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Q04119

- PPN1_YEAST

UniProt

Q04119 - PPN1_YEAST

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Protein
Endopolyphosphatase
Gene
PPN1, PHM5, YDR452W, D9461.37
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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.2 Publications
(Polyphosphate)(n) + H2O = (polyphosphate)(n-1) + phosphate.2 Publications

Cofactori

Metal ions. Manganese is more active than magnesium.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.

GO - Molecular functioni

  1. endopolyphosphatase activity Source: SGD
  2. exopolyphosphatase activity Source: SGD
  3. metal ion binding Source: UniProtKB-KW
Complete GO annotation...

GO - Biological processi

  1. polyphosphate catabolic process Source: SGD
  2. 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.

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: Chromosome IV

Organism-specific databases

CYGDiYDR452w.
SGDiS000002860. PPN1.

Subcellular locationi

Vacuole membrane; Single-pass type II membrane protein 5 Publications

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2121Cytoplasmic Reviewed prediction
Add
BLAST
Transmembranei22 – 4221Helical; Signal-anchor for type II membrane protein; Reviewed prediction
Add
BLAST
Topological domaini43 – 674632Vacuolar Reviewed prediction
Add
BLAST

GO - Cellular componenti

  1. fungal-type vacuole membrane Source: SGD
  2. integral component of membrane Source: UniProtKB-KW
  3. 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 form
PRO_0000022089Add
BLAST
Chaini84 – 384301Endopolyphosphatase
PRO_0000022090Add
BLAST
Propeptidei385 – 674290Removed in mature form
PRO_0000022091Add
BLAST

Amino acid modifications

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

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.3 Publications
N-glycosylated Inferred. N-glycosylation is essential for the protease-mediated maturation.1 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. 18 interactions.
DIPiDIP-2584N.
IntActiQ04119. 13 interactions.
MINTiMINT-426113.
STRINGi4932.YDR452W.

Structurei

3D structure databases

ProteinModelPortaliQ04119.

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.
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

MVVVGKSEVR NVSMSRPKKK SLIAILSTCV LFFLVFIIGA KFQYVSVFSK    50
FLDDRGDNES LQLLNDIEFT RLGLTPREPV IIKDVKTGKE RKLHGRFLHI 100
TDIHPDPYYV EGSSIDAVCH TGKPSKKKDV APKFGKAMSG CDSPVILMEE 150
TLRWIKENLR DKIDFVIWTG DNIRHDNDRK HPRTEAQIFD MNNIVADKMT 200
ELFSAGNEED PRDFDVSVIP SLGNNDVFPH NMFALGPTLQ TREYYRIWKN 250
FVPQQQQRTF DRSASFLTEV IPGKLAVLSI NTLYLFKANP LVDNCNSKKE 300
PGYQLLLWFG YVLEELRSRG MKVWLSGHVP PIAKNFDQSC YDKFTLWTHE 350
YRDIIIGGLY GHMNIDHFIP TDGKKARKSL LKAMEQSTRV QQGEDSNEED 400
EETELNRILD HAMAAKEVFL MGAKPSNKEA YMNTVRDTYY RKVWNKLERV 450
DEKNVENEKK KKEKKDKKKK KPITRKELIE RYSIVNIGGS VIPTFNPSFR 500
IWEYNITDIV NDSNFAVSEY KPWDEFFESL NKIMEDSLLE DEMDSSNIEV 550
GINREKMGEK KNKKKKKNDK TMPIEMPDKY ELGPAYVPQL FTPTRFVQFY 600
ADLEKINQEL HNSFVESKDI FRYEIEYTSD EKPYSMDSLT VGSYLDLAGR 650
LYENKPAWEK YVEWSFASSG YKDD 674
Length:674
Mass (Da):78,344
Last modified:November 1, 1996 - v1
Checksum:iEEC78BC7568098B3
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
AF322107 Genomic DNA. Translation: AAG37278.1 .
U33007 Genomic DNA. Translation: AAB64872.1 .
BK006938 Genomic DNA. Translation: DAA12287.1 .
PIRi S69731.
RefSeqi NP_010740.3. NM_001180760.3.

3D structure databases

ProteinModelPortali Q04119.
ModBasei Search...

Protein-protein interaction databases

BioGridi 32507. 18 interactions.
DIPi DIP-2584N.
IntActi Q04119. 13 interactions.
MINTi MINT-426113.
STRINGi 4932.YDR452W.

Proteomic databases

MaxQBi Q04119.
PaxDbi Q04119.
PeptideAtlasi Q04119.
PRIDEi Q04119.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDR452W ; YDR452W ; YDR452W .
GeneIDi 852063.
KEGGi sce:YDR452W.

Organism-specific databases

CYGDi YDR452w.
SGDi S000002860. PPN1.

Phylogenomic databases

eggNOGi NOG301848.
GeneTreei ENSGT00530000063095.
HOGENOMi HOG000207139.
KOi K06018.
OMAi TQYFANL.
OrthoDBi EOG7RNK7W.

Enzyme and pathway databases

BioCyci YEAST:G3O-29983-MONOMER.
BRENDAi 3.6.1.10. 984.

Miscellaneous databases

NextBioi 970343.

Gene expression databases

Genevestigatori Q04119.

Family and domain databases

Gene3Di 3.60.21.10. 1 hit.
InterProi IPR004843. Calcineurin-like_PHP_apaH.
IPR012358. EndopolyPtase_N1.
IPR029052. Metallo-depent_PP-like.
[Graphical view ]
Pfami PF00149. Metallophos. 1 hit.
[Graphical view ]
PIRSFi PIRSF027093. EndopolyPtase_N1. 1 hit.
SUPFAMi SSF56300. SSF56300. 1 hit.
ProtoNeti Search...

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: June 11, 2014
This is version 118 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.

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