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P35123

- UBP4_MOUSE

UniProt

P35123 - UBP4_MOUSE

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Protein

Ubiquitin carboxyl-terminal hydrolase 4

Gene

Usp4

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

Functioni

Hydrolase that deubiquitinates target proteins such as the receptor ADORA2A, PDPK1 and TRIM21. Deubiquitination of ADORA2A increases the amount of functional receptor at the cell surface. Plays a role in the regulation of quality control in the ER (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 sitei311 – 3111NucleophilePROSITE-ProRule annotation
Metal bindingi461 – 4611ZincBy similarity
Metal bindingi464 – 4641ZincBy similarity
Metal bindingi798 – 7981ZincBy similarity
Metal bindingi801 – 8011ZincBy similarity
Active sitei880 – 8801Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. ubiquitin-specific protease activity Source: UniProtKB
  3. ubiquitin thiolesterase activity Source: UniProtKB

GO - Biological processi

  1. negative regulation of protein ubiquitination Source: UniProtKB
  2. protein deubiquitination Source: UniProtKB
  3. protein localization to cell surface Source: UniProtKB
  4. regulation of protein stability Source: UniProtKB
  5. ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 4 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 4
Ubiquitin thioesterase 4
Ubiquitin-specific-processing protease 4
Ubiquitous nuclear protein
Gene namesi
Name:Usp4
Synonyms:Unp
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 9

Organism-specific databases

MGIiMGI:98905. Usp4.

Subcellular locationi

Cytoplasm 1 Publication. Nucleus 1 Publication
Note: Shuttles between the nucleus and cytoplasm. Exported to the cytoplasm in a CRM1-dependent manner and recycled back to the nucleus via the importin alpha/beta heterodimeric import receptor.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. nucleus Source: UniProtKB
  3. plasma membrane Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi461 – 4611C → Q: Reduces the interaction with RB1. 1 Publication
Mutagenesisi770 – 7712KK → NS: Reduces nuclear localization. 1 Publication

Keywords - Diseasei

Proto-oncogene

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 962962Ubiquitin carboxyl-terminal hydrolase 4PRO_0000080622Add
BLAST

Post-translational modificationi

Monoubiquitinated by TRIM21. Ubiquitination does not lead to its proteasomal degradation. Autodeubiquitinated (By similarity).By similarity

Keywords - PTMi

Ubl conjugation

Proteomic databases

MaxQBiP35123.
PaxDbiP35123.
PRIDEiP35123.

PTM databases

PhosphoSiteiP35123.

Expressioni

Tissue specificityi

Expressed in brain, kidney, liver and spleen (at protein level).1 Publication

Developmental stagei

Overexpression leads to oncogenic transformation of NIH 3T3 cells.

Gene expression databases

BgeeiP35123.
CleanExiMM_USP4.
ExpressionAtlasiP35123. baseline and differential.
GenevestigatoriP35123.

Interactioni

Subunit structurei

Interacts with RB1 (both dephosphorylated and hypophosphorylated forms). Interacts with ADORA2A (via cytoplasmic C-terminus); the interaction is direct (By similarity). Interacts with RB1, RBL1 and RBL2.By similarity1 Publication

Protein-protein interaction databases

IntActiP35123. 1 interaction.
MINTiMINT-4139272.

Structurei

Secondary structure

1
962
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 219
Turni22 – 254
Beta strandi33 – 386
Helixi39 – 4911
Beta strandi51 – 533
Turni56 – 605
Helixi62 – 643
Helixi72 – 743
Beta strandi75 – 773
Turni78 – 814
Turni89 – 913
Beta strandi92 – 976
Helixi98 – 10811
Beta strandi118 – 1247
Beta strandi126 – 1283
Beta strandi130 – 1334
Beta strandi138 – 1447
Beta strandi147 – 15610
Helixi162 – 17211
Beta strandi181 – 1855
Beta strandi187 – 1915
Turni202 – 2065
Beta strandi211 – 2177

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3JYUX-ray2.37A/B1-229[»]
ProteinModelPortaliP35123.
SMRiP35123. Positions 7-226, 297-483, 775-924.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP35123.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini11 – 122112DUSPPROSITE-ProRule annotationAdd
BLAST
Domaini142 – 22685Ubiquitin-like 1Add
BLAST
Domaini302 – 922621USPAdd
BLAST
Domaini483 – 57189Ubiquitin-like 2Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni405 – 4073Necessary for interaction with RBL2
Regioni459 – 4635Necessary for interaction with RB1 and RBL2

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi133 – 1419Nuclear export signal
Motifi766 – 7716Nuclear localization signal

Domaini

The Ubiquitin-like domain 2 inserts into the catalytic domain and competes with the ubiquitin substrate, partially inhibiting DUB activity.By similarity

Sequence similaritiesi

Belongs to the peptidase C19 family. USP4 subfamily.Curated
Contains 1 DUSP domain.PROSITE-ProRule annotation
Contains 2 ubiquitin-like domains.Curated
Contains 1 USP domain.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG5560.
GeneTreeiENSGT00670000097750.
HOGENOMiHOG000264375.
HOVERGENiHBG000864.
InParanoidiP35123.
KOiK11835.
OMAiCHSEGCM.
OrthoDBiEOG77Q4VW.
TreeFamiTF106276.

