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D3ZJ96

- UBP28_RAT

UniProt

D3ZJ96 - UBP28_RAT

Protein

Ubiquitin carboxyl-terminal hydrolase 28

Gene

Usp28

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 33 (01 Oct 2014)
      Sequence version 2 (13 Jul 2010)
      Previous versions | rss
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    Functioni

    Deubiquitinase involved in DNA damage response checkpoint and MYC proto-oncogene stability. Involved in DNA damage induced apoptosis by specifically deubiquitinating proteins of the DNA damage pathway such as CLSPN. Also involved in G2 DNA damage checkpoint, by deubiquitinating CLSPN, and preventing its degradation by the anaphase promoting complex/cyclosome (APC/C). In contrast, it does not deubiquitinate PLK1. Specifically deubiquitinates MYC in the nucleoplasm, leading to prevent MYC degradation by the proteasome: acts by specifically interacting with FBXW7 (FBW7alpha) in the nucleoplasm and counteracting ubiquitination of MYC by the SCF(FBXW7) complex 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 sitei171 – 1711NucleophilePROSITE-ProRule annotation
    Active sitei606 – 6061Proton acceptorPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ubiquitin-specific protease activity Source: UniProtKB
    2. ubiquitin thiolesterase activity Source: UniProtKB

    GO - Biological processi

    1. cell proliferation Source: UniProtKB
    2. cellular response to UV Source: Ensembl
    3. DNA damage checkpoint Source: UniProtKB
    4. DNA repair Source: UniProtKB-KW
    5. intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator Source: UniProtKB
    6. protein deubiquitination Source: UniProtKB
    7. response to ionizing radiation Source: UniProtKB
    8. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    DNA damage, DNA repair, Ubl conjugation pathway

    Protein family/group databases

    MEROPSiC19.054.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 28 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 28
    Ubiquitin thioesterase 28
    Ubiquitin-specific-processing protease 28
    Gene namesi
    Name:Usp28
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 8

    Organism-specific databases

    RGDi1311555. Usp28.

    Subcellular locationi

    Nucleusnucleoplasm By similarity

    GO - Cellular componenti

    1. nucleolus Source: Ensembl
    2. nucleoplasm Source: UniProtKB
    3. protein complex Source: Ensembl

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 10831083Ubiquitin carboxyl-terminal hydrolase 28PRO_0000395809Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei67 – 671PhosphoserineBy similarity
    Modified residuei720 – 7201PhosphoserineBy similarity

    Post-translational modificationi

    Degradaded upon nickel ion level or hypoxia exposure.By similarity
    Phosphorylated upon DNA damage at Ser-67 and Ser-720, by ATM or ATR.By similarity

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PRIDEiD3ZJ96.

    Interactioni

    Subunit structurei

    Interacts with FBXW7; following DNA damage, dissociates from FBXW7 leading to degradation of MYC.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati97 – 11620UIMAdd
    BLAST
    Domaini162 – 656495USPAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase C19 family. USP28 subfamily.Curated
    Contains 1 USP domain.Curated

    Phylogenomic databases

    GeneTreeiENSGT00390000016082.
    HOGENOMiHOG000007956.
    KOiK11849.
    OMAiCIASTTQ.
    OrthoDBiEOG761BSZ.
    PhylomeDBiD3ZJ96.
    TreeFamiTF329035.

    Family and domain databases

    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR009060. UBA-like.
    IPR003903. Ubiquitin-int_motif.
    IPR028889. UCH/PAN2.
    [Graphical view]
    PfamiPF00443. UCH. 1 hit.
    [Graphical view]
    SMARTiSM00726. UIM. 1 hit.
    [Graphical view]
    SUPFAMiSSF46934. SSF46934. 1 hit.
    PROSITEiPS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: D3ZJ96-1) [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

