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Protein

Ubiquitin carboxyl-terminal hydrolase 3

Gene

Usp3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

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 (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 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. chromatin binding Source: Ensembl
  2. core promoter sequence-specific DNA binding Source: Ensembl
  3. cysteine-type endopeptidase activity Source: GO_Central
  4. histone binding Source: MGI
  5. ubiquitin-specific protease activity Source: GO_Central
  6. zinc ion binding Source: InterPro

GO - Biological processi

  1. DNA repair Source: MGI
  2. histone deubiquitination Source: MGI
  3. mitotic cell cycle Source: MGI
  4. negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
  5. proteasome-mediated ubiquitin-dependent protein catabolic process Source: GO_Central
  6. regulation of proteasomal protein catabolic process Source: GO_Central
  7. regulation of protein stability Source: MGI
  8. regulation of transcription, DNA-templated Source: GO_Central
Complete GO annotation...

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

Organism-specific databases

MGIiMGI:2152450. Usp3.

Subcellular locationi

Nucleus
Note: Localizes preferentially with monoubiquitinated H2A to chromatin.

GO - Cellular componenti

  1. nuclear chromatin Source: MGI
  2. nucleus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 520520Ubiquitin carboxyl-terminal hydrolase 3PRO_0000080620Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ91W36.
PaxDbiQ91W36.
PRIDEiQ91W36.

PTM databases

PhosphoSiteiQ91W36.

Expressioni

Gene expression databases

BgeeiQ91W36.
CleanExiMM_USP3.
ExpressionAtlasiQ91W36. baseline and differential.
GenevestigatoriQ91W36.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

IntActiQ91W36. 1 interaction.
MINTiMINT-4139221.

Structurei

3D structure databases

ProteinModelPortaliQ91W36.
SMRiQ91W36. Positions 3-508.
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

eggNOGiCOG5560.
GeneTreeiENSGT00780000121880.
HOGENOMiHOG000231498.
HOVERGENiHBG103589.
InParanoidiQ91W36.
KOiK11986.
OMAiGPESCLY.
OrthoDBiEOG7992Q2.
PhylomeDBiQ91W36.
TreeFamiTF315281.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
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]

Sequencei

Sequence statusi: Complete.

Q91W36-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MECPHLSSSV CIAPDSAKFP NGSPSSWCCS VCRSNKSPWV CLTCSSVHCG
60 70 80 90 100
RYVNGHAKKH YEDAQIPLLN HKRSEKQEKA QHTVCMDCSS YSTYCYRCDD
110 120 130 140 150
FVVNDTKLGL VQKVREHLQN LENSAFTADR HRKRKLLENS SLNSKLLKVN
160 170 180 190 200
GSTTAICATG LRNLGNTCFM NAILQSLSNI EQFCCYFKEL PAVELRNGKT
210 220 230 240 250
AGRRTYHTRS QGDSNVSLVE EFRKTLCALW QGSQTAFSPE SLFYVVWKIM
260 270 280 290 300
PNFRGYQQQD AHEFMRYLLD HLHLELQGGF NGVSRSAILQ ENSTLSASNK
310 320 330 340 350
CCINGASTVV TAIFGGILQN EVNCLICGTE SRKFDPFLDL SLDIPSQFRS
360 370 380 390 400
KRSKNQENGP VCSLRDCLRS FTDLEELDET ELYMCHKCKK KQKSTKKFWI
410 420 430 440 450
QKLPKALCLH LKRFHWTAYL RNKVDTYVQF PLRGLDMKCY LLEPENSGPD
460 470 480 490 500
SCLYDLAAVV VHHGSGVGSG HYTAYAVHEG RWFHFNDSTV TVTDEETVGK
510 520
AKAYILFYVE RQARAGAEKL
Length:520
Mass (Da):58,868
Last modified:December 1, 2001 - v1
Checksum:iE160B48ECA47483D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK031141 mRNA. Translation: BAC27276.1.
BC017156 mRNA. Translation: AAH17156.1.
CCDSiCCDS23305.1.
RefSeqiNP_659186.1. NM_144937.4.
UniGeneiMm.32465.
Mm.38976.
Mm.472571.

Genome annotation databases

EnsembliENSMUST00000127569; ENSMUSP00000122199; ENSMUSG00000032376.
GeneIDi235441.
KEGGimmu:235441.
UCSCiuc009qey.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK031141 mRNA. Translation: BAC27276.1.
BC017156 mRNA. Translation: AAH17156.1.
CCDSiCCDS23305.1.
RefSeqiNP_659186.1. NM_144937.4.
UniGeneiMm.32465.
Mm.38976.
Mm.472571.

3D structure databases

ProteinModelPortaliQ91W36.
SMRiQ91W36. Positions 3-508.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ91W36. 1 interaction.
MINTiMINT-4139221.

Protein family/group databases

MEROPSiC19.026.

PTM databases

PhosphoSiteiQ91W36.

Proteomic databases

MaxQBiQ91W36.
PaxDbiQ91W36.
PRIDEiQ91W36.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000127569; ENSMUSP00000122199; ENSMUSG00000032376.
GeneIDi235441.
KEGGimmu:235441.
UCSCiuc009qey.1. mouse.

Organism-specific databases

CTDi9960.
MGIiMGI:2152450. Usp3.

Phylogenomic databases

eggNOGiCOG5560.
GeneTreeiENSGT00780000121880.
HOGENOMiHOG000231498.
HOVERGENiHBG103589.
InParanoidiQ91W36.
KOiK11986.
OMAiGPESCLY.
OrthoDBiEOG7992Q2.
PhylomeDBiQ91W36.
TreeFamiTF315281.

Miscellaneous databases

NextBioi382674.
PROiQ91W36.
SOURCEiSearch...

Gene expression databases

BgeeiQ91W36.
CleanExiMM_USP3.
ExpressionAtlasiQ91W36. baseline and differential.
GenevestigatoriQ91W36.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001394. Peptidase_C19_UCH.
IPR018200. USP_CS.
IPR028889. USP_dom.
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]
ProtoNetiSearch...

Publicationsi

  1. "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(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Forelimb.
  2. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Salivary gland.

Entry informationi

Entry nameiUBP3_MOUSE
AccessioniPrimary (citable) accession number: Q91W36
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 9, 2003
Last sequence update: December 1, 2001
Last modified: March 4, 2015
This is version 107 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.