ID   YND1_YEAST              Reviewed;         630 AA.
AC   P40009; D3DLQ1; Q6B252;
DT   01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1995, sequence version 1.
DT   02-SEP-2026, entry version 191.
DE   RecName: Full=Golgi apyrase;
DE            EC=3.6.1.5;
DE   AltName: Full=ATP-diphosphatase;
DE   AltName: Full=ATP-diphosphohydrolase;
DE   AltName: Full=Adenosine diphosphatase;
DE            Short=ADPase;
DE   AltName: Full=Golgi nucleoside diphosphatase;
DE   AltName: Full=Yeast nucleoside diphosphatase 1;
GN   Name=YND1; OrderedLocusNames=YER005W;
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], FUNCTION, AND SUBCELLULAR LOCATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=10409709; DOI=10.1074/jbc.274.30.21450;
RA   Gao X.D., Kaigorodov V., Jigami Y.;
RT   "YND1, a homologue of GDA1, encodes membrane-bound apyrase required for
RT   Golgi N- and O-glycosylation in Saccharomyces cerevisiae.";
RL   J. Biol. Chem. 274:21450-21456(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169868; DOI=10.1038/387s078;
RA   Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA   Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA   Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA   Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA   Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA   Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA   Botstein D., Davis R.W.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL   Nature 387:78-81(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   ENZYMATIC ACTIVITY, ACTIVITY REGULATION, AND INTERACTION WITH VMA13.
RX   PubMed=10954728; DOI=10.1074/jbc.m006932200;
RA   Zhong X., Malhotra R., Guidotti G.;
RT   "Regulation of yeast ectoapyrase ynd1p activity by activator subunit Vma13p
RT   of vacuolar H+-ATPase.";
RL   J. Biol. Chem. 275:35592-35599(2000).
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   FUNCTION, ENZYMATIC ACTIVITY, INTERACTION WITH CDC55, DISRUPTION PHENOTYPE,
RP   AND MUTAGENESIS OF GLU-152 AND SER-189.
RX   PubMed=16227198; DOI=10.1074/jbc.m507281200;
RA   Maoz T., Koren R., Ben-Ari I., Kleinberger T.;
RT   "YND1 interacts with CDC55 and is a novel mediator of E4orf4-induced
RT   toxicity.";
RL   J. Biol. Chem. 280:41270-41277(2005).
RN   [9]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=16702413; DOI=10.1534/genetics.105.053025;
RA   Valachovic M., Bareither B.M., Bhuiyan M.S.A., Eckstein J., Barbuch R.,
RA   Balderes D., Wilcox L., Sturley S.L., Dickson R.C., Bard M.;
RT   "Cumulative mutations affecting sterol biosynthesis in the yeast
RT   Saccharomyces cerevisiae result in synthetic lethality that is suppressed
RT   by alterations in sphingolipid profiles.";
RL   Genetics 173:1893-1908(2006).
RN   [10]
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   [11]
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: Catalyzes the hydrolysis of phosphoanhydride bonds of
CC       nucleoside tri- and di-phosphates. Has equal high activity toward
CC       ADP/ATP, GDP/GTP, and UDP/UTP and approximately 50% less toward CDP/CTP
CC       and thiamine pyrophosphate. Has no activity toward GMP. Required for
CC       Golgi glycosylation and cell wall integrity. Together with CDC55,
CC       required for adenovirus E4orf4 (early region 4 open reading frame 4)
CC       induced toxicity, the apyrase activity is not required for this
CC       function. Plays a role in sphingolipid synthesis.
CC       {ECO:0000269|PubMed:10409709, ECO:0000269|PubMed:16227198,
CC       ECO:0000269|PubMed:16702413}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a ribonucleoside 5'-triphosphate + 2 H2O = a ribonucleoside
CC         5'-phosphate + 2 phosphate + 2 H(+); Xref=Rhea:RHEA:36795,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58043, ChEBI:CHEBI:61557; EC=3.6.1.5;
CC         Evidence={ECO:0000269|PubMed:10954728, ECO:0000269|PubMed:16227198};
CC   -!- COFACTOR:
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000250};
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=A divalent cation Ca(2+), Mg(2+) or Mn(2+). {ECO:0000250};
CC   -!- ACTIVITY REGULATION: Activity is inhibited both by interaction with
CC       VMA13 and by V-ATPase acidification of the lumen. The activity of VMA13
CC       is not required for YND1 inhibition. {ECO:0000269|PubMed:10954728}.
