APA1_YEAST
ID APA1_YEAST Reviewed; 321 AA.
AC P16550; D6VQW6;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=Protein APA1;
DE Includes:
DE RecName: Full=Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 1 {ECO:0000303|PubMed:2556364};
DE Short=Ap4A phosphorylase 1;
DE EC=2.7.7.53 {ECO:0000269|PubMed:2556364};
DE AltName: Full=ADP-sulfurylase {ECO:0000303|PubMed:2556364};
DE EC=2.7.7.5 {ECO:0000269|PubMed:2556364};
DE AltName: Full=ATP adenylyltransferase;
DE AltName: Full=Diadenosine tetraphosphate alpha,beta-phosphorylase (ADP-forming) {ECO:0000303|PubMed:2982863};
GN Name=APA1 {ECO:0000303|PubMed:2556364};
GN Synonyms=DTP {ECO:0000303|PubMed:2174812};
GN OrderedLocusNames=YCL050C {ECO:0000312|SGD:S000000555}; ORFNames=YCL50C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 15-33 AND 39-321,
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=2556364; DOI=10.1128/jb.171.12.6437-6445.1989;
RA Plateau P., Fromant M., Schmitter J.-M., Buhler J.-M., Blanquet S.;
RT "Isolation, characterization, and inactivation of the APA1 gene encoding
RT yeast diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase.";
RL J. Bacteriol. 171:6437-6445(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2174812; DOI=10.1016/0378-1119(90)90416-o;
RA Kaushal V., Avila D.M., Hardies S.C., Barnes L.D.;
RT "Sequencing and enhanced expression of the gene encoding diadenosine
RT 5',5'''-P1,P4-tetraphosphate (Ap4A) phosphorylase in Saccharomyces
RT cerevisiae.";
RL Gene 95:79-84(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=1574125; DOI=10.1038/357038a0;
RA Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M.,
RA Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G.,
RA Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A.,
RA Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M., Carcano C.,
RA Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M.,
RA Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C.,
RA Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F.,
RA Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C.,
RA Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E.,
RA Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P.,
RA Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J.,
RA Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P.,
RA Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M.,
RA Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P.,
RA Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G.,
RA Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E.,
RA Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F.,
RA Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L.,
RA Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J.,
RA Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M.,
RA Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A.,
RA Richterich P., Roberts A.B., Rodriguez F., Sanz E.,
RA Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J.,
RA Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I.,
RA Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M.,
RA Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M.,
RA Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D.,
RA Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K.,
RA Sgouros J.G.;
RT "The complete DNA sequence of yeast chromosome III.";
RL Nature 357:38-46(1992).
RN [4]
RP SEQUENCE REVISION TO 100.
RA Mewes H.-W.;
RL Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [6]
RP CATALYTIC ACTIVITY.
RX PubMed=2982863; DOI=10.1016/s0021-9258(19)83656-6;
RA Guranowski A., Blanquet S.;
RT "Phosphorolytic cleavage of diadenosine 5',5'''-P1,P4-tetraphosphate.
RT Properties of homogeneous diadenosine 5',5'''-P1,P4-tetraphosphate alpha,
RT beta-phosphorylase from Saccharomyces cerevisiae.";
RL J. Biol. Chem. 260:3542-3547(1985).
RN [7]
RP FUNCTION.
RX PubMed=3009435; DOI=10.1016/s0021-9258(17)38474-0;
RA Guranowski A., Blanquet S.;
RT "Diadenosine 5',5'''-P1, P4-tetraphosphate alpha, beta-phosphorylase from
RT yeast supports nucleoside diphosphate-phosphate exchange.";
RL J. Biol. Chem. 261:5943-5946(1986).
RN [8]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=2840953; DOI=10.1021/bi00408a044;
RA Guranowski A., Just G., Holler E., Jakubowski H.;
RT "Synthesis of diadenosine 5',5'''-P1,P4-tetraphosphate (AppppA) from
RT adenosine 5'-phosphosulfate and adenosine 5'-triphosphate catalyzed by
RT yeast AppppA phosphorylase.";
RL Biochemistry 27:2959-2964(1988).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=2174863; DOI=10.1128/jb.172.12.6892-6899.1990;
RA Plateau P., Fromant M., Schmitter J.-M., Blanquet S.;
RT "Catabolism of bis(5'-nucleosidyl) tetraphosphates in Saccharomyces
RT cerevisiae.";
RL J. Bacteriol. 172:6892-6899(1990).
