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P00729

- CBPY_YEAST

UniProt

P00729 - CBPY_YEAST

Protein

Carboxypeptidase Y

Gene

PRC1

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 162 (01 Oct 2014)
      Sequence version 1 (01 Nov 1988)
      Previous versions | rss
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    Functioni

    Involved in degradation of small peptides. Digests preferentially peptides containing an aliphatic or hydrophobic residue in P1' position, as well as methionine, leucine or phenylalanine in P1 position of ester substrate.

    Catalytic activityi

    Release of a C-terminal amino acid with broad specificity.PROSITE-ProRule annotation

    Enzyme regulationi

    Inhibited by ZPCK.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei257 – 25712 Publications
    Active sitei449 – 4491By similarity
    Binding sitei452 – 4521Substrate
    Active sitei508 – 50811 Publication
    Binding sitei509 – 5091Substrate

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. serine-type carboxypeptidase activity Source: SGD

    GO - Biological processi

    1. phytochelatin biosynthetic process Source: SGD
    2. protein catabolic process in the vacuole Source: SGD

    Keywords - Molecular functioni

    Carboxypeptidase, Hydrolase, Protease

    Enzyme and pathway databases

    BioCyciYEAST:YMR297W-MONOMER.

    Protein family/group databases

    MEROPSiS10.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Carboxypeptidase Y (EC:3.4.16.5)
    Short name:
    cpY
    Alternative name(s):
    Carboxypeptidase YSCY
    Gene namesi
    Name:PRC1
    Ordered Locus Names:YMR297W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIII

    Organism-specific databases

    CYGDiYMR297w.
    SGDiS000004912. PRC1.

    Subcellular locationi

    Vacuole
    Note: Lysosome-like vacuoles.

    GO - Cellular componenti

    1. fungal-type vacuole Source: SGD

    Keywords - Cellular componenti

    Vacuole

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi508 – 5081H → A or R: Inactivates enzyme. 1 Publication

    Protein family/group databases

    Allergomei8267. Sac c Carboxypeptidase Y.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2020Sequence AnalysisAdd
    BLAST
    Propeptidei21 – 111911 PublicationPRO_0000004293Add
    BLAST
    Chaini112 – 532421Carboxypeptidase YPRO_0000004294Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi124 – 1241N-linked (GlcNAc...)
    Disulfide bondi167 ↔ 409
    Glycosylationi198 – 1981N-linked (GlcNAc...)
    Glycosylationi279 – 2791N-linked (GlcNAc...)
    Disulfide bondi304 ↔ 318
    Disulfide bondi328 ↔ 351
    Disulfide bondi335 ↔ 344
    Disulfide bondi373 ↔ 379
    Glycosylationi479 – 4791N-linked (GlcNAc...)

    Post-translational modificationi

    Enters the endoplasmic reticulum as an inactive zymogen and is modified by four N-linked core oligosaccharides, giving rise to a precursor known as P1 (67 kDa). As P1 transits through the Golgi, extension of its core oligosaccharides leads to the Golgi-modified P2 precursor (69 kDa). P2 is sorted away from secretory proteins at or beyond a late Golgi compartment and is subsequently delivered to the vacuole via a prevacuolar endosome-like compartment. Upon arrival in the vacuole, the N-terminal prosegment of P2 is cleaved to yield the enzymatically active mature vacuolar form of CPY (61 kDa).

    Keywords - PTMi

    Disulfide bond, Glycoprotein, Zymogen

    Proteomic databases

    MaxQBiP00729.
    PaxDbiP00729.
    PeptideAtlasiP00729.

    Expressioni

    Gene expression databases

    GenevestigatoriP00729.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    DER1P383072EBI-4153,EBI-5761
    HRD1Q081094EBI-4153,EBI-37613
    HRD3Q057876EBI-4153,EBI-31647
    SEC61P329154EBI-4153,EBI-16400
    YOS9Q992202EBI-4153,EBI-34938

    Protein-protein interaction databases

    BioGridi35477. 31 interactions.
    DIPiDIP-2394N.
    IntActiP00729. 16 interactions.
    MINTiMINT-1956986.
    STRINGi4932.YMR297W.

