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Protein

Protein APA1

Gene

APA1

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

Ap4A phosphorylase catalyzes the phosphorolytic degradation of bis(5'-adenosyl) tetraphosphate (Ap4A) into ADP and ATP. Can also use other Np4N' nucleotides (where N and N' stand for A,C,G or U) as substrates with equal efficiency. Cannot catalyze the reverse reaction. Additionally, this enzyme can also catalyze the phosphorolytic degradation of adenosine 5'-phosphosulfate (AMPS) into ADP and sulfate, the reversible exchange recation between inorganic phosphate and the beta-phosphate of a nucleoside diphosphate (NDP), and the synthesis of Ap4A from AMPS plus ATP.6 Publications

Catalytic activityi

ADP + ATP = phosphate + P1,P(4)-bis(5'-adenosyl) tetraphosphate.3 Publications
ADP + sulfate = phosphate + adenylyl sulfate.2 Publications

Cofactori

a divalent metal cation1 Publication

Kineticsi

kcat is 81.2 sec(-1) with Ap4A as substrate.1 Publication

  1. KM=39.3 µM for Ap4A1 Publication

    pH dependencei

    Optimum pH is 7.5.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei54 – 541SubstrateBy similarity
    Binding sitei145 – 1451SubstrateBy similarity
    Active sitei158 – 1581NucleophileBy similarity
    Binding sitei160 – 1601SubstrateBy similarity
    Sitei160 – 1601Transition state stabilizerBy similarity
    Binding sitei280 – 2801Substrate; via carbonyl oxygenBy similarity
    Binding sitei284 – 2841SubstrateBy similarity

    GO - Molecular functioni

    • ATP adenylyltransferase activity Source: UniProtKB-EC
    • ATP binding Source: UniProtKB-KW
    • bis(5'-nucleosyl)-tetraphosphatase activity Source: SGD
    • sulfate adenylyltransferase (ADP) activity Source: SGD

    GO - Biological processi

    • nucleoside catabolic process Source: SGD
    • nucleotide biosynthetic process Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Nucleotidyltransferase, Transferase

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-12462.
    YEAST:YCL050C-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein APA1
    Including the following 1 domains:
    Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 11 Publication (EC:2.7.7.531 Publication)
    Short name:
    Ap4A phosphorylase 1
    Alternative name(s):
    ADP-sulfurylase1 Publication (EC:2.7.7.51 Publication)
    ATP adenylyltransferase
    Diadenosine tetraphosphate alpha,beta-phosphorylase (ADP-forming)1 Publication
    Gene namesi
    Name:APA11 Publication
    Synonyms:DTP1 Publication
    Ordered Locus Names:YCL050CImported
    ORF Names:YCL50C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome III

    Organism-specific databases

    EuPathDBiFungiDB:YCL050C.
    SGDiS000000555. APA1.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Inactivation of both APA1 and APA2 promotes a great increase in the cellular concentration of bis(5'-nuceleosidyl) tetraphosphate nucleotides.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 321321Protein APA1PRO_0000064611Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei60 – 601PhosphothreonineCombined sources

    Post-translational modificationi

    The N-terminus is blocked.1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP16550.

    PTM databases

    iPTMnetiP16550.

    Interactioni

    Subunit structurei

    Monomer.By similarity

    Protein-protein interaction databases

    BioGridi30935. 24 interactions.
    DIPiDIP-5139N.
    IntActiP16550. 64 interactions.
    MINTiMINT-561161.

    Structurei

    3D structure databases

    ProteinModelPortaliP16550.
    SMRiP16550. Positions 3-321.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni93 – 942Substrate bindingBy similarity
    Regioni151 – 1544Substrate bindingBy similarity
    Regioni273 – 2753Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the ATP adenylyltransferase family.Curated

    Phylogenomic databases

    GeneTreeiENSGT00390000006636.
    HOGENOMiHOG000248604.
    InParanoidiP16550.
    KOiK00988.
    OMAiECGFPNT.
    OrthoDBiEOG78D7W2.

    Family and domain databases

    InterProiIPR009163. ATP_adenylyltransferase.
    IPR019200. ATP_adenylylTrfase_C.
    IPR011146. HIT-like.
    [Graphical view]
    PfamiPF09830. ATP_transf. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000846. ATP_adenylyltr. 1 hit.
    SUPFAMiSSF54197. SSF54197. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P16550-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSIPADIASL ISDKYKSAFD NGNLKFIQTE TTKTKDPKTS MPYLISHMPS
    60 70 80 90 100
    LIEKPERGQT PEGEDPLGKP EEELTVIPEF GGADNKAYKL LLNKFPVIPE
    110 120 130 140 150
    HTLLVTNEYQ HQTDALTPTD LLTAYKLLCA LDNEESDKRH MVFYNSGPAS
    160 170 180 190 200
    GSSLDHKHLQ ILQMPEKFVT FQDRLCNGKE HFLPTFNTEP LQDAKVSFAH
    210 220 230 240 250
    FVLPMPESEE TVDEDLLAMC YISILQRALT FFQDWLNENP ELKKSYNLML
    260 270 280 290 300
    TKEWICVVPR SKAFSDEMKI GFNSTGYCGM ILTKNDEVFS KITEKPELIN
    310 320
    DILLECGFPN TSGQKPNEYN Y
    Length:321
    Mass (Da):36,493
    Last modified:January 23, 2007 - v4
    Checksum:iA1273537D91482A5
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti100 – 1001E → G in AAA34581 (PubMed:2174812).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M31791 Genomic DNA. Translation: AAA34427.1.
    M35204 Genomic DNA. Translation: AAA34581.1.
    X59720 Genomic DNA. Translation: CAA42394.2.
    BK006937 Genomic DNA. Translation: DAA07435.1.
    PIRiS12946. XXBYP1.
    RefSeqiNP_009880.2. NM_001178695.1.

