APA2_YEAST
ID APA2_YEAST Reviewed; 325 AA.
AC P22108; D6VTF1;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1991, sequence version 1.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2 {ECO:0000303|PubMed:2174863};
DE Short=Ap4A phosphorylase 2;
DE EC=2.7.7.53 {ECO:0000269|PubMed:2174863};
DE AltName: Full=ADP-sulfurylase {ECO:0000305|PubMed:2174863};
DE EC=2.7.7.5 {ECO:0000269|PubMed:2174863};
DE AltName: Full=ATP adenylyltransferase;
GN Name=APA2 {ECO:0000303|PubMed:2174863};
GN OrderedLocusNames=YDR530C {ECO:0000312|SGD:S000002938}; ORFNames=D9719.33;
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 1-11, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, SUBSTRATE SPECIFICITY, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=YPAL16;
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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [3]
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 [4]
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 [5]
RP 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 [6]
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 [7]
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 [8]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH AMP AND SUBSTRATE,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT, MUTAGENESIS OF HIS-161,
RP AND ACTIVE SITE.
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, but prefers A-containing substrates. Cannot catalyze the
CC reverse reaction. Additionally, this enzyme can also catalyze the
CC phosphorolytic degradation of adenosine 5'-phosphosulfate (AMPS) into
CC ADP and sulfate, the reversible exchange reaction between inorganic
CC phosphate and the beta-phosphate of a nucleoside diphosphate (NDP), and
CC the synthesis of Ap4A from AMPS plus ATP. {ECO:0000269|PubMed:2174863}.
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;
CC Evidence={ECO:0000269|PubMed:2174863};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:2174863, ECO:0000269|PubMed:23628156};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.5 uM for Ap4A {ECO:0000269|PubMed:23628156};
CC Note=kcat is 93.8 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:0000269|PubMed:2174863,
CC ECO:0000269|PubMed:23628156}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
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 1770 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the ATP adenylyltransferase family.
CC {ECO:0000305}.
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DR EMBL; M60265; AAA34428.1; -; Genomic_DNA.
DR EMBL; U33057; AAB64969.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12361.1; -; Genomic_DNA.
DR PIR; A37836; A37836.
DR RefSeq; NP_010819.1; NM_001180838.1.
DR PDB; 4I5T; X-ray; 2.30 A; A/B=1-325.
DR PDB; 4I5V; X-ray; 2.70 A; A/B=1-325.
DR PDB; 4I5W; X-ray; 2.79 A; A/B=1-325.
DR PDBsum; 4I5T; -.
DR PDBsum; 4I5V; -.
DR PDBsum; 4I5W; -.
DR AlphaFoldDB; P22108; -.
DR SMR; P22108; -.
DR BioGRID; 32579; 126.
DR DIP; DIP-4729N; -.
DR STRING; 4932.YDR530C; -.
DR MaxQB; P22108; -.
DR PaxDb; P22108; -.
DR PRIDE; P22108; -.
DR EnsemblFungi; YDR530C_mRNA; YDR530C; YDR530C.
DR GeneID; 852143; -.
DR KEGG; sce:YDR530C; -.
DR SGD; S000002938; APA2.
DR VEuPathDB; FungiDB:YDR530C; -.
DR eggNOG; ENOG502QRAQ; Eukaryota.
DR GeneTree; ENSGT00940000176550; -.
DR HOGENOM; CLU_049915_1_0_1; -.
DR OMA; LPYANHV; -.
DR BioCyc; YEAST:YDR530C-MON; -.
DR PRO; PR:P22108; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P22108; 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; IBA:GO_Central.
DR GO; GO:0009164; P:nucleoside catabolic process; IDA:SGD.
DR GO; GO:0009165; P:nucleotide biosynthetic process; IBA:GO_Central.
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 3D-structure; ATP-binding; Cytoplasm; Direct protein sequencing; Hydrolase;
KW Nucleotide-binding; Nucleotidyltransferase; Nucleus; Reference proteome;
KW Transferase.
FT CHAIN 1..325
FT /note="Diadenosine 5',5'''-P1,P4-tetraphosphate
FT phosphorylase 2"
FT /id="PRO_0000064613"
FT ACT_SITE 161
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 53
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 92..93
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 148
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 154..157
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 163
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 277..279
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 284
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT BINDING 288
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23628156"
FT MUTAGEN 161
FT /note="H->A: Completely abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:23628156"
FT HELIX 6..19
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 21..23
FT /evidence="ECO:0007829|PDB:4I5W"
FT STRAND 29..34
FT /evidence="ECO:0007829|PDB:4I5T"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 41..46
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:4I5T"
FT TURN 67..69
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 76..79
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 81..91
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 101..107
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 117..130
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 143..150
FT /evidence="ECO:0007829|PDB:4I5T"
FT TURN 151..154
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 174..179
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:4I5V"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 204..207
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 217..232
FT /evidence="ECO:0007829|PDB:4I5T"
FT TURN 233..235
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 249..253
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 255..264
FT /evidence="ECO:0007829|PDB:4I5T"
FT TURN 270..272
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 278..282
FT /evidence="ECO:0007829|PDB:4I5T"
FT STRAND 284..287
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 290..298
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 301..310
FT /evidence="ECO:0007829|PDB:4I5T"
FT HELIX 320..322
FT /evidence="ECO:0007829|PDB:4I5T"
SQ SEQUENCE 325 AA; 36841 MW; F2F2A2C900F1144F CRC64;
MIEENLKQKI HDKFVAAKKN GHLKVTHAES KKLKDPQTTT QYWVTFAPSL ALKPDANKNS
DSKAEDPFAN PDEELVVTED LNGDGEYKLL LNKFPVVPEH SLLVTSEFKD QRSALTPSDL
MTAYNVLCSL QGDKDDDVTC ERYLVFYNCG PHSGSSQDHK HLQIMQMPEK FIPFQDVLCN
GKDHFLPTFN AEPLQDDKVS FAHFVLPLPE SSDQVDEDLL AMCYVSLMQR ALTFFQDWTN
ESPELTKSYN VLLTKKWICV VPRSHAKSGP PLMLNINSTG YCGMILVKDR EKLENLTEDP
HLVDKSLLQC GFPNTAGQKP TEYHY
