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Protein

Ubiquitin carboxyl-terminal hydrolase 28

Gene

Usp28

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: 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 sitei605 – 6051Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

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
Synonyms:Kiaa1515
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:2442293. Usp28.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10511051Ubiquitin carboxyl-terminal hydrolase 28PRO_0000080658Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei67 – 671PhosphoserineBy similarity
Modified residuei720 – 7201PhosphoserineBy similarity
Modified residuei1022 – 10221PhosphothreonineBy 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

MaxQBiQ5I043.
PaxDbiQ5I043.
PRIDEiQ5I043.

PTM databases

PhosphoSiteiQ5I043.

Expressioni

Gene expression databases

BgeeiQ5I043.
CleanExiMM_USP28.
ExpressionAtlasiQ5I043. baseline and differential.
GenevestigatoriQ5I043.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi231641. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ5I043.
SMRiQ5I043. Positions 22-132.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini97 – 11620UIMCuratedAdd
BLAST
Domaini162 – 655494USPAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG5077.
GeneTreeiENSGT00390000016082.
HOGENOMiHOG000007956.
HOVERGENiHBG056030.
InParanoidiQ5I043.
KOiK11849.
OMAiCIASTTQ.
OrthoDBiEOG761BSZ.
PhylomeDBiQ5I043.
TreeFamiTF329035.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR009060. UBA-like.
IPR003903. Ubiquitin-int_motif.
IPR018200. USP_CS.
IPR028889. USP_dom.
[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. AlignAdd to basket

Isoform 1 (identifier: Q5I043-1) [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
MTAELQQDDS AGAADGHGSS CQMLLNQLRE ITGIQDPSFL HEALKASNGD
60 70 80 90 100
ITQAVSLLTD QRVKEPSHDT TAAEPSEVEE SATSKDLLAK VIDLTHDNKD
110 120 130 140 150
DLQAAIALSL LESPNIQADN RDLNRAHEAN SAETKRSKRK RCEVWGENHN
160 170 180 190 200
PNNWRRVDGW PVGLKNVGNT CWFSAVIQSL FQLPEFRRLV LSYNLPQNIL
210 220 230 240 250
ENCRSHTEKR NIMFMQELQY LFALLLGSNR KFVDPSAALD LLKGAFRSSE
260 270 280 290 300
EQQQDVSEFT HKLLDWLEDA FQLAVNVNSH LRNKSENPMV QLFYGTFLTE
310 320 330 340 350
GVREGKPFCN NETFGQYPLQ VNGYHNLDEC LEGAMVEGDI ALLPSDRSVK
360 370 380 390 400
YGQERWFTKL PPVLTFELSR FEFNQSLGQP EKIHNKLEFP QIIYMDRYMY
410 420 430 440 450
KSKELIRSKR ESVRKLKEEI QVLQQKLERY VKYGSGPSRF PLPDMLKYVI
460 470 480 490 500
EFASTKPASE SCLSGSAEHV TLPLPSVHCP ISDLTPKESS SPESCSQNAG
510 520 530 540 550
STFSSPEDAL PSSEGMNGPF TSPHSSLETP APPAPRTVTD EEMNFVKTCL
560 570 580 590 600
QRWRSEIEQD IQDLKNCISS STKAIEQMYC DPLLRQVPYR LHAVLVHEGQ
610 620 630 640 650
ASAGHYWAYI YNQPRQTWLK YNDISVTESS WEELERDSYG GLRNVSAYCL
660 670 680 690 700
MYINDNLPHF SAEASSNESD ETAGEVEALS VELRQYIQED NWRFQQEVEE
710 720 730 740 750
WEEEQSCKIP QMESSPNSSS QDFSTSQESP AVSSHEVRCL SSEHAVIAKE
760 770 780 790 800
QTAQAIANTA HAYEKSGVEA ALSEAFHEEY SRLYQLAKET PTSHSDPRLQ
810 820 830 840 850
HVLVYFFQNE APKRVVERTL LEQFADRNLS YDERSISIMK VAQAKLMEIG
860 870 880 890 900
PDDMNMEEYK RWHEDYSLFR KVSVYLLTGL ELFQKGKYQE ALSYLVYAYQ
910 920 930 940 950
SNAGLLVKGP RRGVKESVIA LYRRKCLLEL NAKAASLFET NDDHSVTEGI
960 970 980 990 1000
NVMNELIIPC IHLIINNDIS KDDLDAIEVM RNHWCSYLGK DIAENLQLCL
1010 1020 1030 1040 1050
GEFLPRLLDP SAEIIVLKEP PTIRPNSPYD LCNRFAAVME SIQGVSTVTV

K
Length:1,051
Mass (Da):119,318
Last modified:February 15, 2005 - v1
Checksum:i72623C4668860749
GO
Isoform 2 (identifier: Q5I043-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     429-453: Missing.

