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Protein

Endopolyphosphatase

Gene

PPN1

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

Catalyzes the hydrolysis of inorganic polyphosphate (polyP) chains of many hundreds of phosphate residues into shorter lengths both by cleaving phosphate from the chain end and by fragmenting long-chain polymers into shorter ones. The limited digestion products are 1 and 3 P(i) residues (PubMed:11102525, PubMed:11447286, PubMed:15170373, PubMed:15342119, PubMed:15792812, PubMed:8900207, Ref. 16). Also releases phosphate from dATP. dATP phosphohydrolase activity is about 7-fold lower than the exopolyphosphatase activity (Ref. 16).7 Publications

Catalytic activityi

Polyphosphate + n H2O = (n+1) oligophosphate.1 Publication
(Polyphosphate)(n) + H2O = (polyphosphate)(n-1) + phosphate.1 Publication
dATP + H2O = dADP + phosphate.1 Publication

Cofactori

Mn2+1 Publication, Mg2+1 Publication, Co2+1 PublicationNote: Divalent metal cations. Exopolyphosphatase activity is predominant in the presence of Co2+, while endopolyphosphatase activity is predominant in the presence of Mg2+ (PubMed:8900207, PubMed:25742176). Co2+ is more effective than Mn2+ for dATP phosphohydrolase activity (Ref.16).3 Publications

Enzyme regulationi

Inhibited by heparin and EDTA.1 Publication

Kineticsi

  1. KM=185 nM for polyP(750)1 Publication
  2. KM=3.5 µM for polyP(208)1 Publication
  3. KM=75 µM for polyP(15)1 Publication
  4. KM=1100 µM for polyP31 Publication
  5. KM=0.88 mM for dATP1 Publication

    pH dependencei

    Optimum pH is about 7.5.1 Publication

    GO - Molecular functioni

    • endopolyphosphatase activity Source: SGD
    • exopolyphosphatase activity Source: SGD
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    • polyphosphate catabolic process Source: SGD
    • polyphosphate metabolic process Source: SGD

    Keywordsi

    Molecular functionHydrolase
    LigandMetal-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29983-MONOMER.
    BRENDAi3.6.1.10. 984.
    ReactomeiR-SCE-1660662. Glycosphingolipid metabolism.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Endopolyphosphatase1 Publication (EC:3.6.1.101 Publication)
    Alternative name(s):
    Deoxyadenosine triphosphate phosphohydrolase1 Publication (EC:3.6.1.-1 Publication)
    Short name:
    dATP phosphohydrolase1 Publication
    Exopolyphosphatase (EC:3.6.1.111 Publication)
    Phosphate metabolism protein 51 Publication
    Gene namesi
    Name:PPN11 Publication
    Synonyms:PHM51 Publication
    Ordered Locus Names:YDR452WImported
    ORF Names:D9461.37
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome IV

    Organism-specific databases

    EuPathDBiFungiDB:YDR452W.
    SGDiS000002860. PPN1.

    Subcellular locationi

    Topology

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Topological domaini1 – 21CytoplasmicSequence analysisAdd BLAST21
    Transmembranei22 – 42Helical; Signal-anchor for type II membrane proteinSequence analysisAdd BLAST21
    Topological domaini43 – 674VacuolarSequence analysisAdd BLAST632

    GO - Cellular componenti

    • cytosol Source: SGD
    • fungal-type vacuole membrane Source: SGD
    • integral component of membrane Source: UniProtKB-KW
    • nucleus Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Membrane, Vacuole

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi6K → R or G: Causes accumulation in vacuoles and abolishes sorting into internal vesicles in late endosomes. 1 Publication1
    Mutagenesisi11N → A: Abolishes enzyme activity; when associated with A-505 and A-511. 1 Publication1
    Mutagenesisi505N → A: Abolishes enzyme activity; when associated with A-11 and A-511. 1 Publication1
    Mutagenesisi511N → A: Abolishes enzyme activity; when associated with A-11 and A-505. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    PropeptideiPRO_00000220891 – 83Removed in mature form1 PublicationAdd BLAST83
    ChainiPRO_000002209084 – 384EndopolyphosphataseAdd BLAST301
    PropeptideiPRO_0000022091385 – 674Removed in mature form1 PublicationAdd BLAST290

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Cross-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Glycosylationi58N-linked (GlcNAc...)Sequence analysis1
    Glycosylationi505N-linked (GlcNAc...)Sequence analysis1
    Glycosylationi511N-linked (GlcNAc...)Sequence analysis1

    Post-translational modificationi

    Processing by proteases in the vacuole is required for activation.1 Publication
    Ubiquitinated. Ubiquitination mediates sorting into internal vesicles in late endosomes. TUL1 and RSP5 are required for ubiquitination. Other cytoplasmic Lys residues than Lys-6 may also be ubiquitinated.1 Publication
    N-glycosylated (Probable). N-glycosylation is essential for the protease-mediated maturation.Curated1 Publication

    Keywords - PTMi

    Glycoprotein, Isopeptide bond, Ubl conjugation, Zymogen

    Proteomic databases

    MaxQBiQ04119.
    PRIDEiQ04119.

    PTM databases

    iPTMnetiQ04119.

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    BioGridi32507. 27 interactors.
    DIPiDIP-2584N.
    IntActiQ04119. 13 interactors.
    MINTiMINT-426113.

    Structurei

    3D structure databases

    ProteinModelPortaliQ04119.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domaini

    The transmembrane domain contains polar residues that mediate the recognition by TUL1.1 Publication

    Sequence similaritiesi

    Belongs to the endopolyphosphatase PPN1 family.Curated

    Keywords - Domaini

    Signal-anchor, Transmembrane, Transmembrane helix

    Phylogenomic databases

    GeneTreeiENSGT00530000063095.
    HOGENOMiHOG000207139.
    InParanoidiQ04119.
    KOiK06018.
    OMAiTQYFANL.
    OrthoDBiEOG092C27EW.