CC   -!- PATHWAY: Protein modification; protein glycosylation.
CC   -!- SUBUNIT: Interacts with activator subunit VMA13 of vacuolar H(+)-
CC       ATPase. Interacts with CDC55; this interaction is disrupted by
CC       adenovirus E4orf4, which remains associated with both YND1 and CDC55.
CC       {ECO:0000269|PubMed:10954728, ECO:0000269|PubMed:16227198}.
CC   -!- SUBCELLULAR LOCATION: Golgi apparatus {ECO:0000269|PubMed:10409709,
CC       ECO:0000269|PubMed:14562095}. Membrane {ECO:0000305}; Single-pass
CC       membrane protein {ECO:0000305}.
CC   -!- DISRUPTION PHENOTYPE: Cells are partially resistant to E4orf4 and can
CC       partially suppress the spindle checkpoint defect in CDC55 deletion
CC       mutant. Does not suppress the rapamycin-resistance of CDC55 deletion
CC       mutant. YND1 and CDC55 double mutant is fully resistant to E4orf4.
CC       Deletion mutant suppresses the synthetic lethality of triple mutants,
CC       where UPC2 and ECM22 are knocked out along with either HAP1, ERG6 or
CC       ERG28. {ECO:0000269|PubMed:16227198, ECO:0000269|PubMed:16702413}.
CC   -!- MISCELLANEOUS: Present with 450 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the GDA1/CD39 NTPase family. {ECO:0000305}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AF203695; AAF17573.1; -; Genomic_DNA.
DR   EMBL; U18778; AAB64538.1; -; Genomic_DNA.
DR   EMBL; AY692878; AAT92897.1; -; Genomic_DNA.
DR   EMBL; BK006939; DAA07655.1; -; Genomic_DNA.
DR   PIR; S50463; S50463.
DR   RefSeq; NP_010920.3; NM_001178896.3.
DR   AlphaFoldDB; P40009; -.
DR   SMR; P40009; -.
DR   BioGRID; 36735; 106.
DR   DIP; DIP-7607N; -.
DR   FunCoup; P40009; 316.
DR   IntAct; P40009; 8.
DR   MINT; P40009; -.
DR   STRING; 4932.YER005W; -.
DR   iPTMnet; P40009; -.
DR   PaxDb; 4932-YER005W; -.
DR   PeptideAtlas; P40009; -.
DR   EnsemblFungi; YER005W_mRNA; YER005W; YER005W.
DR   GeneID; 856722; -.
DR   KEGG; sce:YER005W; -.
DR   AGR; SGD:S000000807; -.
DR   SGD; S000000807; YND1.
DR   VEuPathDB; FungiDB:YER005W; -.
DR   eggNOG; KOG1386; Eukaryota.
DR   HOGENOM; CLU_010246_3_3_1; -.
DR   InParanoid; P40009; -.
DR   OMA; HESIGFM; -.
DR   OrthoDB; 6372431at2759; -.
DR   BioCyc; MetaCyc:G3O-30192-MONOMER; -.
DR   BioCyc; YEAST:G3O-30192-MONOMER; -.
DR   Reactome; R-SCE-8850843; Phosphate bond hydrolysis by NTPDase proteins.
DR   UniPathway; UPA00378; -.
DR   BioGRID-ORCS; 856722; 4 hits in 10 CRISPR screens.
DR   PRO; PR:P40009; -.
DR   Proteomes; UP000002311; Chromosome V.
DR   RNAct; P40009; protein.
DR   GO; GO:0005794; C:Golgi apparatus; HDA:SGD.
DR   GO; GO:0000139; C:Golgi membrane; IDA:SGD.
DR   GO; GO:0016020; C:membrane; IBA:GO_Central.
DR   GO; GO:0004050; F:apyrase activity; IEA:UniProtKB-EC.
