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D3ZJ96

- UBP28_RAT

UniProt

D3ZJ96 - UBP28_RAT

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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

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
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

DNA damage, DNA repair, Ubl conjugation pathway

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
Complete GO annotation...

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.
InParanoidiD3ZJ96.
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

        10         20         30         40         50
MTAELQQDDA AGAADGHGSS CQMLLNQLRE ITGIQDPSFL HEALKASNGD
60 70 80 90 100
ITQAVSLLTD QRVKEPSHDT AATEPSEVEE SATSKDLLAK VIDLTHDNKD
110 120 130 140 150
DLQAAIALSL LESPNIQTDS RDLNRIHEAN SAETKRSKRK RCEVWGENHN
160 170 180 190 200
PNNWRRVDGW PVGLKNVGNT CWFSAVIQSL FQLPEFRRLV LSYSLPQNIL
210 220 230 240 250
ENCRSHTEKR NIMFMQELQY LFALLLGSNR KFVDPSAALD LLKGAFRSSE
260 270 280 290 300
EQQQDVSEFT HKLLDWLEDA FQLAVNVNSN PRTKSENPMV QLFYGTFLTE
310 320 330 340 350
GVREGKPFCN NETFGQYPLQ VNGYHNLDEC LEGAMVEGDI ALLPSDRSVK
360 370 380 390 400
YGQERWFTKL PPVLTFELSR FEFNQSLGQP EKIHNKLEFP QVIYMDRYMY
410 420 430 440 450
KSKELIRSKR ESIRKLKEEI QVLQQKLERY VKYGSGPSRF PLPDMLKYVI
460 470 480 490 500
EFASTKPASE SCLSGSVEHM TLPLPSVHCP ISDLTAKESS SPKSCSQNAE
510 520 530 540 550
GSFSSPEDAL PNSEVMNGPF TSPHSSLEMP APPPAPRTVT DEEMNFVKTC
560 570 580 590 600
LQRWRSEIEQ DIQDLKNCIS STTQAIEQMY CDPLLRQVPY RLHAVLVHEG
610 620 630 640 650
QASAGHYWAY IYNQPRQIWL KYNDISVTES SWEELERDSY GGLRNVSAYC
660 670 680 690 700
LMYINDKLPH CSAEAAHGES DQTAEVEALS VELRQYIQED NWRFEQEVEE
710 720 730 740 750
WEEEQSCKIP QMESSPNSSS QDFSTSQESS AASSHGVRCL SSEHAVIAKE
760 770 780 790 800
QTAQAIANTA HAYEKSGVEA ALSEVMLSPA MQGVLLAIAK ARQTFDRDGS
810 820 830 840 850
EAGLIKAFHE EYSRLYQLAK ETPTSHSDPR LQHVLVYFFQ NEAPKRVVER
860 870 880 890 900
TLLEQFADRN LSYDERSISI MKVAQAKLME IGPEDMNMEE YKRWHEDYSL
910 920 930 940 950
FRKVSVYLLT GLELFQKGKY QEALSYLVYA YQSNAGLLVK GPRRGVKESV
960 970 980 990 1000
IALYRRKCLL ELNAKAASLF ETNDDHSVTE GINVMNELII PCIHLIINND
1010 1020 1030 1040 1050
ISKDDLDAIE VMRNHWCSYL GKDIAENLQL CLGEFLPRLL DPSAEIIVLK
1060 1070 1080
EPPTIRPNSP YDLCSRFAAV MESIQGVSTV TVK
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:
EMBLi
GenBanki
DDBJi
Links Updated
AB240643 mRNA. Translation: BAF97608.1.
CH473975 Genomic DNA. Translation: EDL95433.1.
RefSeqiNP_001101614.1. NM_001108144.1.
XP_006243070.1. XM_006243008.2. [D3ZJ96-1]
XP_006243073.1. XM_006243011.2. [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:
EMBLi
GenBanki
DDBJi
Links Updated
AB240643 mRNA. Translation: BAF97608.1 .
CH473975 Genomic DNA. Translation: EDL95433.1 .
RefSeqi NP_001101614.1. NM_001108144.1.
XP_006243070.1. XM_006243008.2. [D3ZJ96-1 ]
XP_006243073.1. XM_006243011.2. [D3ZJ96-2 ]
UniGenei Rn.6599.

3D structure databases

ModBasei Search...
MobiDBi Search...

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.
InParanoidi D3ZJ96.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 34 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