RN [10]
RP FUNCTION.
RX PubMed=1660456; DOI=10.1128/jb.173.24.7875-7880.1991;
RA Avila D.M., Robinson A.K., Kaushal V., Barnes L.D.;
RT "A paradoxical increase of a metabolite upon increased expression of its
RT catabolic enzyme: the case of diadenosine tetraphosphate (Ap4A) and Ap4A
RT phosphorylase I in Saccharomyces cerevisiae.";
RL J. Bacteriol. 173:7875-7880(1991).
RN [11]
RP FUNCTION.
RX PubMed=7642617; DOI=10.1074/jbc.270.33.19377;
RA Booth J.W., Guidotti G.;
RT "An alleged yeast polyphosphate kinase is actually diadenosine-5', 5'''-
RT P1,P4-tetraphosphate alpha,beta-phosphorylase.";
RL J. Biol. Chem. 270:19377-19382(1995).
RN [12]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [13]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-60, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-60, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-60, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [17]
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=23628156; DOI=10.1016/j.jmb.2013.04.018;
RA Hou W.T., Li W.Z., Chen Y., Jiang Y.L., Zhou C.Z.;
RT "Structures of yeast Apa2 reveal catalytic insights into a canonical AP(4)A
RT phosphorylase of the histidine triad superfamily.";
RL J. Mol. Biol. 425:2687-2698(2013).
CC -!- FUNCTION: Ap4A phosphorylase catalyzes the phosphorolytic degradation
CC of bis(5'-adenosyl) tetraphosphate (Ap4A) into ADP and ATP. Can also
CC use other Np4N' nucleotides (where N and N' stand for A,C,G or U) as
CC substrates with equal efficiency. Cannot catalyze the reverse reaction.
CC Additionally, this enzyme can also catalyze the phosphorolytic
CC degradation of adenosine 5'-phosphosulfate (AMPS) into ADP and sulfate,
CC the reversible exchange reaction between inorganic phosphate and the
CC beta-phosphate of a nucleoside diphosphate (NDP), and the synthesis of
CC Ap4A from AMPS plus ATP. {ECO:0000269|PubMed:1660456,
CC ECO:0000269|PubMed:2174863, ECO:0000269|PubMed:2556364,
CC ECO:0000269|PubMed:2840953, ECO:0000269|PubMed:3009435,
CC ECO:0000269|PubMed:7642617}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ADP + ATP + H(+) = P(1),P(4)-bis(5'-adenosyl) tetraphosphate +
CC phosphate; Xref=Rhea:RHEA:16577, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58141,
CC ChEBI:CHEBI:456216; EC=2.7.7.53;
CC Evidence={ECO:0000269|PubMed:2174863, ECO:0000269|PubMed:2556364,
CC ECO:0000269|PubMed:2982863};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ADP + H(+) + sulfate = adenosine 5'-phosphosulfate +
CC phosphate; Xref=Rhea:RHEA:16529, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16189, ChEBI:CHEBI:43474, ChEBI:CHEBI:58243,
CC ChEBI:CHEBI:456216; EC=2.7.7.5; Evidence={ECO:0000269|PubMed:2174863,
CC ECO:0000269|PubMed:2556364};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:2174863};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=39.3 uM for Ap4A {ECO:0000269|PubMed:23628156};
CC Note=kcat is 81.2 sec(-1) with Ap4A as substrate.
CC {ECO:0000269|PubMed:23628156};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:23628156};
CC -!- SUBUNIT: Monomer. {ECO:0000250|UniProtKB:P22108}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- PTM: The N-terminus is blocked. {ECO:0000305|PubMed:2556364}.
CC -!- DISRUPTION PHENOTYPE: Inactivation of both APA1 and APA2 promotes a
CC great increase in the cellular concentration of bis(5'-nuceleosidyl)
CC tetraphosphate nucleotides. {ECO:0000269|PubMed:2174863}.
CC -!- MISCELLANEOUS: Present with 19600 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the ATP adenylyltransferase family.
