DDP1_YEAST
ID DDP1_YEAST Reviewed; 188 AA.
AC Q99321; D6W2M1;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=Diphosphoinositol polyphosphate phosphohydrolase DDP1;
DE EC=3.6.1.52;
DE AltName: Full=Diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase;
DE Short=Ap6A hydrolase;
DE AltName: Full=Diadenosine and diphosphoinositol polyphosphate phosphohydrolase 1;
DE AltName: Full=Diadenosine hexaphosphate hydrolase (AMP-forming);
DE EC=3.6.1.60;
GN Name=DDP1; OrderedLocusNames=YOR163W; ORFNames=O3575;
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].
RC STRAIN=S288c / FY1678;
RX PubMed=8972579;
RX DOI=10.1002/(sici)1097-0061(199612)12:15<1563::aid-yea44>3.0.co;2-m;
RA Madania A., Poch O., Tarassov I.A., Winsor B., Martin R.P.;
RT "Analysis of a 22,956 bp region on the right arm of Saccharomyces
RT cerevisiae chromosome XV.";
RL Yeast 12:1563-1573(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP CHARACTERIZATION, PROTEIN SEQUENCE OF 2-13, AND MASS SPECTROMETRY.
RX PubMed=10085096; DOI=10.1074/jbc.274.13.8604;
RA Cartwright J.L., McLennan A.G.;
RT "The Saccharomyces cerevisiae YOR163w gene encodes a diadenosine 5', 5'''-
RT P1,P6-hexaphosphate (Ap6A) hydrolase member of the MutT motif (Nudix
RT hydrolase) family.";
RL J. Biol. Chem. 274:8604-8610(1999).
RN [6]
RP CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=10419486; DOI=10.1074/jbc.274.31.21735;
RA Safrany S.T., Ingram S.W., Cartwright J.L., Falck J.R., McLennan A.G.,
RA Barnes L.D., Shears S.B.;
RT "The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe
RT and Saccharomyces cerevisiae are homologues of the human diphosphoinositol
RT polyphosphate phosphohydrolase. Overlapping substrate specificities in a
RT MutT-type protein.";
RL J. Biol. Chem. 274:21735-21740(1999).
RN [7]
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 [8]
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 [9]
RP IDENTIFICATION BY 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 [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: May eliminate potentially toxic dinucleoside polyphosphates
CC during sporulation. Most active against diadenosine 5',5'''-P1,P6-
CC hexaphosphate (Ap6A). Can also hydrolyze diadenosine 5',5'''-P1,P5-
CC pentaphosphate (Ap5A), adenosine 5'-pentaphosphate, and adenosine 5'-
CC tetraphosphate are also substrates, but not diadenosine 5',5'''-P1,P4-
CC tetraphosphate (Ap4A) or other dinucleotides, mononucleotides,
CC nucleotide sugars, or nucleotide alcohols. Also cleaves a beta-
CC phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol
CC pentakisphosphate) and [PP]2-InsP4 (bisdiphosphoinositol
CC tetrakisphosphate).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=diphospho-myo-inositol polyphosphate + H2O = myo-inositol
CC polyphosphate + phosphate.; EC=3.6.1.52;
CC Evidence={ECO:0000269|PubMed:10419486};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + P(1),P(6)-bis(5'-adenosyl) hexaphosphate = adenosine 5'-
CC pentaphosphate + AMP + 2 H(+); Xref=Rhea:RHEA:32047,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:63740,
CC ChEBI:CHEBI:63813, ChEBI:CHEBI:456215; EC=3.6.1.60;
CC Evidence={ECO:0000269|PubMed:10419486};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + P(1),P(5)-bis(5'-adenosyl) pentaphosphate = adenosine
CC 5'-tetraphosphate + AMP + 2 H(+); Xref=Rhea:RHEA:32051,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:58450,
CC ChEBI:CHEBI:62041, ChEBI:CHEBI:456215; EC=3.6.1.60;
CC Evidence={ECO:0000269|PubMed:10419486};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=31 nM for PP-InsP5 {ECO:0000269|PubMed:10419486};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MASS SPECTROMETRY: Mass=21443; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:10085096};
CC -!- MISCELLANEOUS: Present with 3340 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. DIPP subfamily.
CC {ECO:0000305}.
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DR EMBL; Z75071; CAA99369.1; -; Genomic_DNA.
DR EMBL; U55021; AAB47410.1; -; Genomic_DNA.
DR EMBL; AY558436; AAS56762.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10937.1; -; Genomic_DNA.
DR PIR; S67051; S67051.
DR RefSeq; NP_014806.1; NM_001183582.1.
DR PDB; 7AUI; X-ray; 1.98 A; A=1-188.
DR PDB; 7AUJ; X-ray; 2.10 A; A=1-188.
DR PDB; 7AUK; X-ray; 2.00 A; A=1-188.
DR PDB; 7AUL; X-ray; 1.85 A; A=1-188.
DR PDB; 7AUM; X-ray; 2.07 A; A=1-188.
DR PDB; 7AUN; X-ray; 1.95 A; A=1-188.
DR PDB; 7AUO; X-ray; 2.65 A; A=1-188.
DR PDB; 7AUP; X-ray; 1.85 A; A=1-188.
