Reviewed, UniProtKB/Swiss-Prot Q04119 (PPN1_YEAST)

Names and origin

Protein names

Recommended name:
    Endopolyphosphatase
    EC=3.6.1.10
    EC=3.6.1.11
Alternative name(s):
    Exopolyphosphatase
    Phosphate metabolism protein 5

Gene names

Name:	PPN1
Synonyms:	PHM5
Ordered Locus Names:	YDR452W
ORF Names:	D9461.37

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	674 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. Ref.1 Ref.3 Ref.5 Ref.6 Ref.11 Ref.12
Catalytic activity	Polyphosphate + n H2O = (n+1) oligophosphate. Ref.3 Ref.12 (Polyphosphate)(n) + H2O = (polyphosphate)(n-1) + phosphate. Ref.3 Ref.12
Cofactor	Metal ions. Manganese is more active than magnesium. Ref.5
Enzyme regulation	Inhibited by heparin and EDTA. Ref.12
Subunit structure	Homotetramer.
Subcellular location	Vacuole membrane; Single-pass type II membrane protein. Ref.5 Ref.7 Ref.8 Ref.9 Ref.13
Domain	The transmembrane domain contains polar residues that mediate the recognition by TUL1.
Post-translational modification	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. Ref.7 Ref.8 Ref.13 N-glycosylated Probable. N-glycosylation is essential for the protease-mediated maturation.
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. Ref.10
biophysicochemical properties	Kinetic parameters: KM=185 nM for polyP(750) pH dependence: Optimum pH is about 7.5.