    Family and domain databases

    Gene3Di3.60.21.10. 1 hit.
    InterProiView protein in InterPro
    IPR004843. Calcineurin-like_PHP_ApaH.
    IPR012358. EndopolyPtase_N1.
    IPR029052. Metallo-depent_PP-like.
    PfamiView protein in Pfam
    PF00149. Metallophos. 1 hit.
    PIRSFiPIRSF027093. EndopolyPtase_N1. 1 hit.
    SUPFAMiSSF56300. SSF56300. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    Q04119-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVVVGKSEVR NVSMSRPKKK SLIAILSTCV LFFLVFIIGA KFQYVSVFSK
    60 70 80 90 100
    FLDDRGDNES LQLLNDIEFT RLGLTPREPV IIKDVKTGKE RKLHGRFLHI
    110 120 130 140 150
    TDIHPDPYYV EGSSIDAVCH TGKPSKKKDV APKFGKAMSG CDSPVILMEE
    160 170 180 190 200
    TLRWIKENLR DKIDFVIWTG DNIRHDNDRK HPRTEAQIFD MNNIVADKMT
    210 220 230 240 250
    ELFSAGNEED PRDFDVSVIP SLGNNDVFPH NMFALGPTLQ TREYYRIWKN
    260 270 280 290 300
    FVPQQQQRTF DRSASFLTEV IPGKLAVLSI NTLYLFKANP LVDNCNSKKE
    310 320 330 340 350
    PGYQLLLWFG YVLEELRSRG MKVWLSGHVP PIAKNFDQSC YDKFTLWTHE
    360 370 380 390 400
    YRDIIIGGLY GHMNIDHFIP TDGKKARKSL LKAMEQSTRV QQGEDSNEED
    410 420 430 440 450
    EETELNRILD HAMAAKEVFL MGAKPSNKEA YMNTVRDTYY RKVWNKLERV
    460 470 480 490 500
    DEKNVENEKK KKEKKDKKKK KPITRKELIE RYSIVNIGGS VIPTFNPSFR
    510 520 530 540 550
    IWEYNITDIV NDSNFAVSEY KPWDEFFESL NKIMEDSLLE DEMDSSNIEV
    560 570 580 590 600
    GINREKMGEK KNKKKKKNDK TMPIEMPDKY ELGPAYVPQL FTPTRFVQFY
    610 620 630 640 650
    ADLEKINQEL HNSFVESKDI FRYEIEYTSD EKPYSMDSLT VGSYLDLAGR
    660 670
    LYENKPAWEK YVEWSFASSG YKDD
    Length:674
    Mass (Da):78,344
    Last modified:November 1, 1996 - v1
    Checksum:iEEC78BC7568098B3
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF322107 Genomic DNA. Translation: AAG37278.1.
    U33007 Genomic DNA. Translation: AAB64872.1.
    BK006938 Genomic DNA. Translation: DAA12287.1.
    PIRiS69731.
    RefSeqiNP_010740.3. NM_001180760.3.

    Genome annotation databases

    EnsemblFungiiYDR452W; YDR452W; YDR452W.
    GeneIDi852063.
    KEGGisce:YDR452W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF322107 Genomic DNA. Translation: AAG37278.1.
    U33007 Genomic DNA. Translation: AAB64872.1.
    BK006938 Genomic DNA. Translation: DAA12287.1.
    PIRiS69731.
    RefSeqiNP_010740.3. NM_001180760.3.

    3D structure databases

    ProteinModelPortaliQ04119.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi32507. 27 interactors.
    DIPiDIP-2584N.
    IntActiQ04119. 13 interactors.
    MINTiMINT-426113.

    PTM databases

    iPTMnetiQ04119.

    Proteomic databases

    MaxQBiQ04119.
    PRIDEiQ04119.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYDR452W; YDR452W; YDR452W.
    GeneIDi852063.
    KEGGisce:YDR452W.

    Organism-specific databases

    EuPathDBiFungiDB:YDR452W.
    SGDiS000002860. PPN1.

    Phylogenomic databases

    GeneTreeiENSGT00530000063095.
    HOGENOMiHOG000207139.
    InParanoidiQ04119.
    KOiK06018.
    OMAiTQYFANL.
    OrthoDBiEOG092C27EW.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29983-MONOMER.
    BRENDAi3.6.1.10. 984.
    ReactomeiR-SCE-1660662. Glycosphingolipid metabolism.

    Miscellaneous databases

    PROiQ04119.

    Family and domain databases

    Gene3Di3.60.21.10. 1 hit.
    InterProiView protein in InterPro
    IPR004843. Calcineurin-like_PHP_ApaH.
    IPR012358. EndopolyPtase_N1.
    IPR029052. Metallo-depent_PP-like.
    PfamiView protein in Pfam
    PF00149. Metallophos. 1 hit.
    PIRSFiPIRSF027093. EndopolyPtase_N1. 1 hit.
    SUPFAMiSSF56300. SSF56300. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPPN1_YEAST
    AccessioniPrimary (citable) accession number: Q04119
    Secondary accession number(s): D6VT77
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 10, 2005
    Last sequence update: November 1, 1996
    Last modified: March 15, 2017
    This is version 141 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Inactivation of PPN1 leads to the inhibition of expression of both exopolyphosphatase PPX1 and high-molecular-mass exopolyphosphatase not encoded by PPX1.
    Present with 319 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: 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.