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P25451

- PSB3_YEAST

UniProt

P25451 - PSB3_YEAST

Protein

Proteasome subunit beta type-3

Gene

PUP3

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 149 (01 Oct 2014)
      Sequence version 1 (01 May 1992)
      Previous versions | rss
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    Functioni

    The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity. This subunit may participate in the trypsin-like activity of the enzyme complex.

    Catalytic activityi

    Cleavage of peptide bonds with very broad specificity.

    GO - Molecular functioni

    1. endopeptidase activator activity Source: SGD
    2. protein binding Source: IntAct
    3. threonine-type endopeptidase activity Source: UniProtKB-KW

    GO - Biological processi

    1. positive regulation of endopeptidase activity Source: GOC
    2. proteasomal ubiquitin-independent protein catabolic process Source: SGD
    3. proteasome-mediated ubiquitin-dependent protein catabolic process Source: SGD

    Keywords - Molecular functioni

    Hydrolase, Protease, Threonine protease

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30261-MONOMER.
    ReactomeiREACT_100522. Regulation of activated PAK-2p34 by proteasome mediated degradation.
    REACT_189025. ER-Phagosome pathway.
    REACT_189047. Cross-presentation of soluble exogenous antigens (endosomes).
    REACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_189250. AUF1 (hnRNP D0) destabilizes mRNA.
    REACT_83036. Orc1 removal from chromatin.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Proteasome subunit beta type-3 (EC:3.4.25.1)
    Alternative name(s):
    Macropain subunit PUP3
    Multicatalytic endopeptidase complex subunit PUP3
    Proteasome component PUP3
    Gene namesi
    Name:PUP3
    Ordered Locus Names:YER094C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYER094c.
    SGDiS000000896. PUP3.

    Subcellular locationi

    GO - Cellular componenti

    1. endoplasmic reticulum membrane Source: SGD
    2. nucleus Source: SGD
    3. proteasome core complex, beta-subunit complex Source: SGD
    4. proteasome storage granule Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Nucleus, Proteasome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 205205Proteasome subunit beta type-3PRO_0000148070Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei31 – 311Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP25451.
    PaxDbiP25451.
    PeptideAtlasiP25451.

    Expressioni

    Gene expression databases

    GenevestigatoriP25451.

    Interactioni

    Subunit structurei

    The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PUP1P250433EBI-13993,EBI-14009

    Protein-protein interaction databases

    BioGridi36840. 33 interactions.
    DIPiDIP-2039N.
    IntActiP25451. 12 interactions.
    MINTiMINT-498393.
    STRINGi4932.YER094C.

    Structurei

    Secondary structure

    1
    205
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 63
    Beta strandi11 – 166
    Beta strandi18 – 269
    Beta strandi29 – 313
    Beta strandi34 – 385
    Beta strandi43 – 464
    Beta strandi49 – 557
    Helixi57 – 7822
    Helixi84 – 9613
    Turni97 – 1004
    Beta strandi105 – 1128
    Turni114 – 1163
    Beta strandi119 – 1246
    Beta strandi130 – 1323
    Beta strandi134 – 1407
    Helixi143 – 15311
    Helixi160 – 17516
    Beta strandi178 – 1814
    Beta strandi185 – 1939
    Beta strandi195 – 2006

