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Protein

Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2

Gene

APA2

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, but prefers A-containing substrates. 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.1 Publication

Catalytic activityi

ADP + ATP = phosphate + P1,P(4)-bis(5'-adenosyl) tetraphosphate.3 Publications
ADP + sulfate = phosphate + adenylyl sulfate.1 Publication

Cofactori

a divalent metal cation2 Publications

Kineticsi

kcat is 93.8 sec(-1) with Ap4A as substrate.1 Publication

  1. KM=4.5 µM for Ap4A1 Publication

    pH dependencei

    Optimum pH is 7.5.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei53 – 531Substrate1 Publication
    Binding sitei148 – 1481Substrate1 Publication
    Active sitei161 – 1611Nucleophile1 Publication
    Binding sitei163 – 1631Substrate1 Publication
    Binding sitei284 – 2841Substrate; via carbonyl oxygen1 Publication
    Binding sitei288 – 2881Substrate1 Publication

    GO - Molecular functioni

    GO - Biological processi

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

    Keywords - Molecular functioni

    Hydrolase, Nucleotidyltransferase, Transferase

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:YDR530C-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 21 Publication (EC:2.7.7.531 Publication)
    Short name:
    Ap4A phosphorylase 2
    Alternative name(s):
    ADP-sulfurylase1 Publication (EC:2.7.7.51 Publication)
    ATP adenylyltransferase
    Gene namesi
    Name:APA21 Publication
    Ordered Locus Names:YDR530CImported
    ORF Names:D9719.33
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome IV

    Organism-specific databases

    EuPathDBiFungiDB:YDR530C.
    SGDiS000002938. APA2.

    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

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi161 – 1611H → A: Completely abolishes catalytic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 325325Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2PRO_0000064613Add
    BLAST

    Proteomic databases

    MaxQBiP22108.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    BioGridi32579. 26 interactions.
    DIPiDIP-4729N.
    MINTiMINT-546233.

    Structurei

    Secondary structure

    1
    325
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1914Combined sources
    Beta strandi21 – 233Combined sources
    Beta strandi29 – 346Combined sources
    Turni36 – 383Combined sources
    Beta strandi41 – 466Combined sources
    Helixi48 – 514Combined sources
    Turni67 – 693Combined sources
    Helixi73 – 753Combined sources
    Beta strandi76 – 794Combined sources
    Beta strandi81 – 9111Combined sources
    Beta strandi101 – 1077Combined sources
    Helixi117 – 13014Combined sources
    Beta strandi137 – 1393Combined sources
    Beta strandi143 – 1508Combined sources
    Turni151 – 1544Combined sources
    Beta strandi161 – 1666Combined sources
    Helixi174 – 1796Combined sources
    Beta strandi188 – 1903Combined sources
    Beta strandi197 – 2015Combined sources
    Beta strandi204 – 2074Combined sources
    Helixi212 – 2143Combined sources
    Helixi217 – 23216Combined sources
    Turni233 – 2353Combined sources
    Beta strandi249 – 2535Combined sources
    Beta strandi255 – 26410Combined sources
    Turni270 – 2723Combined sources
    Helixi278 – 2825Combined sources
    Beta strandi284 – 2874Combined sources
    Helixi290 – 2989Combined sources
    Helixi301 – 31010Combined sources
    Helixi320 – 3223Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4I5TX-ray2.30A/B1-325[»]
    4I5VX-ray2.70A/B1-325[»]
    4I5WX-ray2.79A/B1-325[»]
    ProteinModelPortaliP22108.
    SMRiP22108. Positions 1-316.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni92 – 932Substrate binding1 Publication
    Regioni154 – 1574Substrate binding1 Publication
    Regioni277 – 2793Substrate binding1 Publication

    Sequence similaritiesi

    Belongs to the ATP adenylyltransferase family.Curated

    Phylogenomic databases

    GeneTreeiENSGT00390000006636.
    HOGENOMiHOG000248604.
    KOiK00988.
    OMAiCERYLVF.
    OrthoDBiEOG78D7W2.

    Family and domain databases

    Gene3Di3.30.428.10. 1 hit.
    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.

    P22108-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIEENLKQKI HDKFVAAKKN GHLKVTHAES KKLKDPQTTT QYWVTFAPSL
    60 70 80 90 100
    ALKPDANKNS DSKAEDPFAN PDEELVVTED LNGDGEYKLL LNKFPVVPEH
    110 120 130 140 150
    SLLVTSEFKD QRSALTPSDL MTAYNVLCSL QGDKDDDVTC ERYLVFYNCG
    160 170 180 190 200
    PHSGSSQDHK HLQIMQMPEK FIPFQDVLCN GKDHFLPTFN AEPLQDDKVS
    210 220 230 240 250
    FAHFVLPLPE SSDQVDEDLL AMCYVSLMQR ALTFFQDWTN ESPELTKSYN
    260 270 280 290 300
    VLLTKKWICV VPRSHAKSGP PLMLNINSTG YCGMILVKDR EKLENLTEDP
    310 320
    HLVDKSLLQC GFPNTAGQKP TEYHY
    Length:325
    Mass (Da):36,841
    Last modified:August 1, 1991 - v1
    Checksum:iF2F2A2C900F1144F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M60265 Genomic DNA. Translation: AAA34428.1.
    U33057 Genomic DNA. Translation: AAB64969.1.
    BK006938 Genomic DNA. Translation: DAA12361.1.
    PIRiA37836.
    RefSeqiNP_010819.1. NM_001180838.1.

    Genome annotation databases

    EnsemblFungiiYDR530C; YDR530C; YDR530C.
    GeneIDi852143.
    KEGGisce:YDR530C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M60265 Genomic DNA. Translation: AAA34428.1.
    U33057 Genomic DNA. Translation: AAB64969.1.
    BK006938 Genomic DNA. Translation: DAA12361.1.
    PIRiA37836.
    RefSeqiNP_010819.1. NM_001180838.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4I5TX-ray2.30A/B1-325[»]
    4I5VX-ray2.70A/B1-325[»]
    4I5WX-ray2.79A/B1-325[»]
    ProteinModelPortaliP22108.
    SMRiP22108. Positions 1-316.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi32579. 26 interactions.
    DIPiDIP-4729N.
    MINTiMINT-546233.

    Proteomic databases

    MaxQBiP22108.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYDR530C; YDR530C; YDR530C.
    GeneIDi852143.
    KEGGisce:YDR530C.

    Organism-specific databases

    EuPathDBiFungiDB:YDR530C.
    SGDiS000002938. APA2.

    Phylogenomic databases

    GeneTreeiENSGT00390000006636.
    HOGENOMiHOG000248604.
    KOiK00988.
    OMAiCERYLVF.
    OrthoDBiEOG78D7W2.

    Enzyme and pathway databases

    BioCyciYEAST:YDR530C-MONOMER.

    Miscellaneous databases

    PROiP22108.

    Family and domain databases

    Gene3Di3.30.428.10. 1 hit.
    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. "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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-11, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE.
      Strain: YPAL16.
    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. "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.
    5. "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: CATALYTIC ACTIVITY.
    6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    8. "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: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH AMP AND SUBSTRATE, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT, MUTAGENESIS OF HIS-161, ACTIVE SITE.

    Entry informationi

    Entry nameiAPA2_YEAST
    AccessioniPrimary (citable) accession number: P22108
    Secondary accession number(s): D6VTF1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1991
    Last sequence update: August 1, 1991
    Last modified: June 8, 2016
    This is version 128 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 1770 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 IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: 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.