (NOV-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) OF 1-229.

    Entry informationi

    Entry nameiUBP4_MOUSE
    AccessioniPrimary (citable) accession number: P35123
    Secondary accession number(s): O54704, Q8BTL9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1994
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 122 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Peptidase families
      Classification of peptidase families and list of entries
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3