Ontologies

Keywords
Cellular component	Membrane Vacuole
Domain	Signal-anchor Transmembrane
Ligand	Metal-binding
Molecular function	Hydrolase
PTM	Glycoprotein Isopeptide bond Phosphoprotein Ubl conjugation Zymogen
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	polyphosphate catabolic process Inferred from direct assay. Source: SGD
Cellular component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from mutant phenotype. Source: SGD vacuolar membrane Ref.7 Inferred from direct assay. Source: SGD
Molecular function	endopolyphosphatase activity Ref.1 Inferred from direct assay. Source: SGD exopolyphosphatase activity Inferred from direct assay. Source: SGD metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Propeptide	1 – 83	83	Removed in mature form Ref.3		PRO_0000022089
	Chain	84 – 384	301	Endopolyphosphatase		PRO_0000022090
	Propeptide	385 – 674	290	Removed in mature form		PRO_0000022091
Regions
	Topological domain	1 – 21	21	Cytoplasmic Potential
	Transmembrane	22 – 42	21	Signal-anchor for type II membrane protein Potential
	Topological domain	43 – 674	632	Vacuolar Potential
Amino acid modifications
	Modified residue	282	1	Phosphothreonine Ref.14
	Glycosylation	58	1	N-linked (GlcNAc...) Potential
	Glycosylation	505	1	N-linked (GlcNAc...) Potential
	Glycosylation	511	1	N-linked (GlcNAc...) Potential
	Cross-link	6		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Probable
Experimental info
	Mutagenesis	6	1	K → R or G: Causes accumulation in vacuoles and abolishes sorting into internal vesicles in late endosomes. Ref.7
	Mutagenesis	11	1	N → A: Abolishes enzyme activity; when associated with A-505 and A-511. Ref.3
	Mutagenesis	505	1	N → A: Abolishes enzyme activity; when associated with A-11 and A-511. Ref.3
	Mutagenesis	511	1	N → A: Abolishes enzyme activity; when associated with A-11 and A-505. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q04119-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: EEC78BC7568098B3	FASTA	674	78,344
	10 20 30 40 50 60 MVVVGKSEVR NVSMSRPKKK SLIAILSTCV LFFLVFIIGA KFQYVSVFSK FLDDRGDNES 70 80 90 100 110 120 LQLLNDIEFT RLGLTPREPV IIKDVKTGKE RKLHGRFLHI TDIHPDPYYV EGSSIDAVCH 130 140 150 160 170 180 TGKPSKKKDV APKFGKAMSG CDSPVILMEE TLRWIKENLR DKIDFVIWTG DNIRHDNDRK 190 200 210 220 230 240 HPRTEAQIFD MNNIVADKMT ELFSAGNEED PRDFDVSVIP SLGNNDVFPH NMFALGPTLQ 250 260 270 280 290 300 TREYYRIWKN FVPQQQQRTF DRSASFLTEV IPGKLAVLSI NTLYLFKANP LVDNCNSKKE 310 320 330 340 350 360 PGYQLLLWFG YVLEELRSRG MKVWLSGHVP PIAKNFDQSC YDKFTLWTHE YRDIIIGGLY 370 380 390 400 410 420 GHMNIDHFIP TDGKKARKSL LKAMEQSTRV QQGEDSNEED EETELNRILD HAMAAKEVFL 430 440 450 460 470 480 MGAKPSNKEA YMNTVRDTYY RKVWNKLERV DEKNVENEKK KKEKKDKKKK KPITRKELIE 490 500 510 520 530 540 RYSIVNIGGS VIPTFNPSFR IWEYNITDIV NDSNFAVSEY KPWDEFFESL NKIMEDSLLE 550 560 570 580 590 600 DEMDSSNIEV GINREKMGEK KNKKKKKNDK TMPIEMPDKY ELGPAYVPQL FTPTRFVQFY 610 620 630 640 650 660 ADLEKINQEL HNSFVESKDI FRYEIEYTSD EKPYSMDSLT VGSYLDLAGR LYENKPAWEK 670 YVEWSFASSG YKDD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 11447286] [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: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"Endopolyphosphatase in Saccharomyces cerevisiae undergoes post-translational activations to produce short-chain polyphosphates." Shi X., Kornberg A. FEBS Lett. 579:2014-2018(2005) [PubMed: 15792812] [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.
[4]	Kulakovskaya T.V. Submitted (APR-2006) to UniProtKB Cited for: PROTEIN SEQUENCE OF 97-126; 184-198; 243-258; 320-334 AND 580-605.
[5]	"Endopolyphosphatases for long chain inorganic polyphosphate in yeast and mammals." Kumble K.D., Kornberg A. J. Biol. Chem. 271:27146-27151(1996) [PubMed: 8900207] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
[6]	"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: 11102525] [Abstract] Cited for: FUNCTION.
[7]	"Sorting of proteins into multivesicular bodies: ubiquitin-dependent and -independent targeting." Reggiori F., Pelham H.R.B. EMBO J. 20:5176-5186(2001) [PubMed: 11566881] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, UBIQUITINATION AT LYS-6, MUTAGENESIS OF LYS-6.
[8]	"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: 11788821] [Abstract] Cited for: SUBCELLULAR LOCATION, ROLE OF UBIQUITINATION.
[9]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[10]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]	"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: 15342119] [Abstract] Cited for: FUNCTION.
[12]	"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. Biokhimiia 69:387-393(2004) [PubMed: 15170373] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION.
[13]	"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: 15086787] [Abstract] Cited for: SUBCELLULAR LOCATION, ROLE OF UBIQUITINATION.
[14]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-282, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF322107 Genomic DNA. Translation: AAG37278.1. U33007 Genomic DNA. Translation: AAB64872.1.
PIR	S69731.
RefSeq	NP_010740.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:2584N.
IntAct	Q04119. 8 interactions.
Proteomic databases
PeptideAtlas	Q04119.
PRIDE	Q04119.
Genome annotation databases
Ensembl	YDR452W. Saccharomyces cerevisiae. [Contig view]
GeneID	852063.
GenomeReviews	Gene locus YDR452W in contig Z71256_GR.
KEGG	sce:YDR452W.
NMPDR	fig|4932.3.peg.1513.
Organism-specific databases
CYGD	YDR452w.
SGD	S000002860. PPN1.
Yeast-GFP	Search...
Phylogenomic databases
HOGENOM	Q04119.
OMA	Q04119. GGLYGHM.
Enzyme and pathway databases
BRENDA	3.6.1.10. 250. 3.6.1.11. 250.
Gene expression databases
ArrayExpress	Q04119.
GermOnline	YDR452W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR012358. EndopolyPtase_N1. IPR004843. M-pesterase. [Graphical view]
PANTHER	PTHR10340:SF4. EndopolyPtase_N1. 1 hit.
Pfam	PF00149. Metallophos. 1 hit. [Graphical view]
PIRSF	PIRSF027093. EndopolyPtase_N1. 1 hit.
ProtoNet	Search...
Other Resources
NextBio	970343.

Entry information

Entry name

PPN1_YEAST

Accession

Primary (citable) accession number: Q04119

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	November 1, 1996
Last modified:	June 16, 2009
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)