Family and domain databases

Gene3Di3.30.2230.10. 1 hit.
InterProiIPR006615. Pept_C19_DUSP.
IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028135. Ub_USP-typ.
IPR028889. UCH/PAN2.
IPR028134. USP.
[Graphical view]
PANTHERiPTHR24006:SF360. PTHR24006:SF360. 1 hit.
PfamiPF06337. DUSP. 1 hit.
PF14836. Ubiquitin_3. 1 hit.
PF00443. UCH. 1 hit.
[Graphical view]
SMARTiSM00695. DUSP. 1 hit.
[Graphical view]
SUPFAMiSSF143791. SSF143791. 1 hit.
PROSITEiPS51283. DUSP. 1 hit.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P35123-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAEGRGSRER PDVETQKTEL GALMGTTLQR GAQWYLIDSR WFKQWKKYVG
60 70 80 90 100
FDSWDMYNVG EHNLFPGPID NSGLFSDPES QTLKEHLIDE LDYVLVPAEA
110 120 130 140 150
WNKLLNWYGC VEGQQPIVRK VVEHGLFVKH CKVEVYLLEL KLCENSDPTN
160 170 180 190 200
VLSCHFSKAD TIATIEKEMR KLFNIPAERE TRLWNKYMSN TYEQLSKLDN
210 220 230 240 250
TIQDAGLYQG QVLVIEPQNE DGTWPRQSLQ SKSSTAPSRN FTTSSKPSAS
260 270 280 290 300
PYCSVSASLI ANGDSTNSSG MHSSGVSRGG SGFSASYNCQ EPPSPHIQPG
310 320 330 340 350
LCGLGNLGNT CFMNSALQCL SNTAPLTEYF LKDEYEAEIN RDNPLGMKGE
360 370 380 390 400
IAEAYAELIK QMWSGRDTHV APRMFKTQVG RFAPQFSGYQ QQDSQELLAF
410 420 430 440 450
ILDGLHEDLN RVKKKPYLEP KDANGRPDAV VAKEAWENHR LRNDSVIVDT
460 470 480 490 500
FHGLFKSTLV CPECAKVSVT FDPFCYLTLP LPLKKDRIME VFLVPADPQC
510 520 530 540 550
RPIQYRVTVP LMGAISDLCE ALSKLSGIAA ENMVVTDVYN HRFHKIFQMD
560 570 580 590 600
EGLSHITPRD DIFVYEVCNT SMDGSECITL PVYFREKKSR PSSASSGAVL
610 620 630 640 650
YGQPLLVSVP KHKLTLESLY QAVCDRISRY IKQPLPDEFL SSPLEPGACN
660 670 680 690 700
GSRSSYEGDE EEEMDHQEEG KEQLSEVEGS GEDDQGDDHS ESAQKVKGQP
710 720 730 740 750
RHKRLFTFSL VNSCGTADIN SLATDGKLLK LNSRSTLAID WDSETRSLYF
760 770 780 790 800
DEQESEACEK HLSMSQPQKK KKAAVALREC IELFTTMETL GEHDPWYCPT
810 820 830 840 850
CKKHQQATKK FDLWSLPKIL VVHLKRFSYN RYWRDKLDTV VEFPVRALNM
860 870 880 890 900
SEFVCDRSAR PYVYDLIAVS NHYGAMGVGH YTAYAKNRLN GKWYYFDDSS
910 920 930 940 950
VSLASEDQIV TKAAYVLFYQ RRDDECSSTS SLGSFPGSDG GVKLSSSHQG
960
MGDEEAYNMD TN
Length:962
Mass (Da):108,343
Last modified:July 27, 2011 - v3
Checksum:i95F95BE86186DA52
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti123 – 1242EH → DD in AAB82339. (PubMed:8336951)Curated
Sequence conflicti123 – 1242EH → DD in AAC53587. (PubMed:9602026)Curated
Sequence conflicti292 – 2921P → A in AAB82339. (PubMed:8336951)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L00681 mRNA. Translation: AAB82339.1.
AF026469 Genomic DNA. Translation: AAC53587.1.
AK089425 mRNA. Translation: BAC40877.1.
AK143582 mRNA. Translation: BAE25450.1.
AK149964 mRNA. Translation: BAE29198.1.
AK169933 mRNA. Translation: BAE41468.1.
AK171271 mRNA. Translation: BAE42357.1.
CH466560 Genomic DNA. Translation: EDL21282.1.
CCDSiCCDS23523.1.
PIRiI58376.
RefSeqiNP_035808.2. NM_011678.2.
UniGeneiMm.3974.

