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P00817

- IPYR_YEAST

UniProt

P00817 - IPYR_YEAST

Protein

Inorganic pyrophosphatase

Gene

IPP1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 162 (01 Oct 2014)
      Sequence version 4 (24 Jul 2007)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    Diphosphate + H2O = 2 phosphate.

    Cofactori

    Binds 4 magnesium ions per subunit. Other metal ions can support activity, but at a lower rate. Two magnesium ions are required for the activation of the enzyme and are present before substrate binds, two additional magnesium ions form complexes with substrate and product By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei79 – 791Diphosphate
    Active sitei90 – 901Proton donor2 Publications
    Metal bindingi116 – 1161Magnesium 1
    Metal bindingi121 – 1211Magnesium 1
    Metal bindingi121 – 1211Magnesium 2
    Metal bindingi153 – 1531Magnesium 1

    GO - Molecular functioni

    1. inorganic diphosphatase activity Source: SGD
    2. magnesium ion binding Source: InterPro
    3. protein binding Source: IntAct

    GO - Biological processi

    1. phosphate-containing compound metabolic process Source: SGD

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciYEAST:YBR011C-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Inorganic pyrophosphatase (EC:3.6.1.1)
    Alternative name(s):
    Pyrophosphate phospho-hydrolase
    Short name:
    PPase
    Gene namesi
    Name:IPP1
    Synonyms:PPA, PPA1
    Ordered Locus Names:YBR011C
    ORF Names:YBR0202
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    SGDiS000000215. IPP1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 287286Inorganic pyrophosphatasePRO_0000137588Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei65 – 651Phosphothreonine1 Publication
    Modified residuei251 – 2511Phosphothreonine2 Publications
    Modified residuei266 – 2661Phosphoserine2 Publications
    Modified residuei286 – 2861Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP00817.
    PaxDbiP00817.
    PeptideAtlasiP00817.

    2D gel databases

    COMPLUYEAST-2DPAGEP00817.
    SWISS-2DPAGEP00817.

    Expressioni

    Gene expression databases

    GenevestigatoriP00817.

    Interactioni

    Subunit structurei

    Homodimer.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    RSP5P399402EBI-9338,EBI-16219

    Protein-protein interaction databases

    BioGridi32712. 76 interactions.
    DIPiDIP-5753N.
    IntActiP00817. 34 interactions.
    MINTiMINT-614477.
    STRINGi4932.YBR011C.

    Structurei

    Secondary structure

    1
    287
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 108
    Beta strandi13 – 153
    Beta strandi17 – 226
    Beta strandi25 – 273
    Turni29 – 324
    Beta strandi35 – 384
    Turni39 – 424
    Beta strandi43 – 508
    Beta strandi58 – 603
    Beta strandi62 – 643
    Beta strandi69 – 713
    Beta strandi75 – 773
    Beta strandi85 – 873
    Beta strandi91 – 966
    Beta strandi106 – 1083
    Turni109 – 1124
    Beta strandi113 – 1153
    Beta strandi117 – 1193
    Beta strandi121 – 1244
    Beta strandi126 – 1283
    Beta strandi135 – 14410
    Beta strandi146 – 1483
    Beta strandi155 – 1606
    Beta strandi163 – 1653
    Helixi166 – 1683
    Helixi172 – 1787
    Helixi182 – 19211
    Helixi195 – 1973
    Helixi205 – 2084
    Beta strandi210 – 2123
    Helixi213 – 23119
    Beta strandi245 – 2473
    Helixi256 – 2583
    Turni259 – 2613
    Beta strandi266 – 2683
    Helixi275 – 2784

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    117EX-ray2.15A/B2-287[»]
    1E6AX-ray1.90A/B2-287[»]
    1E9GX-ray1.15A/B2-287[»]
    1HUJX-ray2.10A/B2-282[»]
    1HUKX-ray2.20A/B2-282[»]
    1M38X-ray1.80A/B1-287[»]
    1PYPX-ray3.00A/B2-287[»]
    1WGIX-ray2.20A/B2-287[»]
    1WGJX-ray2.00A/B2-287[»]
    1YPPX-ray2.40A/B2-287[»]
    2IHPX-ray1.50A/B2-287[»]
    2IK0X-ray1.70A/B2-287[»]
    2IK1X-ray1.70A/B2-287[»]
    2IK2X-ray1.80A/B2-287[»]
    2IK4X-ray1.80A/B2-287[»]
    2IK6X-ray1.80A/B2-287[»]
    2IK7X-ray1.90A/B2-287[»]
    2IK9X-ray1.50A/B2-287[»]
    8PRKX-ray1.85A/B1-287[»]
    ProteinModelPortaliP00817.
    SMRiP00817. Positions 2-285.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00817.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PPase family.Curated

    Phylogenomic databases

    eggNOGiCOG0221.
    GeneTreeiENSGT00390000017004.
    HOGENOMiHOG000195569.
    KOiK01507.
    OMAiANTLEHR.
    OrthoDBiEOG7K0ZP6.

