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Q01477

- UBP3_YEAST

UniProt

Q01477 - UBP3_YEAST

Protein

Ubiquitin carboxyl-terminal hydrolase 3

Gene

UBP3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 128 (01 Oct 2014)
      Sequence version 1 (01 Jul 1993)
      Previous versions | rss
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    Functioni

    Has an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety in natural or engineered linear fusion proteins, irrespective of their size or the presence of an N-terminal extension to ubiquitin. Plays a role in regulation of silencing by interacting with SIR4. Also, in conjunction with BRE5, cleaves ubiquitin, leading to the subsequent mono-ubiquitination of SEC23.2 Publications

    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).1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei469 – 4691NucleophilePROSITE-ProRule annotation
    Active sitei861 – 8611Proton acceptorPROSITE-ProRule annotation

    GO - Molecular functioni

    1. mRNA binding Source: SGD
    2. protein binding Source: IntAct
    3. ubiquitin-specific protease activity Source: SGD

    GO - Biological processi

    1. protein deubiquitination Source: SGD
    2. regulation of ER to Golgi vesicle-mediated transport Source: SGD
    3. regulation of response to osmotic stress Source: SGD
    4. ribophagy Source: SGD
    5. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Ubl conjugation pathway

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30312-MONOMER.

    Protein family/group databases

    MEROPSiC19.004.

    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:UBP3
    Ordered Locus Names:YER151C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYER151c.
    SGDiS000000953. UBP3.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: SGD

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 912912Ubiquitin carboxyl-terminal hydrolase 3PRO_0000080588Add
    BLAST

    Proteomic databases

    MaxQBiQ01477.
    PaxDbiQ01477.
    PeptideAtlasiQ01477.

    Expressioni

    Gene expression databases

    GenevestigatoriQ01477.

    Interactioni

    Subunit structurei

    Heterotetramer with BRE5; contains two molecules of BRE5 and two molecules of UBP3.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    BRE5P537417EBI-19834,EBI-28528
    CDC48P256944EBI-19834,EBI-4308
    DOA1P360374EBI-19834,EBI-6017
    HOG1P324853EBI-19834,EBI-8437

    Protein-protein interaction databases

    BioGridi36901. 865 interactions.
    DIPiDIP-4255N.
    IntActiQ01477. 401 interactions.
    MINTiMINT-527025.
    STRINGi4932.YER151C.

    Structurei

    Secondary structure

    1
    912
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi208 – 2125
    Helixi214 – 22815

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2QIYX-ray1.69C/D190-233[»]
    ProteinModelPortaliQ01477.
    SMRiQ01477. Positions 573-912.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ01477.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini460 – 911452USPAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG5533.
    GeneTreeiENSGT00550000074994.
    HOGENOMiHOG000141876.
    KOiK11841.
    OMAiANICFMS.
    OrthoDBiEOG7F2546.

    Family and domain databases

    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [Graphical view]
    PfamiPF00443. UCH. 1 hit.
    [Graphical view]
    PROSITEiPS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q01477-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNMQDANKEE SYSMYPKTSS PPPPTPTNMQ IPIYQAPLQM YGYTQAPYLY    50
    PTQIPAYSFN MVNQNQPIYH QSGSPHHLPP QNNINGGSTT NNNNINKKKW 100
    HSNGITNNNG SSGNQGANSS GSGMSYNKSH TYHHNYSNNH IPMMASPNSG 150
    SNAGMKKQTN SSNGNGSSAT SPSYSSYNSS SQYDLYKFDV TKLKNLKENS 200
    SNLIQLPLFI NTTEAEFAAA SVQRYELNMK ALNLNSESLE NSSVEKSSAH 250
    HHTKSHSIPK HNEEVKTETH GEEEDAHDKK PHASKDAHEL KKKTEVKKED 300
    AKQDRNEKVI QEPQATVLPV VDKKEPEESV EENTSKTSSP SPSPPAAKSW 350
    SAIASDAIKS RQASNKTVSG SMVTKTPISG TTAGVSSTNM AAATIGKSSS 400
    PLLSKQPQKK DKKYVPPSTK GIEPLGSIAL RMCFDPDFIS YVLRNKDVEN 450
    KIPVHSIIPR GIINRANICF MSSVLQVLLY CKPFIDVINV LSTRNTNSRV 500
    GTSSCKLLDA CLTMYKQFDK ETYEKKFLEN ADDAEKTTES DAKKSSKSKS 550
    FQHCATADAV KPDEFYKTLS TIPKFKDLQW GHQEDAEEFL THLLDQLHEE 600
    LISAIDGLTD NEIQNMLQSI NDEQLKVFFI RNLSRYGKAE FIKNASPRLK 650
    ELIEKYGVIN DDSTEENGWH EVSGSSKRGK KTKTAAKRTV EIVPSPISKL 700
    FGGQFRSVLD IPNNKESQSI TLDPFQTIQL DISDAGVNDL ETAFKKFSEY 750
    ELLPFKSSSG NDVEAKKQTF IDKLPQVLLI QFKRFSFINN VNKDNAMTNY 800
    NAYNGRIEKI RKKIKYGHEL IIPEESMSSI TLKNNTSGID DRRYKLTGVI 850
    YHHGVSSDGG HYTADVYHSE HNKWYRIDDV NITELEDDDV LKGGEEASDS 900
    RTAYILMYQK RN 912
    Length:912
    Mass (Da):101,917
    Last modified:July 1, 1993 - v1
    Checksum:i337FD05527C5542D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M94917 Genomic DNA. Translation: AAA35191.1.
    U18917 Genomic DNA. Translation: AAB64678.1.
    BK006939 Genomic DNA. Translation: DAA07812.1.
    PIRiB44450.
    RefSeqiNP_011078.3. NM_001179041.3.

    Genome annotation databases

    EnsemblFungiiYER151C; YER151C; YER151C.
    GeneIDi856895.
    KEGGisce:YER151C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M94917 Genomic DNA. Translation: AAA35191.1 .
    U18917 Genomic DNA. Translation: AAB64678.1 .
    BK006939 Genomic DNA. Translation: DAA07812.1 .
    PIRi B44450.
    RefSeqi NP_011078.3. NM_001179041.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2QIY X-ray 1.69 C/D 190-233 [» ]
    ProteinModelPortali Q01477.
    SMRi Q01477. Positions 573-912.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36901. 865 interactions.
    DIPi DIP-4255N.
    IntActi Q01477. 401 interactions.
    MINTi MINT-527025.
    STRINGi 4932.YER151C.

    Protein family/group databases

    MEROPSi C19.004.

    Proteomic databases

    MaxQBi Q01477.
    PaxDbi Q01477.
    PeptideAtlasi Q01477.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YER151C ; YER151C ; YER151C .
    GeneIDi 856895.
    KEGGi sce:YER151C.

    Organism-specific databases

    CYGDi YER151c.
    SGDi S000000953. UBP3.

    Phylogenomic databases

    eggNOGi COG5533.
    GeneTreei ENSGT00550000074994.
    HOGENOMi HOG000141876.
    KOi K11841.
    OMAi ANICFMS.
    OrthoDBi EOG7F2546.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30312-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q01477.
    NextBioi 983307.
    PROi Q01477.

    Gene expression databases

    Genevestigatori Q01477.

    Family and domain databases

    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    [Graphical view ]
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family."
      Baker R.T., Tobias J.W., Varshavsky A.
      J. Biol. Chem. 267:23364-23375(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae."
      Moazed D., Johnson D.
      Cell 86:667-677(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    5. "Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23."
      Cohen M., Stutz F., Belgareh N., Haguenauer-Tsapis R., Dargemont C.
      Nat. Cell Biol. 5:661-667(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme."
      Li K., Ossareh-Nazari B., Liu X., Dargemont C., Marmorstein R.
      J. Mol. Biol. 372:194-204(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 190-233 IN COMPLEX WITH BRE5, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.

    Entry informationi

    Entry nameiUBP3_YEAST
    AccessioniPrimary (citable) accession number: Q01477
    Secondary accession number(s): D3DM58
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 1993
    Last sequence update: July 1, 1993
    Last modified: October 1, 2014
    This is version 128 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 2210 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    External Data

    Dasty 3