Genome annotation databases

EnsembliENSMUST00000035237; ENSMUSP00000035237; ENSMUSG00000032612.
GeneIDi22258.
KEGGimmu:22258.
UCSCiuc009rph.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L00681 mRNA. Translation: AAB82339.1 .
AF026469 Genomic DNA. Translation: AAC53587.1 .
AK089425 mRNA. Translation: BAC40877.1 .
AK143582 mRNA. Translation: BAE25450.1 .
AK149964 mRNA. Translation: BAE29198.1 .
AK169933 mRNA. Translation: BAE41468.1 .
AK171271 mRNA. Translation: BAE42357.1 .
CH466560 Genomic DNA. Translation: EDL21282.1 .
CCDSi CCDS23523.1.
PIRi I58376.
RefSeqi NP_035808.2. NM_011678.2.
UniGenei Mm.3974.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3JYU X-ray 2.37 A/B 1-229 [» ]
ProteinModelPortali P35123.
SMRi P35123. Positions 7-226, 297-483, 775-924.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P35123. 1 interaction.
MINTi MINT-4139272.

PTM databases

PhosphoSitei P35123.

Proteomic databases

MaxQBi P35123.
PaxDbi P35123.
PRIDEi P35123.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000035237 ; ENSMUSP00000035237 ; ENSMUSG00000032612 .
GeneIDi 22258.
KEGGi mmu:22258.
UCSCi uc009rph.2. mouse.

Organism-specific databases

CTDi 7375.
MGIi MGI:98905. Usp4.

Phylogenomic databases

eggNOGi COG5560.
GeneTreei ENSGT00670000097750.
HOGENOMi HOG000264375.
HOVERGENi HBG000864.
InParanoidi P35123.
KOi K11835.
OMAi CHSEGCM.
OrthoDBi EOG77Q4VW.
TreeFami TF106276.

Miscellaneous databases

EvolutionaryTracei P35123.
NextBioi 302345.
PROi P35123.
SOURCEi Search...

Gene expression databases

Bgeei P35123.
CleanExi MM_USP4.
ExpressionAtlasi P35123. baseline and differential.
Genevestigatori P35123.

Family and domain databases

Gene3Di 3.30.2230.10. 1 hit.
InterProi IPR006615. Pept_C19_DUSP.
IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028135. Ub_USP-typ.
IPR028889. UCH/PAN2.
IPR028134. USP.
[Graphical view ]
PANTHERi PTHR24006:SF360. PTHR24006:SF360. 1 hit.
Pfami PF06337. DUSP. 1 hit.
PF14836. Ubiquitin_3. 1 hit.
PF00443. UCH. 1 hit.
[Graphical view ]
SMARTi SM00695. DUSP. 1 hit.
[Graphical view ]
SUPFAMi SSF143791. SSF143791. 1 hit.
PROSITEi PS51283. DUSP. 1 hit.
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. "Unp, a mouse gene related to the tre oncogene."
    Gupta K., Copeland N.G., Gilbert D.J., Jenkins N.A., Gray D.A.
    Oncogene 8:2307-2310(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [MRNA].
  2. "Genomic structure of Unp, a murine gene encoding a ubiquitin-specific protease."
    di Fruscio M., Gilchrist C.A., Baker R.T., Gray D.A.
    Biochim. Biophys. Acta 1398:9-17(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 129.
    Tissue: Testis.
  3. "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].
    Strain: C57BL/6J and NOD.
    Tissue: Bone marrow and Spleen.
  4. 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].
  5. "Association of UNP, a ubiquitin-specific protease, with the pocket proteins pRb, p107 and p130."
    Blanchette P., Gilchrist C.A., Baker R.T., Gray D.A.
    Oncogene 20:5533-5537(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RB1; RBL1 AND RBL2, MUTAGENESIS OF CYS-461.
  6. "Nuclear-cytoplasmic shuttling of the oncogenic mouse UNP/USP4 deubiquitylating enzyme."
    Soboleva T.A., Jans D.A., Johnson-Saliba M., Baker R.T.
    J. Biol. Chem. 280:745-752(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF 770-GLN--LYS-771, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  7. "Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)."
    Structural genomics consortium (SGC)
    Submitted (NOV-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) OF 1-229.

Entry informationi

Entry nameiUBP4_MOUSE
AccessioniPrimary (citable) accession number: P35123
Secondary accession number(s): O54704, Q8BTL9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: July 27, 2011
Last modified: October 29, 2014
This is version 123 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3