    MTAELQQDDA AGAADGHGSS CQMLLNQLRE ITGIQDPSFL HEALKASNGD     50
    ITQAVSLLTD QRVKEPSHDT AATEPSEVEE SATSKDLLAK VIDLTHDNKD 100
    DLQAAIALSL LESPNIQTDS RDLNRIHEAN SAETKRSKRK RCEVWGENHN 150
    PNNWRRVDGW PVGLKNVGNT CWFSAVIQSL FQLPEFRRLV LSYSLPQNIL 200
    ENCRSHTEKR NIMFMQELQY LFALLLGSNR KFVDPSAALD LLKGAFRSSE 250
    EQQQDVSEFT HKLLDWLEDA FQLAVNVNSN PRTKSENPMV QLFYGTFLTE 300
    GVREGKPFCN NETFGQYPLQ VNGYHNLDEC LEGAMVEGDI ALLPSDRSVK 350
    YGQERWFTKL PPVLTFELSR FEFNQSLGQP EKIHNKLEFP QVIYMDRYMY 400
    KSKELIRSKR ESIRKLKEEI QVLQQKLERY VKYGSGPSRF PLPDMLKYVI 450
    EFASTKPASE SCLSGSVEHM TLPLPSVHCP ISDLTAKESS SPKSCSQNAE 500
    GSFSSPEDAL PNSEVMNGPF TSPHSSLEMP APPPAPRTVT DEEMNFVKTC 550
    LQRWRSEIEQ DIQDLKNCIS STTQAIEQMY CDPLLRQVPY RLHAVLVHEG 600
    QASAGHYWAY IYNQPRQIWL KYNDISVTES SWEELERDSY GGLRNVSAYC 650
    LMYINDKLPH CSAEAAHGES DQTAEVEALS VELRQYIQED NWRFEQEVEE 700
    WEEEQSCKIP QMESSPNSSS QDFSTSQESS AASSHGVRCL SSEHAVIAKE 750
    QTAQAIANTA HAYEKSGVEA ALSEVMLSPA MQGVLLAIAK ARQTFDRDGS 800
    EAGLIKAFHE EYSRLYQLAK ETPTSHSDPR LQHVLVYFFQ NEAPKRVVER 850
    TLLEQFADRN LSYDERSISI MKVAQAKLME IGPEDMNMEE YKRWHEDYSL 900
    FRKVSVYLLT GLELFQKGKY QEALSYLVYA YQSNAGLLVK GPRRGVKESV 950
    IALYRRKCLL ELNAKAASLF ETNDDHSVTE GINVMNELII PCIHLIINND 1000
    ISKDDLDAIE VMRNHWCSYL GKDIAENLQL CLGEFLPRLL DPSAEIIVLK 1050
    EPPTIRPNSP YDLCSRFAAV MESIQGVSTV TVK 1083
    Length:1,083
    Mass (Da):122,688
    Last modified:July 13, 2010 - v2
    Checksum:iA0E69DE733BB921E
    GO
    Isoform 2 (identifier: D3ZJ96-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         775-806: Missing.

    Show »
    Length:1,051
    Mass (Da):119,318
    Checksum:iBBEE038814F4BB46
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti73 – 731T → S in BAF97608. 1 PublicationCurated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei775 – 80632Missing in isoform 2. CuratedVSP_039547Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB240643 mRNA. Translation: BAF97608.1.
    CH473975 Genomic DNA. Translation: EDL95433.1.
    RefSeqiNP_001101614.1. NM_001108144.1.
    XP_006243070.1. XM_006243008.1. [D3ZJ96-1]
    XP_006243073.1. XM_006243011.1. [D3ZJ96-2]
    UniGeneiRn.6599.

    Genome annotation databases

    EnsembliENSRNOT00000009724; ENSRNOP00000009724; ENSRNOG00000007325. [D3ZJ96-2]
    ENSRNOT00000067420; ENSRNOP00000060005; ENSRNOG00000007325. [D3ZJ96-1]
    GeneIDi315639.
    KEGGirno:315639.
    UCSCiRGD:1311555. rat. [D3ZJ96-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB240643 mRNA. Translation: BAF97608.1 .
    CH473975 Genomic DNA. Translation: EDL95433.1 .
    RefSeqi NP_001101614.1. NM_001108144.1.
    XP_006243070.1. XM_006243008.1. [D3ZJ96-1 ]
    XP_006243073.1. XM_006243011.1. [D3ZJ96-2 ]
    UniGenei Rn.6599.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi C19.054.

    Proteomic databases

    PRIDEi D3ZJ96.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000009724 ; ENSRNOP00000009724 ; ENSRNOG00000007325 . [D3ZJ96-2 ]
    ENSRNOT00000067420 ; ENSRNOP00000060005 ; ENSRNOG00000007325 . [D3ZJ96-1 ]
    GeneIDi 315639.
    KEGGi rno:315639.
    UCSCi RGD:1311555. rat. [D3ZJ96-1 ]

    Organism-specific databases

    CTDi 57646.
    RGDi 1311555. Usp28.

    Phylogenomic databases

    GeneTreei ENSGT00390000016082.
    HOGENOMi HOG000007956.
    KOi K11849.
    OMAi CIASTTQ.
    OrthoDBi EOG761BSZ.
    PhylomeDBi D3ZJ96.
    TreeFami TF329035.

    Miscellaneous databases

    NextBioi 669544.
    PROi D3ZJ96.

    Family and domain databases

    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR009060. UBA-like.
    IPR003903. Ubiquitin-int_motif.
    IPR028889. UCH/PAN2.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    [Graphical view ]
    SMARTi SM00726. UIM. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46934. SSF46934. 1 hit.
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Expression of deubiquitination enzyme (USP28) in rat spermatogenic cell. Immunocytochemical analysis."
      Haraguchi C.M., Mabuchi T., Yokota S.
      Submitted (NOV-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Tissue: Testis.
    2. 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].
      Strain: Brown Norway.

    Entry informationi

    Entry nameiUBP28_RAT
    AccessioniPrimary (citable) accession number: D3ZJ96
    Secondary accession number(s): D2Y8W6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 13, 2010
    Last sequence update: July 13, 2010
    Last modified: October 1, 2014
    This is version 33 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