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Q9Y6I4

- UBP3_HUMAN

UniProt

Q9Y6I4 - UBP3_HUMAN

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Protein

Ubiquitin carboxyl-terminal hydrolase 3

Gene

USP3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein 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.1 Publication

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. histone binding Source: UniProtKB
  2. ubiquitin-specific protease activity Source: ProtInc
  3. ubiquitin thiolesterase activity Source: UniProtKB
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. DNA repair Source: UniProtKB
  2. histone deubiquitination Source: UniProtKB
  3. mitotic cell cycle Source: UniProtKB
  4. regulation of protein stability Source: UniProtKB
  5. ubiquitin-dependent protein catabolic process Source: InterPro
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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 15

Organism-specific databases

HGNCiHGNC:12626. USP3.

Subcellular locationi

Nucleus 1 Publication
Note: Localizes preferentially with monoubiquitinated H2A to chromatin.

GO - Cellular componenti

  1. nuclear chromatin Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi56 – 561H → A: Does not reduce monoubiquitinated H2A and H2B stability. Interaction with monoubiquitinated H2A is strongly inhibited. 1 Publication
Mutagenesisi168 – 1681C → S: Does not reduce H2A stability. Interacts more strongly with monoubiquitinated H2A than with nonubiquitinated H2A. Its nuclear localization to chromatin is enhanced. 1 Publication

Organism-specific databases

PharmGKBiPA37251.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 520520Ubiquitin carboxyl-terminal hydrolase 3PRO_0000080619Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ9Y6I4.
PaxDbiQ9Y6I4.
PRIDEiQ9Y6I4.

PTM databases

PhosphoSiteiQ9Y6I4.

Expressioni

Tissue specificityi

Expressed in all tissues examined, with strongest expression in pancreas.

Gene expression databases

BgeeiQ9Y6I4.
CleanExiHS_USP3.
ExpressionAtlasiQ9Y6I4. baseline and differential.
GenevestigatoriQ9Y6I4.

Interactioni

Subunit structurei

Interacts (via UBP-type domain) with H2A; the interaction is less efficient than with monoubiquitinated H2A.1 Publication

Protein-protein interaction databases

BioGridi115285. 29 interactions.
DIPiDIP-53585N.
IntActiQ9Y6I4. 20 interactions.
STRINGi9606.ENSP00000369681.

Structurei

3D structure databases

ProteinModelPortaliQ9Y6I4.
SMRiQ9Y6I4. Positions 3-512.
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

eggNOGiCOG5533.
GeneTreeiENSGT00760000119203.
HOGENOMiHOG000231498.
HOVERGENiHBG103589.
InParanoidiQ9Y6I4.
KOiK11986.
OMAiESCLYDL.
PhylomeDBiQ9Y6I4.
TreeFamiTF315281.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9Y6I4-1) [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
MECPHLSSSV CIAPDSAKFP NGSPSSWCCS VCRSNKSPWV CLTCSSVHCG
60 70 80 90 100
RYVNGHAKKH YEDAQVPLTN HKKSEKQDKV QHTVCMDCSS YSTYCYRCDD
110 120 130 140 150
FVVNDTKLGL VQKVREHLQN LENSAFTADR HKKRKLLENS TLNSKLLKVN
160 170 180 190 200
GSTTAICATG LRNLGNTCFM NAILQSLSNI EQFCCYFKEL PAVELRNGKT
210 220 230 240 250
AGRRTYHTRS QGDNNVSLVE 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
QKLPKVLCLH LKRFHWTAYL RNKVDTYVEF PLRGLDMKCY LLEPENSGPE
460 470 480 490 500
SCLYDLAAVV VHHGSGVGSG HYTAYATHEG RWFHFNDSTV TLTDEETVVK
510 520
AKAYILFYVE HQAKAGSDKL
Length:520
Mass (Da):58,897
Last modified:September 2, 2008 - v2
Checksum:iAC27FE9BD0438893
GO
Isoform 2 (identifier: Q9Y6I4-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     51-95: RYVNGHAKKHYEDAQVPLTNHKKSEKQDKVQHTVCMDCSSYSTYC → S

Note: No experimental confirmation available.

Show »
Length:476
Mass (Da):53,743
Checksum:i5F201F63795E938A
GO

Sequence cautioni

The sequence AAD42992.1 differs from that shown. Reason: Frameshift at positions 265, 274 and 299. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti439 – 4391C → W in AAD42992. (PubMed:10480896)Curated
Sequence conflicti473 – 4731T → I in BAG62807. (PubMed:14702039)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti360 – 3601P → T.
Corresponds to variant rs34776764 [ dbSNP | Ensembl ].
VAR_051521

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei51 – 9545RYVNG…YSTYC → S in isoform 2. 1 PublicationVSP_044712Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF073344 mRNA. Translation: AAD42992.1. Frameshift.
BT007269 mRNA. Translation: AAP35933.1.
AK301236 mRNA. Translation: BAG62807.1.
AC007950 Genomic DNA. No translation available.
AC118274 Genomic DNA. No translation available.
CH471082 Genomic DNA. Translation: EAW77651.1.
BC018113 mRNA. Translation: AAH18113.1.
BC065300 mRNA. Translation: AAH65300.1.
BC107137 mRNA. Translation: AAI07138.1.
BC107138 mRNA. Translation: AAI07139.1.
CCDSiCCDS32265.1. [Q9Y6I4-1]
CCDS58370.1. [Q9Y6I4-2]
RefSeqiNP_001243631.1. NM_001256702.1. [Q9Y6I4-2]
NP_006528.2. NM_006537.3. [Q9Y6I4-1]
UniGeneiHs.458499.