    Genome annotation databases

    EnsemblFungiiCAA42394; CAA42394; CAA42394.
    YCL050C; YCL050C; YCL050C.
    GeneIDi850307.
    KEGGisce:YCL050C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M31791 Genomic DNA. Translation: AAA34427.1.
    M35204 Genomic DNA. Translation: AAA34581.1.
    X59720 Genomic DNA. Translation: CAA42394.2.
    BK006937 Genomic DNA. Translation: DAA07435.1.
    PIRiS12946. XXBYP1.
    RefSeqiNP_009880.2. NM_001178695.1.

    3D structure databases

    ProteinModelPortaliP16550.
    SMRiP16550. Positions 3-321.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi30935. 24 interactions.
    DIPiDIP-5139N.
    IntActiP16550. 64 interactions.
    MINTiMINT-561161.

    PTM databases

    iPTMnetiP16550.

    Proteomic databases

    MaxQBiP16550.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiCAA42394; CAA42394; CAA42394.
    YCL050C; YCL050C; YCL050C.
    GeneIDi850307.
    KEGGisce:YCL050C.

    Organism-specific databases

    EuPathDBiFungiDB:YCL050C.
    SGDiS000000555. APA1.

    Phylogenomic databases

    GeneTreeiENSGT00390000006636.
    HOGENOMiHOG000248604.
    InParanoidiP16550.
    KOiK00988.
    OMAiECGFPNT.
    OrthoDBiEOG78D7W2.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-12462.
    YEAST:YCL050C-MONOMER.

    Miscellaneous databases

    PROiP16550.

    Family and domain databases

    InterProiIPR009163. ATP_adenylyltransferase.
    IPR019200. ATP_adenylylTrfase_C.
    IPR011146. HIT-like.
    [Graphical view]
    PfamiPF09830. ATP_transf. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000846. ATP_adenylyltr. 1 hit.
    SUPFAMiSSF54197. SSF54197. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Isolation, characterization, and inactivation of the APA1 gene encoding yeast diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase."
      Plateau P., Fromant M., Schmitter J.-M., Buhler J.-M., Blanquet S.
      J. Bacteriol. 171:6437-6445(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 15-33 AND 39-321, FUNCTION, CATALYTIC ACTIVITY.
    2. "Sequencing and enhanced expression of the gene encoding diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) phosphorylase in Saccharomyces cerevisiae."
      Kaushal V., Avila D.M., Hardies S.C., Barnes L.D.
      Gene 95:79-84(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "The complete DNA sequence of yeast chromosome III."
      Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
      , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
      Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Mewes H.-W.
      Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION TO 100.
    5. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    6. "Phosphorolytic cleavage of diadenosine 5',5'''-P1,P4-tetraphosphate. Properties of homogeneous diadenosine 5',5'''-P1,P4-tetraphosphate alpha, beta-phosphorylase from Saccharomyces cerevisiae."
      Guranowski A., Blanquet S.
      J. Biol. Chem. 260:3542-3547(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY.
    7. "Diadenosine 5',5'''-P1, P4-tetraphosphate alpha, beta-phosphorylase from yeast supports nucleoside diphosphate-phosphate exchange."
      Guranowski A., Blanquet S.
      J. Biol. Chem. 261:5943-5946(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "Synthesis of diadenosine 5',5'''-P1,P4-tetraphosphate (AppppA) from adenosine 5'-phosphosulfate and adenosine 5'-triphosphate catalyzed by yeast AppppA phosphorylase."
      Guranowski A., Just G., Holler E., Jakubowski H.
      Biochemistry 27:2959-2964(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    9. "Catabolism of bis(5'-nucleosidyl) tetraphosphates in Saccharomyces cerevisiae."
      Plateau P., Fromant M., Schmitter J.-M., Blanquet S.
      J. Bacteriol. 172:6892-6899(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE.
    10. "A paradoxical increase of a metabolite upon increased expression of its catabolic enzyme: the case of diadenosine tetraphosphate (Ap4A) and Ap4A phosphorylase I in Saccharomyces cerevisiae."
      Avila D.M., Robinson A.K., Kaushal V., Barnes L.D.
      J. Bacteriol. 173:7875-7880(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    11. "An alleged yeast polyphosphate kinase is actually diadenosine-5', 5'''-P1,P4-tetraphosphate alpha,beta-phosphorylase."
      Booth J.W., Guidotti G.
      J. Biol. Chem. 270:19377-19382(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    12. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    13. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    14. "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-60, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    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-60, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "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 THR-60, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    17. "Structures of yeast Apa2 reveal catalytic insights into a canonical AP(4)A phosphorylase of the histidine triad superfamily."
      Hou W.T., Li W.Z., Chen Y., Jiang Y.L., Zhou C.Z.
      J. Mol. Biol. 425:2687-2698(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiAPA1_YEAST
    AccessioniPrimary (citable) accession number: P16550
    Secondary accession number(s): D6VQW6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: January 23, 2007
    Last modified: July 6, 2016
    This is version 146 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 19600 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    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 one 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.