DR   GO; GO:0004382; F:GDP phosphatase activity; IBA:GO_Central.
DR   GO; GO:0017110; F:nucleoside diphosphate phosphatase activity; IDA:SGD.
DR   GO; GO:0017111; F:ribonucleoside triphosphate phosphatase activity; IDA:SGD.
DR   GO; GO:0045134; F:UDP phosphatase activity; IBA:GO_Central.
DR   GO; GO:0046036; P:CTP metabolic process; IBA:GO_Central.
DR   GO; GO:0009101; P:glycoprotein biosynthetic process; IMP:SGD.
DR   GO; GO:0006256; P:UDP catabolic process; IBA:GO_Central.
DR   CDD; cd24039; ASKHA_NBD_YND1-like; 1.
DR   Gene3D; 3.30.420.40; -; 1.
DR   Gene3D; 3.30.420.150; Exopolyphosphatase. Domain 2; 1.
DR   InterPro; IPR000407; GDA1_CD39_NTPase.
DR   PANTHER; PTHR11782; ADENOSINE/GUANOSINE DIPHOSPHATASE; 1.
DR   PANTHER; PTHR11782:SF121; NUCLEOSIDE-DIPHOSPHATASE MIG-23; 1.
DR   Pfam; PF01150; GDA1_CD39; 1.
DR   PROSITE; PS01238; GDA1_CD39_NTPASE; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Golgi apparatus; Hydrolase; Lipid metabolism; Membrane;
KW   Nucleotide-binding; Reference proteome; Sphingolipid metabolism;
KW   Transmembrane; Transmembrane helix.
FT   CHAIN           1..630
FT                   /note="Golgi apyrase"
FT                   /id="PRO_0000209920"
FT   TOPO_DOM        1..500
FT                   /note="Lumenal"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        501..517
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TOPO_DOM        518..630
FT                   /note="Cytoplasmic"
FT                   /evidence="ECO:0000255"
FT   REGION          586..606
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        152
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   MUTAGEN         152
FT                   /note="E->Q: Expressed at lower levels. GTPase activity
FT                   reduced."
FT                   /evidence="ECO:0000269|PubMed:16227198"
FT   MUTAGEN         189
FT                   /note="S->A: Expressed at the same level as wild-type.
FT                   GTPase and GDPase activities decreased more than 20-fold
FT                   toward GTP and 3-fold for GDP."
FT                   /evidence="ECO:0000269|PubMed:16227198"
FT   CONFLICT        498
FT                   /note="S -> P (in Ref. 4; AAT92897)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   630 AA;  71852 MW;  02F8D24A78212544 CRC64;
     MLIENTNDRF GIVIDAGSSG SRIHVFKWQD TESLLHATNQ DSQSILQSVP HIHQEKDWTF
     KLNPGLSSFE KKPQDAYKSH IKPLLDFAKN IIPESHWSSC PVFIQATAGM RLLPQDIQSS
     ILDGLCQGLK HPAEFLVEDC SAQIQVIDGE TEGLYGWLGL NYLYGHFNDY NPEVSDHFTF
     GFMDMGGAST QIAFAPHDSG EIARHRDDIA TIFLRSVNGD LQKWDVFVST WLGFGANQAR
     RRYLAQLINT LPENTNDYEN DDFSTRNLND PCMPRGSSTD FEFKDTIFHI AGSGNYEQCT
     KSIYPLLLKN MPCDDEPCLF NGVHAPRIDF ANDKFIGTSE YWYTANDVFK LGGEYNFDKF
     SKSLREFCNS NWTQILANSD KGVYNSIPEN FLKDACFKGN WVLNILHEGF DMPRIDVDAE
     NVNDRPLFQS VEKVEERELS WTLGRILLYA SGSILAGNDD FMVGIAPSER RTKLTGKKFI
     PGKLLESDQL RKQSSSLSNK GFLMWFAIIC CIFYLIFHRS HIIRRRFSGL YNITKDFKTG
     IRRRLKFLRR SDPFSRLEEG ELGTDVDGFK DVYRMKSSSM FDLGKSSATM QREHEPQRTA
     SQSANLAPSN LRPAFSMADF SKFKDSRLYD
//