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FNTX-ray3.20J/X1-205[»]
    1G0UX-ray2.40I/W1-205[»]
    1G65X-ray2.25I/W2-205[»]
    1JD2X-ray3.00I/P2-205[»]
    1RYPX-ray1.90J/X2-205[»]
    1VSYX-ray3.00J/X2-205[»]
    1Z7QX-ray3.22J/X1-205[»]
    2F16X-ray2.80I/W2-205[»]
    2FAKX-ray2.80I/W2-205[»]
    2GPLX-ray2.81I/W2-205[»]
    2ZCYX-ray2.90I/W1-205[»]
    3BDMX-ray2.70I/W1-205[»]
    3D29X-ray2.60I/W2-205[»]
    3DY3X-ray2.81I/W2-205[»]
    3DY4X-ray2.80I/W2-205[»]
    3E47X-ray3.00I/W2-205[»]
    3GPJX-ray2.70I/W2-205[»]
    3GPTX-ray2.41I/W2-205[»]
    3GPWX-ray2.50I/W2-205[»]
    3HYEX-ray2.50I/W2-205[»]
    3L5QX-ray3.00N/Z2-205[»]
    3MG0X-ray2.68I/W2-205[»]
    3MG4X-ray3.11I/W2-205[»]
    3MG6X-ray2.60I/W1-205[»]
    3MG7X-ray2.78I/W1-205[»]
    3MG8X-ray2.59I/W1-205[»]
    3NZJX-ray2.40I/W1-205[»]
    3NZWX-ray2.50I/W1-205[»]
    3NZXX-ray2.70I/W1-205[»]
    3OEUX-ray2.60I/W2-205[»]
    3OEVX-ray2.85I/W2-205[»]
    3OKJX-ray2.70I/W2-205[»]
    3SDIX-ray2.65I/W2-205[»]
    3SDKX-ray2.70I/W2-205[»]
    3SHJX-ray2.80I/W2-205[»]
    3TDDX-ray2.70I/W2-205[»]
    3UN4X-ray3.40I/W1-205[»]
    3UN8X-ray2.70I/W1-205[»]
    4CR2electron microscopy7.7031-205[»]
    4CR3electron microscopy9.3031-205[»]
    4CR4electron microscopy8.8031-205[»]
    4EU2X-ray2.51J/X2-205[»]
    4FZCX-ray2.80I/W2-205[»]
    4FZGX-ray3.00I/W2-205[»]
    4G4SX-ray2.49J1-205[»]
    4GK7X-ray2.80I/W2-205[»]
    4HNPX-ray2.80I/W2-205[»]
    4HRCX-ray2.80I/W2-205[»]
    4HRDX-ray2.80I/W2-205[»]
    4INRX-ray2.70I/W1-205[»]
    4INTX-ray2.90I/W1-205[»]
    4INUX-ray3.10I/W1-205[»]
    4J70X-ray2.80I/W1-205[»]
    4JSQX-ray2.80I/W1-205[»]
    4JSUX-ray2.90I/W1-205[»]
    4JT0X-ray3.10I/W1-205[»]
    4LQIX-ray2.70I/W2-205[»]
    4NNNX-ray2.50I/W1-205[»]
    4NNWX-ray2.60I/W1-205[»]
    4NO1X-ray2.50I/W1-205[»]
    4NO6X-ray3.00I/W1-205[»]
    4NO8X-ray2.70I/W1-205[»]
    4NO9X-ray2.90I/W1-205[»]
    4QBYX-ray3.00I/W1-205[»]
    ProteinModelPortaliP25451.
    SMRiP25451. Positions 2-205.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP25451.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase T1B family.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0638.
    GeneTreeiENSGT00550000074820.
    HOGENOMiHOG000090523.
    KOiK02735.
    OMAiMDLIGCP.
    OrthoDBiEOG7SJDGM.

    Family and domain databases

    Gene3Di3.60.20.10. 1 hit.
    InterProiIPR029055. Ntn_hydrolases_N.
    IPR016050. Proteasome_bsu_CS.
    IPR001353. Proteasome_sua/b.
    IPR023333. Proteasome_suB-type.
    [Graphical view]
    PfamiPF00227. Proteasome. 1 hit.
    [Graphical view]
    SUPFAMiSSF56235. SSF56235. 1 hit.
    PROSITEiPS00854. PROTEASOME_BETA_1. 1 hit.
    PS51476. PROTEASOME_BETA_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P25451-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSDPSSINGG IVVAMTGKDC VAIACDLRLG SQSLGVSNKF EKIFHYGHVF    50
    LGITGLATDV TTLNEMFRYK TNLYKLKEER AIEPETFTQL VSSSLYERRF 100
    GPYFVGPVVA GINSKSGKPF IAGFDLIGCI DEAKDFIVSG TASDQLFGMC 150
    ESLYEPNLEP EDLFETISQA LLNAADRDAL SGWGAVVYII KKDEVVKRYL 200
    KMRQD 205
    Length:205
    Mass (Da):22,605
    Last modified:May 1, 1992 - v1
    Checksum:i5AA92D746454BCB7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M88470 Genomic DNA. Translation: AAA34946.1.
    U18839 Genomic DNA. Translation: AAB64649.1.
    BK006939 Genomic DNA. Translation: DAA07756.1.
    PIRiS29251.
    RefSeqiNP_011020.3. NM_001178985.3.

