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Protein

Carboxypeptidase Y

Gene

PRC1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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.1 Publication

Miscellaneous

Present with 44000 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

Release of a C-terminal amino acid with broad specificity.1 Publication

Enzyme regulationi

Inhibited by ZPCK.

Kineticsi

kcat is 4900 min(-1) with furylacryloyl-Phe-Leu-OH as substrate.1 Publication
  1. KM=0.021 mM for furylacryloyl-Phe-Leu-OH1 Publication

    pH dependencei

    Optimum pH is 6.5. Avtive from pH 4.5 to pH 8.5.1 Publication

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei2572 Publications1
    Active sitei4491 Publication1
    Binding sitei452Substrate1 Publication1
    Active sitei5081 Publication1 Publication1
    Binding sitei509Substrate1 Publication1

    GO - Molecular functioni

    • serine-type carboxypeptidase activity Source: SGD

    GO - Biological processi

    • phytochelatin biosynthetic process Source: SGD
    • protein catabolic process in the vacuole Source: SGD
    • proteolysis involved in cellular protein catabolic process Source: GO_Central

    Keywordsi

    Molecular functionCarboxypeptidase, Hydrolase, Protease

    Enzyme and pathway databases

    BioCyciYEAST:YMR297W-MONOMER.
    BRENDAi3.4.16.5. 984.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.

    Protein family/group databases

    ESTHERiyeast-cbpy1. Carboxypeptidase_S10.
    MEROPSiS10.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Carboxypeptidase Y1 Publication (EC:3.4.16.51 Publication)
    Short name:
    CPD-Y1 Publication
    Short name:
    cpY
    Alternative name(s):
    Carboxypeptidase YSCY
    Gene namesi
    Name:PRC11 Publication
    Ordered Locus Names:YMR297WImported
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XIII

    Organism-specific databases

    EuPathDBiFungiDB:YMR297W.
    SGDiS000004912. PRC1.

    Subcellular locationi

    GO - Cellular componenti

    • fungal-type vacuole Source: SGD

    Keywords - Cellular componenti

    Vacuole

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi508H → A or R: Inactivates enzyme. 1 Publication1

    Protein family/group databases

    Allergomei8267. Sac c Carboxypeptidase Y.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 20Sequence analysisAdd BLAST20
    PropeptideiPRO_000000429321 – 111Mediates translocation across the endoplasmic reticulum, renders the enzyme inactive during transit, and targets the molecule to the vacuole1 Publication1 PublicationAdd BLAST91
    ChainiPRO_0000004294112 – 532Carboxypeptidase YAdd BLAST421

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Glycosylationi124N-linked (GlcNAc...) (high mannose)1 Publication1
    Disulfide bondi167 ↔ 4092 Publications
    Glycosylationi198N-linked (GlcNAc...) (high mannose)3 Publications1
    Glycosylationi279N-linked (GlcNAc...) (high mannose)3 Publications1
    Disulfide bondi304 ↔ 3182 Publications
    Disulfide bondi328 ↔ 3512 Publications
    Disulfide bondi335 ↔ 3442 Publications
    Disulfide bondi373 ↔ 3792 Publications
    Glycosylationi479N-linked (GlcNAc...) (high mannose)3 Publications1

    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 by vacuolar proteases to yield the enzymatically active mature vacuolar form of CPY (61 kDa).1 Publication
    The four high mannose core N-glycans found in mature CPY are Man(11-15)GlcNAc2 at Asn-124, Man(8-12)GlcNAc2 at Asn-198, Man(9-14)GlcNAc2 at Asn-279 and phosphorylated Man(12-17)GlcNAc2 as well as Man(11-16)GlcNAc2 at Asn-479.1 Publication

    Keywords - PTMi

    Disulfide bond, Glycoprotein, Zymogen

    Proteomic databases

    MaxQBiP00729.
    PRIDEiP00729.

    Interactioni

    Binary interactionsi

    Show more details

    Protein-protein interaction databases

    BioGridi35477. 72 interactors.
    DIPiDIP-2394N.
    IntActiP00729. 17 interactors.
    MINTiMINT-1956986.