CC {ECO:0000305}.
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DR EMBL; M31791; AAA34427.1; -; Genomic_DNA.
DR EMBL; M35204; AAA34581.1; -; Genomic_DNA.
DR EMBL; X59720; CAA42394.2; -; Genomic_DNA.
DR EMBL; BK006937; DAA07435.1; -; Genomic_DNA.
DR PIR; S12946; XXBYP1.
DR RefSeq; NP_009880.2; NM_001178695.1.
DR AlphaFoldDB; P16550; -.
DR SMR; P16550; -.
DR BioGRID; 30935; 69.
DR DIP; DIP-5139N; -.
DR IntAct; P16550; 65.
DR MINT; P16550; -.
DR STRING; 4932.YCL050C; -.
DR iPTMnet; P16550; -.
DR MaxQB; P16550; -.
DR PaxDb; P16550; -.
DR PRIDE; P16550; -.
DR EnsemblFungi; YCL050C_mRNA; YCL050C; YCL050C.
DR GeneID; 850307; -.
DR KEGG; sce:YCL050C; -.
DR SGD; S000000555; APA1.
DR VEuPathDB; FungiDB:YCL050C; -.
DR eggNOG; ENOG502QRAQ; Eukaryota.
DR GeneTree; ENSGT00940000176550; -.
DR HOGENOM; CLU_049915_1_0_1; -.
DR InParanoid; P16550; -.
DR OMA; GLWFFNS; -.
DR BioCyc; MetaCyc:YCL050C-MON; -.
DR BioCyc; YEAST:YCL050C-MON; -.
DR PRO; PR:P16550; -.
DR Proteomes; UP000002311; Chromosome III.
DR RNAct; P16550; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0003877; F:ATP adenylyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008796; F:bis(5'-nucleosyl)-tetraphosphatase activity; IDA:SGD.
DR GO; GO:0004780; F:sulfate adenylyltransferase (ADP) activity; IDA:SGD.
DR GO; GO:0009164; P:nucleoside catabolic process; IDA:SGD.
DR GO; GO:0009165; P:nucleotide biosynthetic process; IDA:SGD.
DR Gene3D; 3.30.428.70; -; 1.
DR InterPro; IPR009163; Ap4A_phos1/2.
DR InterPro; IPR043171; Ap4A_phos1/2-like.
DR InterPro; IPR045759; Ap4A_phos1/2_N.
DR InterPro; IPR019200; ATP_adenylylTrfase_C.
DR InterPro; IPR036265; HIT-like_sf.
DR PANTHER; PTHR38420; PTHR38420; 1.
DR Pfam; PF19327; Ap4A_phos_N; 1.
DR Pfam; PF09830; ATP_transf; 1.
DR PIRSF; PIRSF000846; ATP_adenylyltr; 1.
DR SUPFAM; SSF54197; SSF54197; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Direct protein sequencing; Hydrolase;
KW Nucleotide-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein;
KW Reference proteome; Transferase.
FT CHAIN 1..321
FT /note="Protein APA1"
FT /id="PRO_0000064611"
FT REGION 50..70
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 158
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 54
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 93..94
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 145
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 151..154
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 160
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 273..275
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 280
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT BINDING 284
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT SITE 160
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P22108"
FT MOD_RES 60
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT CONFLICT 100
FT /note="E -> G (in Ref. 2; AAA34581)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 321 AA; 36493 MW; A1273537D91482A5 CRC64;
MSIPADIASL ISDKYKSAFD NGNLKFIQTE TTKTKDPKTS MPYLISHMPS LIEKPERGQT
PEGEDPLGKP EEELTVIPEF GGADNKAYKL LLNKFPVIPE HTLLVTNEYQ HQTDALTPTD
LLTAYKLLCA LDNEESDKRH MVFYNSGPAS GSSLDHKHLQ ILQMPEKFVT FQDRLCNGKE
HFLPTFNTEP LQDAKVSFAH FVLPMPESEE TVDEDLLAMC YISILQRALT FFQDWLNENP
ELKKSYNLML TKEWICVVPR SKAFSDEMKI GFNSTGYCGM ILTKNDEVFS KITEKPELIN
DILLECGFPN TSGQKPNEYN Y