    Genome annotation databases

    EnsemblFungiiYER094C; YER094C; YER094C.
    GeneIDi856830.
    KEGGisce:YER094C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M88470 Genomic DNA. Translation: AAA34946.1 .
    U18839 Genomic DNA. Translation: AAB64649.1 .
    BK006939 Genomic DNA. Translation: DAA07756.1 .
    PIRi S29251.
    RefSeqi NP_011020.3. NM_001178985.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1FNT X-ray 3.20 J/X 1-205 [» ]
    1G0U X-ray 2.40 I/W 1-205 [» ]
    1G65 X-ray 2.25 I/W 2-205 [» ]
    1JD2 X-ray 3.00 I/P 2-205 [» ]
    1RYP X-ray 1.90 J/X 2-205 [» ]
    1VSY X-ray 3.00 J/X 2-205 [» ]
    1Z7Q X-ray 3.22 J/X 1-205 [» ]
    2F16 X-ray 2.80 I/W 2-205 [» ]
    2FAK X-ray 2.80 I/W 2-205 [» ]
    2GPL X-ray 2.81 I/W 2-205 [» ]
    2ZCY X-ray 2.90 I/W 1-205 [» ]
    3BDM X-ray 2.70 I/W 1-205 [» ]
    3D29 X-ray 2.60 I/W 2-205 [» ]
    3DY3 X-ray 2.81 I/W 2-205 [» ]
    3DY4 X-ray 2.80 I/W 2-205 [» ]
    3E47 X-ray 3.00 I/W 2-205 [» ]
    3GPJ X-ray 2.70 I/W 2-205 [» ]
    3GPT X-ray 2.41 I/W 2-205 [» ]
    3GPW X-ray 2.50 I/W 2-205 [» ]
    3HYE X-ray 2.50 I/W 2-205 [» ]
    3L5Q X-ray 3.00 N/Z 2-205 [» ]
    3MG0 X-ray 2.68 I/W 2-205 [» ]
    3MG4 X-ray 3.11 I/W 2-205 [» ]
    3MG6 X-ray 2.60 I/W 1-205 [» ]
    3MG7 X-ray 2.78 I/W 1-205 [» ]
    3MG8 X-ray 2.59 I/W 1-205 [» ]
    3NZJ X-ray 2.40 I/W 1-205 [» ]
    3NZW X-ray 2.50 I/W 1-205 [» ]
    3NZX X-ray 2.70 I/W 1-205 [» ]
    3OEU X-ray 2.60 I/W 2-205 [» ]
    3OEV X-ray 2.85 I/W 2-205 [» ]
    3OKJ X-ray 2.70 I/W 2-205 [» ]
    3SDI X-ray 2.65 I/W 2-205 [» ]
    3SDK X-ray 2.70 I/W 2-205 [» ]
    3SHJ X-ray 2.80 I/W 2-205 [» ]
    3TDD X-ray 2.70 I/W 2-205 [» ]
    3UN4 X-ray 3.40 I/W 1-205 [» ]
    3UN8 X-ray 2.70 I/W 1-205 [» ]
    4CR2 electron microscopy 7.70 3 1-205 [» ]
    4CR3 electron microscopy 9.30 3 1-205 [» ]
    4CR4 electron microscopy 8.80 3 1-205 [» ]
    4EU2 X-ray 2.51 J/X 2-205 [» ]
    4FZC X-ray 2.80 I/W 2-205 [» ]
    4FZG X-ray 3.00 I/W 2-205 [» ]
    4G4S X-ray 2.49 J 1-205 [» ]
    4GK7 X-ray 2.80 I/W 2-205 [» ]
    4HNP X-ray 2.80 I/W 2-205 [» ]
    4HRC X-ray 2.80 I/W 2-205 [» ]
    4HRD X-ray 2.80 I/W 2-205 [» ]
    4INR X-ray 2.70 I/W 1-205 [» ]
    4INT X-ray 2.90 I/W 1-205 [» ]
    4INU X-ray 3.10 I/W 1-205 [» ]
    4J70 X-ray 2.80 I/W 1-205 [» ]
    4JSQ X-ray 2.80 I/W 1-205 [» ]
    4JSU X-ray 2.90 I/W 1-205 [» ]
    4JT0 X-ray 3.10 I/W 1-205 [» ]
    4LQI X-ray 2.70 I/W 2-205 [» ]
    4NNN X-ray 2.50 I/W 1-205 [» ]
    4NNW X-ray 2.60 I/W 1-205 [» ]
    4NO1 X-ray 2.50 I/W 1-205 [» ]
    4NO6 X-ray 3.00 I/W 1-205 [» ]
    4NO8 X-ray 2.70 I/W 1-205 [» ]
    4NO9 X-ray 2.90 I/W 1-205 [» ]
    4QBY X-ray 3.00 I/W 1-205 [» ]
    ProteinModelPortali P25451.
    SMRi P25451. Positions 2-205.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36840. 33 interactions.
    DIPi DIP-2039N.
    IntActi P25451. 12 interactions.
    MINTi MINT-498393.
    STRINGi 4932.YER094C.