DR PDB; 7AUQ; X-ray; 2.25 A; A=1-188.
DR PDB; 7AUR; X-ray; 1.65 A; A=1-188.
DR PDB; 7AUS; X-ray; 1.75 A; A=1-188.
DR PDB; 7AUT; X-ray; 1.60 A; A=1-188.
DR PDB; 7AUU; X-ray; 2.45 A; A=1-103, A=127-188.
DR PDBsum; 7AUI; -.
DR PDBsum; 7AUJ; -.
DR PDBsum; 7AUK; -.
DR PDBsum; 7AUL; -.
DR PDBsum; 7AUM; -.
DR PDBsum; 7AUN; -.
DR PDBsum; 7AUO; -.
DR PDBsum; 7AUP; -.
DR PDBsum; 7AUQ; -.
DR PDBsum; 7AUR; -.
DR PDBsum; 7AUS; -.
DR PDBsum; 7AUT; -.
DR PDBsum; 7AUU; -.
DR AlphaFoldDB; Q99321; -.
DR SMR; Q99321; -.
DR BioGRID; 34559; 73.
DR IntAct; Q99321; 3.
DR STRING; 4932.YOR163W; -.
DR iPTMnet; Q99321; -.
DR MaxQB; Q99321; -.
DR PaxDb; Q99321; -.
DR PRIDE; Q99321; -.
DR EnsemblFungi; YOR163W_mRNA; YOR163W; YOR163W.
DR GeneID; 854334; -.
DR KEGG; sce:YOR163W; -.
DR SGD; S000005689; DDP1.
DR VEuPathDB; FungiDB:YOR163W; -.
DR eggNOG; KOG2839; Eukaryota.
DR HOGENOM; CLU_037162_5_3_1; -.
DR InParanoid; Q99321; -.
DR OMA; EDQWPEM; -.
DR BioCyc; YEAST:YOR163W-MON; -.
DR BRENDA; 3.6.1.10; 984.
DR BRENDA; 3.6.1.52; 984.
DR BRENDA; 3.6.1.60; 984.
DR Reactome; R-SCE-1855167; Synthesis of pyrophosphates in the cytosol.
DR SABIO-RK; Q99321; -.
DR PRO; PR:Q99321; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q99321; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0034431; F:bis(5'-adenosyl)-hexaphosphatase activity; IDA:SGD.
DR GO; GO:0034432; F:bis(5'-adenosyl)-pentaphosphatase activity; IDA:SGD.
DR GO; GO:0008486; F:diphosphoinositol-polyphosphate diphosphatase activity; IDA:SGD.
DR GO; GO:0000298; F:endopolyphosphatase activity; IDA:SGD.
DR GO; GO:0052842; F:inositol diphosphate pentakisphosphate diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0052840; F:inositol diphosphate tetrakisphosphate diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0050072; F:m7G(5')pppN diphosphatase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:1990174; F:phosphodiesterase decapping endonuclease activity; IDA:SGD.
DR GO; GO:1901911; P:adenosine 5'-(hexahydrogen pentaphosphate) catabolic process; IBA:GO_Central.
DR GO; GO:1901909; P:diadenosine hexaphosphate catabolic process; IBA:GO_Central.
DR GO; GO:1901907; P:diadenosine pentaphosphate catabolic process; IBA:GO_Central.
DR GO; GO:0015961; P:diadenosine polyphosphate catabolic process; IDA:SGD.
DR GO; GO:0071543; P:diphosphoinositol polyphosphate metabolic process; IBA:GO_Central.
DR GO; GO:0046855; P:inositol phosphate dephosphorylation; IDA:SGD.
DR GO; GO:0006798; P:polyphosphate catabolic process; IDA:SGD.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Hydrolase; Magnesium;
KW Metal-binding; Nucleus; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10085096"
FT CHAIN 2..188
FT /note="Diphosphoinositol polyphosphate phosphohydrolase
FT DDP1"
FT /id="PRO_0000057067"
FT DOMAIN 30..179
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 65..86
FT /note="Nudix box"
FT BINDING 80
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 84
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT TURN 27..29
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 32..40
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 44..51
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:7AUR"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:7AUT"
FT HELIX 73..85
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 87..100
FT /evidence="ECO:0007829|PDB:7AUT"
FT HELIX 107..109
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 120..123
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 129..142
FT /evidence="ECO:0007829|PDB:7AUT"
FT TURN 147..151
FT /evidence="ECO:0007829|PDB:7AUT"
FT STRAND 154..158
FT /evidence="ECO:0007829|PDB:7AUT"
FT HELIX 159..168
FT /evidence="ECO:0007829|PDB:7AUT"
FT HELIX 172..180
FT /evidence="ECO:0007829|PDB:7AUT"
SQ SEQUENCE 188 AA; 21572 MW; 17A39EB060F03184 CRC64;
MGKTADNHGP VRSETAREGR ENQVYSPVTG ARLVAGCICL TPDKKQVLMI TSSAHKKRWI
VPKGGVEKDE PNYETTAQRE TWEEAGCIGK IVANLGTVED MRPPKDWNKD IKQFENSRKD
SEVAKHPPRT EFHFYELEIE NLLDKFPECH KRHRKLYSYT EAKQNLIDAK RPELLEALNR
SAIIKDDK