    Structurei

    Secondary structure

    1
    532
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi116 – 1183
    Beta strandi119 – 1213
    Beta strandi129 – 1346
    Turni135 – 1384
    Beta strandi139 – 1468
    Turni152 – 1543
    Beta strandi157 – 1615
    Turni164 – 1663
    Helixi170 – 1734
    Turni174 – 1774
    Beta strandi178 – 1836
    Turni184 – 1863
    Beta strandi187 – 1904
    Helixi195 – 1984
    Beta strandi199 – 2024
    Beta strandi214 – 2174
    Helixi224 – 24017
    Helixi242 – 2443
    Turni245 – 2484
    Beta strandi251 – 2566
    Helixi259 – 27012
    Beta strandi282 – 2876
    Helixi292 – 2954
    Helixi296 – 2983
    Helixi299 – 3035
    Beta strandi307 – 3093
    Helixi315 – 33824
    Helixi341 – 35515
    Helixi357 – 3626
    Beta strandi368 – 3714
    Beta strandi375 – 3773
    Helixi382 – 39110
    Helixi393 – 3986
    Beta strandi403 – 4053
    Helixi411 – 4188
    Turni419 – 4213
    Helixi422 – 4243
    Helixi428 – 4369
    Beta strandi441 – 4466
    Helixi454 – 46310
    Helixi469 – 4746
    Beta strandi478 – 4814
    Turni483 – 4853
    Beta strandi487 – 4926
    Beta strandi498 – 5036
    Helixi510 – 5134
    Helixi515 – 52612
    Turni527 – 5293

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CPYX-ray2.60A112-532[»]
    1WPXX-ray2.70A112-532[»]
    1YSCX-ray2.80A112-532[»]
    ProteinModelPortaliP00729.
    SMRiP00729. Positions 112-532.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00729.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi24 – 274Vacuolar targeting signal

    Sequence similaritiesi

    Belongs to the peptidase S10 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG2939.
    GeneTreeiENSGT00560000077221.
    HOGENOMiHOG000198296.
    KOiK13289.
    OMAiECSAMED.
    OrthoDBiEOG7XDBR1.

    Family and domain databases

    Gene3Di3.40.50.1820. 2 hits.
    InterProiIPR029058. AB_hydrolase.
    IPR001563. Peptidase_S10.
    IPR018202. Peptidase_S10_AS.
    IPR008442. Propeptide_carboxypepY.
    [Graphical view]
    PANTHERiPTHR11802. PTHR11802. 1 hit.
    PfamiPF05388. Carbpep_Y_N. 1 hit.
    PF00450. Peptidase_S10. 1 hit.
    [Graphical view]
    PRINTSiPR00724. CRBOXYPTASEC.
    SUPFAMiSSF53474. SSF53474. 1 hit.
    PROSITEiPS00560. CARBOXYPEPT_SER_HIS. 1 hit.
    PS00131. CARBOXYPEPT_SER_SER. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P00729-1 [UniParc]FASTAAdd to Basket

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    MKAFTSLLCG LGLSTTLAKA ISLQRPLGLD KDVLLQAAEK FGLDLDLDHL    50
    LKELDSNVLD AWAQIEHLYP NQVMSLETST KPKFPEAIKT KKDWDFVVKN 100
    DAIENYQLRV NKIKDPKILG IDPNVTQYTG YLDVEDEDKH FFFWTFESRN 150
    DPAKDPVILW LNGGPGCSSL TGLFFELGPS SIGPDLKPIG NPYSWNSNAT 200
    VIFLDQPVNV GFSYSGSSGV SNTVAAGKDV YNFLELFFDQ FPEYVNKGQD 250
    FHIAGESYAG HYIPVFASEI LSHKDRNFNL TSVLIGNGLT DPLTQYNYYE 300
    PMACGEGGEP SVLPSEECSA MEDSLERCLG LIESCYDSQS VWSCVPATIY 350
    CNNAQLAPYQ RTGRNVYDIR KDCEGGNLCY PTLQDIDDYL NQDYVKEAVG 400
    AEVDHYESCN FDINRNFLFA GDWMKPYHTA VTDLLNQDLP ILVYAGDKDF 450
    ICNWLGNKAW TDVLPWKYDE EFASQKVRNW TASITDEVAG EVKSYKHFTY 500
    LRVFNGGHMV PFDVPENALS MVNEWIHGGF SL 532
    Length:532
    Mass (Da):59,802
    Last modified:November 1, 1988 - v1
    Checksum:i7227F3489CBDD952
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti260 – 2612GH → HG AA sequence 1 PublicationCurated
    Sequence conflicti389 – 3891Y → E AA sequence 1 PublicationCurated
    Sequence conflicti529 – 5291G → D AA sequence 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M15482 Genomic DNA. Translation: AAA34902.1.
    X80836 Genomic DNA. Translation: CAA56806.1.
    BK006946 Genomic DNA. Translation: DAA10198.1.
    PIRiA26597. CPBYY.
    RefSeqiNP_014026.1. NM_001182806.1.