    Proteomic databases

    MaxQBi P25451.
    PaxDbi P25451.
    PeptideAtlasi P25451.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YER094C ; YER094C ; YER094C .
    GeneIDi 856830.
    KEGGi sce:YER094C.

    Organism-specific databases

    CYGDi YER094c.
    SGDi S000000896. PUP3.

    Phylogenomic databases

    eggNOGi COG0638.
    GeneTreei ENSGT00550000074820.
    HOGENOMi HOG000090523.
    KOi K02735.
    OMAi MDLIGCP.
    OrthoDBi EOG7SJDGM.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30261-MONOMER.
    Reactomei REACT_100522. Regulation of activated PAK-2p34 by proteasome mediated degradation.
    REACT_189025. ER-Phagosome pathway.
    REACT_189047. Cross-presentation of soluble exogenous antigens (endosomes).
    REACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_189250. AUF1 (hnRNP D0) destabilizes mRNA.
    REACT_83036. Orc1 removal from chromatin.

    Miscellaneous databases

    EvolutionaryTracei P25451.
    NextBioi 983127.
    PROi P25451.

    Gene expression databases

    Genevestigatori P25451.

    Family and domain databases

    Gene3Di 3.60.20.10. 1 hit.
    InterProi IPR029055. Ntn_hydrolases_N.
    IPR016050. Proteasome_bsu_CS.
    IPR001353. Proteasome_sua/b.
    IPR023333. Proteasome_suB-type.
    [Graphical view ]
    Pfami PF00227. Proteasome. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56235. SSF56235. 1 hit.
    PROSITEi PS00854. PROTEASOME_BETA_1. 1 hit.
    PS51476. PROTEASOME_BETA_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence and transcriptional regulation of the yeast recombinational repair gene RAD51."
      Basile G.M., Aker M., Mortimer R.K.
      Mol. Cell. Biol. 12:3235-3246(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 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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-31, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    5. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    6. "Structure of 20S proteasome from yeast at 2.4-A resolution."
      Groll M., Ditzel L., Loewe J., Stock D., Bochtler M., Bartunik H.D., Huber R.
      Nature 386:463-471(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEX WITH THE 20S PROTEASOME.
    7. "Structural basis for the activation of 20S proteasomes by 11S regulators."
      Whitby F.G., Masters E.I., Kramer L., Knowlton J.R., Yao Y., Wang C.C., Hill C.P.
      Nature 408:115-120(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF COMPLEX WITH THE 20S PROTEASOME AND A 11S REGULATORY COMPLEX.
    8. Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF COMPLEX WITH THE 20S PROTEASOME.
    9. "TMC-95-based inhibitor design provides evidence for the catalytic versatility of the proteasome."
      Groll M., Goetz M., Kaiser M., Weyher E., Moroder L.
      Chem. Biol. 13:607-614(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.81 ANGSTROMS) OF COMPLEX WITH THE 20S PROTEASOME AND A TMC-95-BASED INHIBITOR.
    10. "Crystal structures of salinosporamide A (NPI-0052) and B (NPI-0047) in complex with the 20S proteasome reveal important consequences of beta-lactone ring opening and a mechanism for irreversible binding."
      Groll M., Huber R., Potts B.C.M.
      J. Am. Chem. Soc. 128:5136-5141(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF COMPLEX WITH THE 20S PROTEASOME AND SALINOSPORAMIDE.
    11. "Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome."
      Groll M., Berkers C.R., Ploegh H.L., Ovaa H.
      Structure 14:451-456(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF COMPLEX WITH THE 20S PROTEASOME AND BORTEZOMIB.
    12. "Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening."
      Sadre-Bazzaz K., Whitby F.G., Robinson H., Formosa T., Hill C.P.
      Mol. Cell 37:728-735(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 2-205 IN COMPLEX WITH THE PROTEASOME.
    13. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (7.4 ANGSTROMS) OF THE 26S PROTEASOME.

    Entry informationi

    Entry nameiPSB3_YEAST
    AccessioniPrimary (citable) accession number: P25451
    Secondary accession number(s): D3DM02
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: May 1, 1992
    Last modified: October 1, 2014
    This is version 149 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    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