YND1_YEAST
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 03-AUG-2022, entry version 173.
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;
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 H(+) + 2 phosphate; 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}.
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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; 99.
DR DIP; DIP-7607N; -.
DR IntAct; P40009; 8.
DR MINT; P40009; -.
DR STRING; 4932.YER005W; -.
DR iPTMnet; P40009; -.
DR MaxQB; P40009; -.
DR PaxDb; P40009; -.
DR PRIDE; P40009; -.
DR EnsemblFungi; YER005W_mRNA; YER005W; YER005W.
DR GeneID; 856722; -.
DR KEGG; sce:YER005W; -.
DR SGD; S000000807; YND1.
DR VEuPathDB; FungiDB:YER005W; -.
DR eggNOG; KOG1386; Eukaryota.
DR GeneTree; ENSGT01050000244974; -.
DR HOGENOM; CLU_010246_3_3_1; -.
DR InParanoid; P40009; -.
DR OMA; QDEIGPP; -.
DR BioCyc; MetaCyc:G3O-30192-MON; -.
DR BioCyc; YEAST:G3O-30192-MON; -.
DR Reactome; R-SCE-8850843; Phosphate bond hydrolysis by NTPDase proteins.
DR UniPathway; UPA00378; -.
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:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0016020; C:membrane; IDA:SGD.
DR GO; GO:0102490; F:8-oxo-dGTP phosphohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0102485; F:dATP phosphohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0102486; F:dCTP phosphohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0102491; F:dGTP phosphohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0102488; F:dTTP phosphohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0102487; F:dUTP phosphohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0102489; F:GTP phosphohydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0004382; F:guanosine-diphosphatase activity; IBA:GO_Central.
DR GO; GO:0017110; F:nucleoside-diphosphatase activity; IDA:SGD.
DR GO; GO:0017111; F:nucleoside-triphosphatase activity; IDA:SGD.
DR GO; GO:0045134; F:uridine-diphosphatase activity; IBA:GO_Central.
DR GO; GO:0009134; P:nucleoside diphosphate catabolic process; IBA:GO_Central.
DR GO; GO:0006486; P:protein glycosylation; IMP:SGD.
DR GO; GO:0006665; P:sphingolipid metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0006256; P:UDP catabolic process; IBA:GO_Central.
DR InterPro; IPR000407; GDA1_CD39_NTPase.
DR PANTHER; PTHR11782; PTHR11782; 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