Note: No experimental confirmation available.

Show »
Length:1,026
Mass (Da):116,402
Checksum:i4620DBD05FE6E55A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti523 – 5231P → L in BAC98190 (PubMed:14621295).Curated
Sequence conflicti617 – 6171T → I in BAC98190 (PubMed:14621295).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei429 – 45325Missing in isoform 2. 1 PublicationVSP_015581Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC066033 mRNA. Translation: AAH66033.1.
BC088733 mRNA. Translation: AAH88733.1.
AK052442 mRNA. Translation: BAC34993.1.
AK129380 mRNA. Translation: BAC98190.1.
CCDSiCCDS40613.1. [Q5I043-1]
RefSeqiNP_780691.2. NM_175482.3. [Q5I043-1]
UniGeneiMm.21630.

Genome annotation databases

EnsembliENSMUST00000047349; ENSMUSP00000047467; ENSMUSG00000032267. [Q5I043-1]
GeneIDi235323.
KEGGimmu:235323.
UCSCiuc009pir.1. mouse. [Q5I043-1]
uc009pis.1. mouse. [Q5I043-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC066033 mRNA. Translation: AAH66033.1.
BC088733 mRNA. Translation: AAH88733.1.
AK052442 mRNA. Translation: BAC34993.1.
AK129380 mRNA. Translation: BAC98190.1.
CCDSiCCDS40613.1. [Q5I043-1]
RefSeqiNP_780691.2. NM_175482.3. [Q5I043-1]
UniGeneiMm.21630.

3D structure databases

ProteinModelPortaliQ5I043.
SMRiQ5I043. Positions 22-132.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi231641. 1 interaction.

Protein family/group databases

MEROPSiC19.054.

PTM databases

PhosphoSiteiQ5I043.

Proteomic databases

MaxQBiQ5I043.
PaxDbiQ5I043.
PRIDEiQ5I043.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000047349; ENSMUSP00000047467; ENSMUSG00000032267. [Q5I043-1]
GeneIDi235323.
KEGGimmu:235323.
UCSCiuc009pir.1. mouse. [Q5I043-1]
uc009pis.1. mouse. [Q5I043-2]

Organism-specific databases

CTDi57646.
MGIiMGI:2442293. Usp28.
RougeiSearch...

Phylogenomic databases

eggNOGiCOG5077.
GeneTreeiENSGT00390000016082.
HOGENOMiHOG000007956.
HOVERGENiHBG056030.
InParanoidiQ5I043.
KOiK11849.
OMAiCIASTTQ.
OrthoDBiEOG761BSZ.
PhylomeDBiQ5I043.
TreeFamiTF329035.

Miscellaneous databases

NextBioi382599.
PROiQ5I043.
SOURCEiSearch...

Gene expression databases

BgeeiQ5I043.
CleanExiMM_USP28.
ExpressionAtlasiQ5I043. baseline and differential.
GenevestigatoriQ5I043.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR009060. UBA-like.
IPR003903. Ubiquitin-int_motif.
IPR018200. USP_CS.
IPR028889. USP_dom.
[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]
ProtoNetiSearch...

Publicationsi

  1. "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] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Brain and Embryonic germ cell.
  2. "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] OF 292-1051.
    Strain: C57BL/6J.
    Tissue: Lung.
  3. "Prediction of the coding sequences of mouse homologues of KIAA gene: III. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
    Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Nagase T., Ohara O., Koga H.
    DNA Res. 10:167-180(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 392-1051.
    Tissue: Embryonic tail.

Entry informationi

Entry nameiUBP28_MOUSE
AccessioniPrimary (citable) accession number: Q5I043
Secondary accession number(s): Q6NZP3, Q6ZPP1, Q8BWI1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 13, 2005
Last sequence update: February 15, 2005
Last modified: May 27, 2015
This is version 91 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.