    Family and domain databases

    Gene3Di3.90.80.10. 1 hit.
    InterProiIPR008162. Pyrophosphatase.
    [Graphical view]
    PANTHERiPTHR10286. PTHR10286. 1 hit.
    PfamiPF00719. Pyrophosphatase. 1 hit.
    [Graphical view]
    SUPFAMiSSF50324. SSF50324. 1 hit.
    PROSITEiPS00387. PPASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P00817-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTYTTRQIGA KNTLEYKVYI EKDGKPVSAF HDIPLYADKE NNIFNMVVEI    50
    PRWTNAKLEI TKEETLNPII QDTKKGKLRF VRNCFPHHGY IHNYGAFPQT 100
    WEDPNVSHPE TKAVGDNDPI DVLEIGETIA YTGQVKQVKA LGIMALLDEG 150
    ETDWKVIAID INDPLAPKLN DIEDVEKYFP GLLRATNEWF RIYKIPDGKP 200
    ENQFAFSGEA KNKKYALDII KETHDSWKQL IAGKSSDSKG IDLTNVTLPD 250
    TPTYSKAASD AIPPASPKAD APIDKSIDKW FFISGSV 287
    Length:287
    Mass (Da):32,300
    Last modified:July 24, 2007 - v4
    Checksum:i1DC19A702A389BA9
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti41 – 411N → D AA sequence (PubMed:340461)Curated
    Sequence conflicti72 – 721D → N AA sequence (PubMed:340461)Curated
    Sequence conflicti75 – 751Missing AA sequence (PubMed:340461)Curated
    Sequence conflicti124 – 1241E → Q AA sequence (PubMed:340461)Curated
    Sequence conflicti137 – 1371Q → E AA sequence (PubMed:340461)Curated
    Sequence conflicti187 – 1871N → D AA sequence (PubMed:340461)Curated
    Sequence conflicti225 – 2251D → N AA sequence (PubMed:340461)Curated
    Sequence conflicti267 – 2671P → L in CAA31629. (PubMed:2849749)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X13253 Genomic DNA. Translation: CAA31629.1.
    Z35880 Genomic DNA. Translation: CAA84949.1.
    AY692953 Genomic DNA. Translation: AAT92972.1.
    BK006936 Genomic DNA. Translation: DAA07132.1.
    PIRiS45864. PWBY.
    RefSeqiNP_009565.1. NM_001178359.1.

    Genome annotation databases

    EnsemblFungiiYBR011C; YBR011C; YBR011C.
    GeneIDi852296.
    KEGGisce:YBR011C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X13253 Genomic DNA. Translation: CAA31629.1 .
    Z35880 Genomic DNA. Translation: CAA84949.1 .
    AY692953 Genomic DNA. Translation: AAT92972.1 .
    BK006936 Genomic DNA. Translation: DAA07132.1 .
    PIRi S45864. PWBY.
    RefSeqi NP_009565.1. NM_001178359.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    117E X-ray 2.15 A/B 2-287 [» ]
    1E6A X-ray 1.90 A/B 2-287 [» ]
    1E9G X-ray 1.15 A/B 2-287 [» ]
    1HUJ X-ray 2.10 A/B 2-282 [» ]
    1HUK X-ray 2.20 A/B 2-282 [» ]
    1M38 X-ray 1.80 A/B 1-287 [» ]
    1PYP X-ray 3.00 A/B 2-287 [» ]
    1WGI X-ray 2.20 A/B 2-287 [» ]
    1WGJ X-ray 2.00 A/B 2-287 [» ]
    1YPP X-ray 2.40 A/B 2-287 [» ]
    2IHP X-ray 1.50 A/B 2-287 [» ]
    2IK0 X-ray 1.70 A/B 2-287 [» ]
    2IK1 X-ray 1.70 A/B 2-287 [» ]
    2IK2 X-ray 1.80 A/B 2-287 [» ]
    2IK4 X-ray 1.80 A/B 2-287 [» ]
    2IK6 X-ray 1.80 A/B 2-287 [» ]
    2IK7 X-ray 1.90 A/B 2-287 [» ]
    2IK9 X-ray 1.50 A/B 2-287 [» ]
    8PRK X-ray 1.85 A/B 1-287 [» ]
    ProteinModelPortali P00817.
    SMRi P00817. Positions 2-285.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32712. 76 interactions.
    DIPi DIP-5753N.
    IntActi P00817. 34 interactions.
    MINTi MINT-614477.
    STRINGi 4932.YBR011C.

    2D gel databases

    COMPLUYEAST-2DPAGE P00817.
    SWISS-2DPAGE P00817.

    Proteomic databases

    MaxQBi P00817.
    PaxDbi P00817.
    PeptideAtlasi P00817.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YBR011C ; YBR011C ; YBR011C .
    GeneIDi 852296.
    KEGGi sce:YBR011C.

    Organism-specific databases

    SGDi S000000215. IPP1.

    Phylogenomic databases

    eggNOGi COG0221.
    GeneTreei ENSGT00390000017004.
    HOGENOMi HOG000195569.
    KOi K01507.
    OMAi ANTLEHR.
    OrthoDBi EOG7K0ZP6.

    Enzyme and pathway databases

    BioCyci YEAST:YBR011C-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P00817.
    NextBioi 970952.
    PROi P00817.

    Gene expression databases

    Genevestigatori P00817.

    Family and domain databases

    Gene3Di 3.90.80.10. 1 hit.
    InterProi IPR008162. Pyrophosphatase.
    [Graphical view ]
    PANTHERi PTHR10286. PTHR10286. 1 hit.
    Pfami PF00719. Pyrophosphatase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50324. SSF50324. 1 hit.
    PROSITEi PS00387. PPASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning, molecular characterization and chromosome localization of the inorganic pyrophosphatase (PPA) gene from S. cerevisiae."
      Kolakowski L.F. Jr., Schloesser M., Cooperman B.S.
      Nucleic Acids Res. 16:10441-10452(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 26109 / X2180.
    2. "Complete DNA sequence of yeast chromosome II."
      Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
      , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
      EMBO J. 13:5795-5809(1994) [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. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "Covalent structural analysis of yeast inorganic pyrophosphatase."
      Cohen S.A., Sterner R., Keim P.S., Heinrikson R.L.
      J. Biol. Chem. 253:889-897(1978) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-287.
    6. Cited for: PROTEIN SEQUENCE OF 26-36 AND 240-252.
      Strain: ATCC 204508 / S288c.
    7. "Protein expression during exponential growth in 0.7 M NaCl medium of Saccharomyces cerevisiae."
      Norbeck J., Blomberg A.
      FEMS Microbiol. Lett. 137:1-8(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 240-250.
      Strain: ATCC 38531 / Y41.
    8. "Tyrosine-89 is important for enzymatic activity of S. cerevisiae inorganic pyrophosphatase."
      Raznikov A.V., Sklyankina V.A., Avaeva S.M.
      FEBS Lett. 308:62-64(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE TYR-90.
    9. "Identification of an arginine important for enzymatic activity within the covalent structure of yeast inorganic pyrophosphatase."
      Bond M.W., Chiu N.Y., Cooperman B.S.
      Biochemistry 19:94-102(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE.
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
      Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
      Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-251 AND SER-286, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: YAL6B.
    12. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-251, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    13. "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-65 AND SER-266, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-266, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "X-ray diffraction study of inorganic pyrophosphatase from baker's yeast at the 3-A resolution."
      Arutiunian E.G., Terzian S.S., Voronova A.A., Kuranova I.P., Smirnova E.A., Vainstein B.K., Hohne W.E., Hansen G.
      Dokl. Akad. Nauk SSSR 258:1481-1492(1981)
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
    17. Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
    18. Swaminathan K., Cooperman B.S., Lahti R., Voet D.
      Submitted (DEC-1997) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
    19. "The R78K and D117E active-site variants of Saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implications."
      Tuominen V., Heikinheimo P., Kajander T., Torkkel T., Hyytia T., Kapyla J., Lahti R., Cooperman B.S., Goldman A.
      J. Mol. Biol. 284:1565-1580(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF MUTANTS LYS-79 AND LYS-118.
    20. "Conservation of functional residues between yeast and E. coli inorganic pyrophosphatases."
      Lahti R., Kolakowski L.F. Jr., Heinonen J., Vihinen M., Pohjanoksa K., Cooperman B.S.
      Biochim. Biophys. Acta 1038:338-345(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: SIMILARITY TO E.COLI AND K.LACTIS PPASES.

    Entry informationi

    Entry nameiIPYR_YEAST
    AccessioniPrimary (citable) accession number: P00817
    Secondary accession number(s): D6VQ12
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 24, 2007
    Last modified: October 1, 2014
    This is version 162 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 68400 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    External Data

    Dasty 3