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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 (poly P) chains of many hundreds of phosphate residues into shorter lengths. The limited digestion products are 1 and 3 P(i) residues.6 Publications

Catalytic activityi

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

Cofactori

Mn2+1 Publication, Mg2+1 PublicationNote: Metal ions. Mn(2+) is more active than Mg2+.1 Publication

Enzyme regulationi

Inhibited by heparin and EDTA.1 Publication

Kineticsi

  1. KM=185 nM for polyP(750)1 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
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29983-MONOMER.
    BRENDAi3.6.1.10. 984.
    ReactomeiREACT_307521. Glycosphingolipid metabolism.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Endopolyphosphatase (EC:3.6.1.10, EC:3.6.1.11)
    Alternative name(s):
    Exopolyphosphatase
    Phosphate metabolism protein 5
    Gene namesi
    Name:PPN1
    Synonyms:PHM5
    Ordered Locus Names:YDR452W
    ORF Names:D9461.37
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311 Componenti: Chromosome IV

    Organism-specific databases

    CYGDiYDR452w.
    EuPathDBiFungiDB:YDR452W.
    SGDiS000002860. PPN1.

    Subcellular locationi

    Topology

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 2121CytoplasmicSequence AnalysisAdd
    BLAST
    Transmembranei22 – 4221Helical; Signal-anchor for type II membrane proteinSequence AnalysisAdd
    BLAST
    Topological domaini43 – 674632VacuolarSequence AnalysisAdd
    BLAST

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Membrane, Vacuole

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi6 – 61K → R or G: Causes accumulation in vacuoles and abolishes sorting into internal vesicles in late endosomes. 1 Publication
    Mutagenesisi11 – 111N → A: Abolishes enzyme activity; when associated with A-505 and A-511. 1 Publication
    Mutagenesisi505 – 5051N → A: Abolishes enzyme activity; when associated with A-11 and A-511. 1 Publication
    Mutagenesisi511 – 5111N → A: Abolishes enzyme activity; when associated with A-11 and A-505. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Propeptidei1 – 8383Removed in mature form1 PublicationPRO_0000022089Add
    BLAST
    Chaini84 – 384301EndopolyphosphatasePRO_0000022090Add
    BLAST
    Propeptidei385 – 674290Removed in mature formPRO_0000022091Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Glycosylationi58 – 581N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi505 – 5051N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi511 – 5111N-linked (GlcNAc...)Sequence Analysis

    Post-translational modificationi

    Processing by proteases in the vacuole is required for activation.
    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.
    PaxDbiQ04119.
    PeptideAtlasiQ04119.
    PRIDEiQ04119.

    Expressioni

    Gene expression databases

    GenevestigatoriQ04119.

    Interactioni

    Subunit structurei

    Homotetramer.

    Protein-protein interaction databases

    BioGridi32507. 19 interactions.
    DIPiDIP-2584N.
    IntActiQ04119. 13 interactions.
    MINTiMINT-426113.
    STRINGi4932.YDR452W.

    Structurei

    3D structure databases

    ProteinModelPortaliQ04119.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domaini

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

    Keywords - Domaini

    Signal-anchor, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG301848.
    GeneTreeiENSGT00530000063095.
    HOGENOMiHOG000207139.
    InParanoidiQ04119.
    KOiK06018.
    OMAiTQYFANL.
    OrthoDBiEOG7RNK7W.

    Family and domain databases

    Gene3Di3.60.21.10. 1 hit.
    InterProiIPR004843. Calcineurin-like_PHP_apaH.
    IPR012358. EndopolyPtase_N1.
    IPR029052. Metallo-depent_PP-like.
    [Graphical view]
    PfamiPF00149. Metallophos. 1 hit.
    [Graphical view]
    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. 19 interactions.
    DIPiDIP-2584N.
    IntActiQ04119. 13 interactions.
    MINTiMINT-426113.
    STRINGi4932.YDR452W.

    Proteomic databases

    MaxQBiQ04119.
    PaxDbiQ04119.
    PeptideAtlasiQ04119.
    PRIDEiQ04119.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    CYGDiYDR452w.
    EuPathDBiFungiDB:YDR452W.
    SGDiS000002860. PPN1.

    Phylogenomic databases

    eggNOGiNOG301848.
    GeneTreeiENSGT00530000063095.
    HOGENOMiHOG000207139.
    InParanoidiQ04119.
    KOiK06018.
    OMAiTQYFANL.
    OrthoDBiEOG7RNK7W.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29983-MONOMER.
    BRENDAi3.6.1.10. 984.
    ReactomeiREACT_307521. Glycosphingolipid metabolism.

    Miscellaneous databases

    NextBioi970343.
    PROiQ04119.

    Gene expression databases

    GenevestigatoriQ04119.

    Family and domain databases

    Gene3Di3.60.21.10. 1 hit.
    InterProiIPR004843. Calcineurin-like_PHP_apaH.
    IPR012358. EndopolyPtase_N1.
    IPR029052. Metallo-depent_PP-like.
    [Graphical view]
    PfamiPF00149. Metallophos. 1 hit.
    [Graphical view]
    PIRSFiPIRSF027093. EndopolyPtase_N1. 1 hit.
    SUPFAMiSSF56300. SSF56300. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The endopolyphosphatase gene: essential in Saccharomyces cerevisiae."
      Sethuraman A., Rao N.N., Kornberg A.
      Proc. Natl. Acad. Sci. U.S.A. 98:8542-8547(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 184-212, FUNCTION, PROTEOLYTIC PROCESSING.
      Strain: ATCC 208353 / W303-1A.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Endopolyphosphatase in Saccharomyces cerevisiae undergoes post-translational activations to produce short-chain polyphosphates."
      Shi X., Kornberg A.
      FEBS Lett. 579:2014-2018(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 84-95 AND 381-384, FUNCTION, CATALYTIC ACTIVITY, GLYCOSYLATION, PROTEOLYTIC PROCESSING, MUTAGENESIS OF ASN-11; ASN-505 AND ASN-511.
    5. Kulakovskaya T.V.
      Submitted (APR-2006) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 97-126; 184-198; 243-258; 320-334 AND 580-605.
    6. "Endopolyphosphatases for long chain inorganic polyphosphate in yeast and mammals."
      Kumble K.D., Kornberg A.
      J. Biol. Chem. 271:27146-27151(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
    7. "New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis."
      Ogawa N., DeRisi J.L., Brown P.O.
      Mol. Biol. Cell 11:4309-4321(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "Sorting of proteins into multivesicular bodies: ubiquitin-dependent and -independent targeting."
      Reggiori F., Pelham H.R.B.
      EMBO J. 20:5176-5186(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, UBIQUITINATION AT LYS-6, MUTAGENESIS OF LYS-6.
    9. "A transmembrane ubiquitin ligase required to sort membrane proteins into multivesicular bodies."
      Reggiori F., Pelham H.R.B.
      Nat. Cell Biol. 4:117-123(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, ROLE OF UBIQUITINATION.
    10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    12. "Inactivation of endopolyphosphatase gene PPN1 results in inhibition of expression of exopolyphosphatase PPX1 and high-molecular-mass exopolyphosphatase not encoded by PPX1 in Saccharomyces cerevisiae."
      Lichko L., Kulakovskaya T., Kulaev I.
      Biochim. Biophys. Acta 1674:98-102(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    13. "Purification and properties of exopolyphosphatase from the cytosol of Saccharomyces cerevisiae not encoded by the PPX1 gene."
      Andreeva N.A., Kulakovskaya T.V., Kulaev I.S.
      Biochemistry (Mosc.) 69:387-393(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION.
    14. "The ubiquitin ligase Rsp5p is required for modification and sorting of membrane proteins into multivesicular bodies."
      Morvan J., Froissard M., Haguenauer-Tsapis R., Urban-Grimal D.
      Traffic 5:383-392(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, ROLE OF UBIQUITINATION.

    Entry informationi

    Entry nameiPPN1_YEAST
    AccessioniPrimary (citable) accession number: Q04119
    Secondary accession number(s): D6VT77
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 10, 2005
    Last sequence update: November 1, 1996
    Last modified: May 27, 2015
    This is version 125 of the entry and version 1 of the sequence. [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. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    2. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3

    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 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.