Genome annotation databases

EnsembliENST00000380324; ENSP00000369681; ENSG00000140455. [Q9Y6I4-1]
ENST00000540797; ENSP00000445828; ENSG00000140455. [Q9Y6I4-2]
GeneIDi9960.
KEGGihsa:9960.
UCSCiuc002amf.4. human. [Q9Y6I4-1]

Polymorphism databases

DMDMi205371844.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF073344 mRNA. Translation: AAD42992.1 . Frameshift.
BT007269 mRNA. Translation: AAP35933.1 .
AK301236 mRNA. Translation: BAG62807.1 .
AC007950 Genomic DNA. No translation available.
AC118274 Genomic DNA. No translation available.
CH471082 Genomic DNA. Translation: EAW77651.1 .
BC018113 mRNA. Translation: AAH18113.1 .
BC065300 mRNA. Translation: AAH65300.1 .
BC107137 mRNA. Translation: AAI07138.1 .
BC107138 mRNA. Translation: AAI07139.1 .
CCDSi CCDS32265.1. [Q9Y6I4-1 ]
CCDS58370.1. [Q9Y6I4-2 ]
RefSeqi NP_001243631.1. NM_001256702.1. [Q9Y6I4-2 ]
NP_006528.2. NM_006537.3. [Q9Y6I4-1 ]
UniGenei Hs.458499.

3D structure databases

ProteinModelPortali Q9Y6I4.
SMRi Q9Y6I4. Positions 3-512.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 115285. 29 interactions.
DIPi DIP-53585N.
IntActi Q9Y6I4. 20 interactions.
STRINGi 9606.ENSP00000369681.

Protein family/group databases

MEROPSi C19.026.

PTM databases

PhosphoSitei Q9Y6I4.

Polymorphism databases

DMDMi 205371844.

Proteomic databases

MaxQBi Q9Y6I4.
PaxDbi Q9Y6I4.
PRIDEi Q9Y6I4.

Protocols and materials databases

DNASUi 9960.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000380324 ; ENSP00000369681 ; ENSG00000140455 . [Q9Y6I4-1 ]
ENST00000540797 ; ENSP00000445828 ; ENSG00000140455 . [Q9Y6I4-2 ]
GeneIDi 9960.
KEGGi hsa:9960.
UCSCi uc002amf.4. human. [Q9Y6I4-1 ]

Organism-specific databases

CTDi 9960.
GeneCardsi GC15P063796.
H-InvDB HIX0012328.
HGNCi HGNC:12626. USP3.
MIMi 604728. gene.
neXtProti NX_Q9Y6I4.
PharmGKBi PA37251.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG5533.
GeneTreei ENSGT00760000119203.
HOGENOMi HOG000231498.
HOVERGENi HBG103589.
InParanoidi Q9Y6I4.
KOi K11986.
OMAi ESCLYDL.
PhylomeDBi Q9Y6I4.
TreeFami TF315281.

Miscellaneous databases

ChiTaRSi USP3. human.
GenomeRNAii 9960.
NextBioi 37582.
PROi Q9Y6I4.
SOURCEi Search...

Gene expression databases

Bgeei Q9Y6I4.
CleanExi HS_USP3.
ExpressionAtlasi Q9Y6I4. baseline and differential.
Genevestigatori Q9Y6I4.

Family and domain databases

Gene3Di 3.30.40.10. 1 hit.
InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
IPR013083. Znf_RING/FYVE/PHD.
IPR001607. Znf_UBP.
[Graphical view ]
Pfami PF00443. UCH. 1 hit.
PF02148. zf-UBP. 1 hit.
[Graphical view ]
PROSITEi PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
PS50271. ZF_UBP. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization and chromosomal localization of USP3, a novel human ubiquitin-specific protease."
    Sloper-Mould K.E., Eyre H.J., Wang X.-W., Sutherland G.R., Baker R.T.
    J. Biol. Chem. 274:26878-26884(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
    Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
    Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Spleen.
  4. "Analysis of the DNA sequence and duplication history of human chromosome 15."
    Zody M.C., Garber M., Sharpe T., Young S.K., Rowen L., O'Neill K., Whittaker C.A., Kamal M., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Kodira C.D., Madan A., Qin S., Yang X., Abbasi N., Abouelleil A.
    , Arachchi H.M., Baradarani L., Birditt B., Bloom S., Bloom T., Borowsky M.L., Burke J., Butler J., Cook A., DeArellano K., DeCaprio D., Dorris L. III, Dors M., Eichler E.E., Engels R., Fahey J., Fleetwood P., Friedman C., Gearin G., Hall J.L., Hensley G., Johnson E., Jones C., Kamat A., Kaur A., Locke D.P., Madan A., Munson G., Jaffe D.B., Lui A., Macdonald P., Mauceli E., Naylor J.W., Nesbitt R., Nicol R., O'Leary S.B., Ratcliffe A., Rounsley S., She X., Sneddon K.M.B., Stewart S., Sougnez C., Stone S.M., Topham K., Vincent D., Wang S., Zimmer A.R., Birren B.W., Hood L., Lander E.S., Nusbaum C.
    Nature 440:671-675(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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] (ISOFORM 1).
    Tissue: Eye and Skin.
  7. Cited for: FUNCTION, INTERACTION WITH H2A, SUBCELLULAR LOCATION, MUTAGENESIS OF HIS-56 AND CYS-168, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiUBP3_HUMAN
AccessioniPrimary (citable) accession number: Q9Y6I4
Secondary accession number(s): B4DVU5, F5H1A6, Q8WVD0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: September 2, 2008
Last modified: October 29, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Peptidase families
    Classification of peptidase families and list of entries
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3