Endopolyphosphatase precursor - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Preferred order of sections

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 (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [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.4 Ref.6 Ref.7 Ref.12 Ref.13
Catalytic activity	Polyphosphate + n H₂O = (n+1) oligophosphate. Ref.4 Ref.13 (Polyphosphate)(n) + H₂O = (polyphosphate)(n-1) + phosphate. Ref.4 Ref.13
Cofactor	Metal ions. Manganese is more active than magnesium. Ref.6
Enzyme regulation	Inhibited by heparin and EDTA. Ref.13
Subunit structure	Homotetramer.
Subcellular location	Vacuole membrane; Single-pass type II membrane protein Ref.6 Ref.8 Ref.9 Ref.10 Ref.14.
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.8 Ref.9 Ref.14 N-glycosylated Probable. N-glycosylation is essential for the protease-mediated maturation. Ref.4
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.
Biophysicochemical properties	Kinetic parameters: K_M=185 nM for polyP(750) Ref.6 pH dependence: Optimum pH is about 7.5.

Ontologies

Keywords
Cellular component	Membrane Vacuole
Domain	Signal-anchor Transmembrane Transmembrane helix
Ligand	Metal-binding
Molecular function	Hydrolase
PTM	Glycoprotein Isopeptide bond Phosphoprotein Ubl conjugation Zymogen
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	polyphosphate catabolic process Inferred from direct assay PubMed 17009950. Source: SGD
Cellular_component	fungal-type vacuole membrane Inferred from mutant phenotype Ref.8. Source: SGD integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from mutant phenotype PubMed 16862600. Source: SGD
Molecular_function	endopolyphosphatase activity Inferred from mutant phenotype Ref.1. Source: SGD exopolyphosphatase activity Inferred from direct assay PubMed 17009950. 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

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

Helical; Signal-anchor for type II membrane protein; Potential

Topological domain

43 – 674

632

Vacuolar Potential

Amino acid modifications

Modified residue

282

1

Phosphothreonine Ref.15

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.8

Mutagenesis

11

1

N → A: Abolishes enzyme activity; when associated with A-505 and A-511. Ref.4

Mutagenesis

505

1

N → A: Abolishes enzyme activity; when associated with A-11 and A-511. Ref.4

Mutagenesis

511

1

N → A: Abolishes enzyme activity; when associated with A-11 and A-505. Ref.4

Sequences

Sequence

Length

Mass (Da)

Tools

Q04119 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: EEC78BC7568098B3
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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

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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] [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. Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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]	"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] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[11]	"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] [Europe PMC] [Abstract] 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. Biokhimiia 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.
[15]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-282, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF322107 Genomic DNA. Translation: AAG37278.1. U33007 Genomic DNA. Translation: AAB64872.1. BK006938 Genomic DNA. Translation: DAA12287.1.
PIR	S69731.
RefSeq	NP_010740.3. NM_001180760.3.
3D structure databases
ProteinModelPortal	Q04119.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2584N.
IntAct	Q04119. 12 interactions.
MINT	MINT-426113.
STRING	4932.YDR452W.
Proteomic databases
PaxDb	Q04119.
PeptideAtlas	Q04119.
PRIDE	Q04119.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDR452W; YDR452W; YDR452W.
GeneID	852063.
KEGG	sce:YDR452W. sce:YDR457W.
Organism-specific databases
CYGD	YDR452w.
SGD	S000002860. PPN1.
Phylogenomic databases
eggNOG	NOG301848.
GeneTree	ENSGT00530000063095.
HOGENOM	HOG000207139.
KO	K06018. K10592.
OMA	GGLYGHM.
OrthoDB	EOG4TMV9Q.
Enzyme and pathway databases
BRENDA	3.6.1.10. 984.
Gene expression databases
Genevestigator	Q04119.
GermOnline	YDR452W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR012358. EndopolyPtase_N1. IPR004843. Metallo_PEstase_dom. [Graphical view]
Pfam	PF00149. Metallophos. 1 hit. [Graphical view]
PIRSF	PIRSF027093. EndopolyPtase_N1. 1 hit.
ProtoNet	Search...
Other
NextBio	970343.

Entry information

Entry name

PPN1_YEAST

Accession

Primary (citable) accession number: Q04119
Secondary accession number(s): D6VT77

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 108 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents