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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

Manual assertion based on experiment ini

  1. KM=4.5 µM for Ap4A1 Publication

    pH dependencei

    Optimum pH is 7.5.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei53Substrate1 Publication1
    Binding sitei148Substrate1 Publication1
    Active sitei161Nucleophile1 Publication1
    Binding sitei163Substrate1 Publication1
    Binding sitei284Substrate; via carbonyl oxygen1 Publication1
    Binding sitei288Substrate1 Publication1

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi161H → A: Completely abolishes catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000646131 – 325Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2Add BLAST325

    Proteomic databases

    MaxQBiP22108.
    PRIDEiP22108.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1325
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 19Combined sources14
    Beta strandi21 – 23Combined sources3
    Beta strandi29 – 34Combined sources6
    Turni36 – 38Combined sources3
    Beta strandi41 – 46Combined sources6
    Helixi48 – 51Combined sources4
    Turni67 – 69Combined sources3
    Helixi73 – 75Combined sources3
    Beta strandi76 – 79Combined sources4
    Beta strandi81 – 91Combined sources11
    Beta strandi101 – 107Combined sources7
    Helixi117 – 130Combined sources14
    Beta strandi137 – 139Combined sources3
    Beta strandi143 – 150Combined sources8
    Turni151 – 154Combined sources4
    Beta strandi161 – 166Combined sources6
    Helixi174 – 179Combined sources6
    Beta strandi188 – 190Combined sources3
    Beta strandi197 – 201Combined sources5
    Beta strandi204 – 207Combined sources4
    Helixi212 – 214Combined sources3
    Helixi217 – 232Combined sources16
    Turni233 – 235Combined sources3
    Beta strandi249 – 253Combined sources5
    Beta strandi255 – 264Combined sources10
    Turni270 – 272Combined sources3
    Helixi278 – 282Combined sources5
    Beta strandi284 – 287Combined sources4
    Helixi290 – 298Combined sources9
    Helixi301 – 310Combined sources10
    Helixi320 – 322Combined sources3

    3D structure databases

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

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni92 – 93Substrate binding1 Publication2
    Regioni154 – 157Substrate binding1 Publication4
    Regioni277 – 279Substrate binding1 Publication3

    Sequence similaritiesi

    Belongs to the ATP adenylyltransferase family.Curated

    Phylogenomic databases

    GeneTreeiENSGT00390000006636.
    HOGENOMiHOG000248604.
    KOiK00988.
    OMAiITREFKS.
    OrthoDBiEOG092C3O1J.

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4I5TX-ray2.30A/B1-325[»]
    4I5VX-ray2.70A/B1-325[»]
    4I5WX-ray2.79A/B1-325[»]
    ProteinModelPortaliP22108.
    SMRiP22108.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    MaxQBiP22108.
    PRIDEiP22108.

    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.
    OMAiITREFKS.
    OrthoDBiEOG092C3O1J.

    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...

    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: November 2, 2016
    This is version 131 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.