    Structurei

    Secondary structure

    1532
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi116 – 118Combined sources3
    Beta strandi119 – 121Combined sources3
    Beta strandi129 – 134Combined sources6
    Turni135 – 138Combined sources4
    Beta strandi139 – 146Combined sources8
    Turni152 – 154Combined sources3
    Beta strandi157 – 161Combined sources5
    Turni164 – 166Combined sources3
    Helixi170 – 173Combined sources4
    Turni174 – 177Combined sources4
    Beta strandi178 – 183Combined sources6
    Turni184 – 186Combined sources3
    Beta strandi187 – 190Combined sources4
    Helixi195 – 198Combined sources4
    Beta strandi199 – 202Combined sources4
    Beta strandi214 – 217Combined sources4
    Helixi224 – 240Combined sources17
    Helixi242 – 244Combined sources3
    Turni245 – 248Combined sources4
    Beta strandi251 – 256Combined sources6
    Helixi259 – 270Combined sources12
    Beta strandi282 – 287Combined sources6
    Helixi292 – 295Combined sources4
    Helixi296 – 298Combined sources3
    Helixi299 – 303Combined sources5
    Beta strandi307 – 309Combined sources3
    Helixi315 – 338Combined sources24
    Helixi341 – 355Combined sources15
    Helixi357 – 362Combined sources6
    Beta strandi368 – 371Combined sources4
    Beta strandi375 – 377Combined sources3
    Helixi382 – 391Combined sources10
    Helixi393 – 398Combined sources6
    Beta strandi403 – 405Combined sources3
    Helixi411 – 418Combined sources8
    Turni419 – 421Combined sources3
    Helixi422 – 424Combined sources3
    Helixi428 – 436Combined sources9
    Beta strandi441 – 446Combined sources6
    Helixi454 – 463Combined sources10
    Helixi469 – 474Combined sources6
    Beta strandi478 – 481Combined sources4
    Turni483 – 485Combined sources3
    Beta strandi487 – 492Combined sources6
    Beta strandi498 – 503Combined sources6
    Helixi510 – 513Combined sources4
    Helixi515 – 526Combined sources12
    Turni527 – 529Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1CPYX-ray2.60A112-532[»]
    1WPXX-ray2.70A112-532[»]
    1YSCX-ray2.80A112-532[»]
    ProteinModelPortaliP00729.
    SMRiP00729.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00729.

    Family & Domainsi

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi24 – 27Vacuolar targeting signal1 Publication4

    Sequence similaritiesi

    Belongs to the peptidase S10 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    GeneTreeiENSGT00860000133774.
    HOGENOMiHOG000198296.
    InParanoidiP00729.
    KOiK13289.
    OMAiPDVKQYS.
    OrthoDBiEOG092C1EU7.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    InterProiView protein in InterPro
    IPR029058. AB_hydrolase.
    IPR001563. Peptidase_S10.
    IPR008442. Propeptide_carboxypepY.
    IPR033124. Ser_caboxypep_his_AS.
    IPR018202. Ser_caboxypep_ser_AS.
    PANTHERiPTHR11802. PTHR11802. 1 hit.
    PfamiView protein in Pfam
    PF05388. Carbpep_Y_N. 1 hit.
    PF00450. Peptidase_S10. 1 hit.
    PRINTSiPR00724. CRBOXYPTASEC.
    SUPFAMiSSF53474. SSF53474. 1 hit.
    PROSITEiView protein in PROSITE
    PS00560. CARBOXYPEPT_SER_HIS. 1 hit.
    PS00131. CARBOXYPEPT_SER_SER. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P00729-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKAFTSLLCG LGLSTTLAKA ISLQRPLGLD KDVLLQAAEK FGLDLDLDHL
    60 70 80 90 100
    LKELDSNVLD AWAQIEHLYP NQVMSLETST KPKFPEAIKT KKDWDFVVKN
    110 120 130 140 150
    DAIENYQLRV NKIKDPKILG IDPNVTQYTG YLDVEDEDKH FFFWTFESRN
    160 170 180 190 200
    DPAKDPVILW LNGGPGCSSL TGLFFELGPS SIGPDLKPIG NPYSWNSNAT
    210 220 230 240 250
    VIFLDQPVNV GFSYSGSSGV SNTVAAGKDV YNFLELFFDQ FPEYVNKGQD
    260 270 280 290 300
    FHIAGESYAG HYIPVFASEI LSHKDRNFNL TSVLIGNGLT DPLTQYNYYE
    310 320 330 340 350
    PMACGEGGEP SVLPSEECSA MEDSLERCLG LIESCYDSQS VWSCVPATIY
    360 370 380 390 400
    CNNAQLAPYQ RTGRNVYDIR KDCEGGNLCY PTLQDIDDYL NQDYVKEAVG
    410 420 430 440 450
    AEVDHYESCN FDINRNFLFA GDWMKPYHTA VTDLLNQDLP ILVYAGDKDF
    460 470 480 490 500
    ICNWLGNKAW TDVLPWKYDE EFASQKVRNW TASITDEVAG EVKSYKHFTY
    510 520 530
    LRVFNGGHMV PFDVPENALS MVNEWIHGGF SL
    Length:532
    Mass (Da):59,802
    Last modified:November 1, 1988 - v1
    Checksum:i7227F3489CBDD952
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti260 – 261GH → HG AA sequence (Ref. 4) Curated2
    Sequence conflicti389Y → E AA sequence (Ref. 4) Curated1
    Sequence conflicti529G → D AA sequence (Ref. 4) Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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:
    EMBLi
    GenBanki
    DDBJi
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1CPYX-ray2.60A112-532[»]
    1WPXX-ray2.70A112-532[»]
    1YSCX-ray2.80A112-532[»]
    ProteinModelPortaliP00729.
    SMRiP00729.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi35477. 72 interactors.
    DIPiDIP-2394N.
    IntActiP00729. 17 interactors.
    MINTiMINT-1956986.

    Protein family/group databases

    Allergomei8267. Sac c Carboxypeptidase Y.
    ESTHERiyeast-cbpy1. Carboxypeptidase_S10.
    MEROPSiS10.001.

    Proteomic databases

    MaxQBiP00729.
    PRIDEiP00729.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    EuPathDBiFungiDB:YMR297W.
    SGDiS000004912. PRC1.

    Phylogenomic databases

    GeneTreeiENSGT00860000133774.
    HOGENOMiHOG000198296.
    InParanoidiP00729.
    KOiK13289.
    OMAiPDVKQYS.
    OrthoDBiEOG092C1EU7.

    Enzyme and pathway databases

    BioCyciYEAST:YMR297W-MONOMER.
    BRENDAi3.4.16.5. 984.
    ReactomeiR-SCE-6798695. Neutrophil degranulation.

    Miscellaneous databases

    EvolutionaryTraceiP00729.
    PROiPR:P00729.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    InterProiView protein in InterPro
    IPR029058. AB_hydrolase.
    IPR001563. Peptidase_S10.
    IPR008442. Propeptide_carboxypepY.
    IPR033124. Ser_caboxypep_his_AS.
    IPR018202. Ser_caboxypep_ser_AS.
    PANTHERiPTHR11802. PTHR11802. 1 hit.
    PfamiView protein in Pfam
    PF05388. Carbpep_Y_N. 1 hit.
    PF00450. Peptidase_S10. 1 hit.
    PRINTSiPR00724. CRBOXYPTASEC.
    SUPFAMiSSF53474. SSF53474. 1 hit.
    PROSITEiView protein in PROSITE
    PS00560. CARBOXYPEPT_SER_HIS. 1 hit.
    PS00131. CARBOXYPEPT_SER_SER. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiCBPY_YEAST
    AccessioniPrimary (citable) accession number: P00729
    Secondary accession number(s): D6W0C4
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: November 1, 1988
    Last modified: April 12, 2017
    This is version 187 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.