    Genome annotation databases

    EnsemblFungiiYMR297W; YMR297W; YMR297W.
    GeneIDi855343.
    KEGGisce:YMR297W.

    Cross-referencesi

    Web resourcesi

    Worthington enzyme manual

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M15482 Genomic DNA. Translation: AAA34902.1 .
    X80836 Genomic DNA. Translation: CAA56806.1 .
    BK006946 Genomic DNA. Translation: DAA10198.1 .
    PIRi A26597. CPBYY.
    RefSeqi NP_014026.1. NM_001182806.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1CPY X-ray 2.60 A 112-532 [» ]
    1WPX X-ray 2.70 A 112-532 [» ]
    1YSC X-ray 2.80 A 112-532 [» ]
    ProteinModelPortali P00729.
    SMRi P00729. Positions 112-532.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35477. 31 interactions.
    DIPi DIP-2394N.
    IntActi P00729. 16 interactions.
    MINTi MINT-1956986.
    STRINGi 4932.YMR297W.

    Protein family/group databases

    Allergomei 8267. Sac c Carboxypeptidase Y.
    MEROPSi S10.001.

    Proteomic databases

    MaxQBi P00729.
    PaxDbi P00729.
    PeptideAtlasi P00729.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YMR297W ; YMR297W ; YMR297W .
    GeneIDi 855343.
    KEGGi sce:YMR297W.

    Organism-specific databases

    CYGDi YMR297w.
    SGDi S000004912. PRC1.

    Phylogenomic databases

    eggNOGi COG2939.
    GeneTreei ENSGT00560000077221.
    HOGENOMi HOG000198296.
    KOi K13289.
    OMAi ECSAMED.
    OrthoDBi EOG7XDBR1.

    Enzyme and pathway databases

    BioCyci YEAST:YMR297W-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P00729.
    NextBioi 979085.

    Gene expression databases

    Genevestigatori P00729.

    Family and domain databases

    Gene3Di 3.40.50.1820. 2 hits.
    InterProi IPR029058. AB_hydrolase.
    IPR001563. Peptidase_S10.
    IPR018202. Peptidase_S10_AS.
    IPR008442. Propeptide_carboxypepY.
    [Graphical view ]
    PANTHERi PTHR11802. PTHR11802. 1 hit.
    Pfami PF05388. Carbpep_Y_N. 1 hit.
    PF00450. Peptidase_S10. 1 hit.
    [Graphical view ]
    PRINTSi PR00724. CRBOXYPTASEC.
    SUPFAMi SSF53474. SSF53474. 1 hit.
    PROSITEi PS00560. CARBOXYPEPT_SER_HIS. 1 hit.
    PS00131. CARBOXYPEPT_SER_SER. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Protein sorting in yeast: the localization determinant of yeast vacuolar carboxypeptidase Y resides in the propeptide."
      Valls L.A., Hunter C.P., Rothman J.H., Stevens T.H.
      Cell 48:887-897(1987) [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. "Amino acid sequence of carboxypeptidase Y. II. Peptides from enzymatic cleavages."
      Svendsen I., Martin B.M., Viswanatha T., Johansen J.T.
      Carlsberg Res. Commun. 47:15-27(1982)
      Cited for: PROTEIN SEQUENCE OF 112-532.
    5. "Identification of methionyl and cysteinyl residues in the substrate binding site of carboxypeptidase Y."
      Breddam K., Svendsen I.
      Carlsberg Res. Commun. 49:639-645(1984)
      Cited for: SEQUENCE REVISION, ACTIVE SITE SER-257.
    6. "Inactivation of carboxypeptidase Y by mutational removal of the putative essential histidyl residue."
      Bech L.M., Breddam K.
      Carlsberg Res. Commun. 54:165-171(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE HIS-508.
    7. "Site-directed mutagenesis on (serine) carboxypeptidase Y. A hydrogen bond network stabilizes the transition state by interaction with the C-terminal carboxylate group of the substrate."
      Mortensen U.H., Remington S.J., Breddam K.
      Biochemistry 33:508-517(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS.
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "2.8-A structure of yeast serine carboxypeptidase."
      Endrizzi J.A., Breddam K., Remington S.J.
      Biochemistry 33:11106-11120(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).

    Entry informationi

    Entry nameiCBPY_YEAST
    AccessioniPrimary (citable) accession number: P00729
    Secondary accession number(s): D6W0C4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: November 1, 1988
    Last modified: October 1, 2014
    This is version 162 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 44000 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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 XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

    External Data

    Dasty 3