P40009 (YND1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Golgi apyrase
EC=3.6.1.5

Alternative name(s):
ATP-diphosphatase
ATP-diphosphohydrolase
Adenosine diphosphatase
Short name=ADPase
Golgi nucleoside diphosphatase
Yeast nucleoside diphosphatase 1

Gene names

Name:	YND1
Ordered Locus Names:	YER005W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	630 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates. Has equal high activity toward ADP/ATP, GDP/GTP, and UDP/UTP and approximately 50% less toward CDP/CTP and thiamine pyrophosphate. Has no activity toward GMP. Required for Golgi glycosylation and cell wall integrity. Together with CDC55, required for adenovirus E4orf4 (early region 4 open reading frame 4) induced toxicity, the apyrase activity is not required for this function. Plays a role in sphingolipid synthesis. Ref.1 Ref.8 Ref.9
Catalytic activity	ATP + 2 H2O = AMP + 2 phosphate. Ref.5 Ref.8
Cofactor	A divalent cation Ca2+, Mg2+ or Mn2+ By similarity.
Enzyme regulation	Activity is inhibited both by interaction with VMA13 and by V-ATPase acidification of the lumen. The activity of VMA13 is not required for YND1 inhibition. Ref.5
Pathway	Protein modification; protein glycosylation.
Subunit structure	Interacts with activator subunit VMA13 of vacuolar H+-ATPase. Interacts with CDC55; this interaction is disrupted by adenovirus E4orf4, which remains associated with both YND1 and CDC55. Ref.5 Ref.8
Subcellular location	Golgi apparatus. Membrane; Single-pass membrane protein Potential Ref.1 Ref.6.
Disruption phenotype	Cells are partially resistant to E4orf4 and can partially suppress the spindle checkpoint defect in CDC55 deletion mutant. Does not suppress the rapamycin-resistance of CDC55 deletion mutant. Double mutant, where both YND1 and CDC55 are deleted, is fully resistant to E4orf4. Deletion mutant suppresses the synthetic lethality of triple mutants that are deleted for HAP1, ERG6, or ERG28, and UPC2 and ECM22. Ref.8 Ref.9
Miscellaneous	Present with 450 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the GDA1/CD39 NTPase family.

Ontologies

Keywords
Biological process	Lipid metabolism Sphingolipid metabolism
Cellular component	Golgi apparatus Membrane
Domain	Transmembrane Transmembrane helix
Ligand	ATP-binding Nucleotide-binding
Molecular function	Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein glycosylation Inferred from mutant phenotype Ref.1. Source: SGD sphingolipid metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	Golgi membrane Inferred from direct assay PubMed 10551827. Source: SGD integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside-diphosphatase activity Inferred from direct assay Ref.1. Source: SGD nucleoside-triphosphatase activity Inferred from direct assay Ref.1. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 630	630	Golgi apyrase		PRO_0000209920
Regions
	Topological domain	1 – 500	500	Lumenal Potential
	Transmembrane	501 – 517	17	Helical; Potential
	Topological domain	518 – 630	113	Cytoplasmic Potential
Sites
	Active site	152	1	Proton acceptor By similarity
Amino acid modifications
	Modified residue	579	1	Phosphoserine Ref.10
	Modified residue	601	1	Phosphoserine Ref.10
Experimental info
	Mutagenesis	152	1	E → Q: Expressed at lower levels. GTPase activity reduced. Ref.8
	Mutagenesis	189	1	S → A: Expressed at the same level as wild-type. GTPase and GDPase activities decreased more than 20-fold toward GTP and 3-fold for GDP. Ref.8
	Sequence conflict	498	1	S → P in AAT92897. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P40009 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 02F8D24A78212544	FASTA	630	71,852
	10 20 30 40 50 60 MLIENTNDRF GIVIDAGSSG SRIHVFKWQD TESLLHATNQ DSQSILQSVP HIHQEKDWTF 70 80 90 100 110 120 KLNPGLSSFE KKPQDAYKSH IKPLLDFAKN IIPESHWSSC PVFIQATAGM RLLPQDIQSS 130 140 150 160 170 180 ILDGLCQGLK HPAEFLVEDC SAQIQVIDGE TEGLYGWLGL NYLYGHFNDY NPEVSDHFTF 190 200 210 220 230 240 GFMDMGGAST QIAFAPHDSG EIARHRDDIA TIFLRSVNGD LQKWDVFVST WLGFGANQAR 250 260 270 280 290 300 RRYLAQLINT LPENTNDYEN DDFSTRNLND PCMPRGSSTD FEFKDTIFHI AGSGNYEQCT 310 320 330 340 350 360 KSIYPLLLKN MPCDDEPCLF NGVHAPRIDF ANDKFIGTSE YWYTANDVFK LGGEYNFDKF 370 380 390 400 410 420 SKSLREFCNS NWTQILANSD KGVYNSIPEN FLKDACFKGN WVLNILHEGF DMPRIDVDAE 430 440 450 460 470 480 NVNDRPLFQS VEKVEERELS WTLGRILLYA SGSILAGNDD FMVGIAPSER RTKLTGKKFI 490 500 510 520 530 540 PGKLLESDQL RKQSSSLSNK GFLMWFAIIC CIFYLIFHRS HIIRRRFSGL YNITKDFKTG 550 560 570 580 590 600 IRRRLKFLRR SDPFSRLEEG ELGTDVDGFK DVYRMKSSSM FDLGKSSATM QREHEPQRTA 610 620 630 SQSANLAPSN LRPAFSMADF SKFKDSRLYD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"YND1, a homologue of GDA1, encodes membrane-bound apyrase required for Golgi N- and O-glycosylation in Saccharomyces cerevisiae." Gao X.D., Kaigorodov V., Jigami Y. J. Biol. Chem. 274:21450-21456(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION. Strain: ATCC 204508 / S288c.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Regulation of yeast ectoapyrase ynd1p activity by activator subunit Vma13p of vacuolar H+-ATPase." Zhong X., Malhotra R., Guidotti G. J. Biol. Chem. 275:35592-35599(2000) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYMATIC ACTIVITY, ENZYME REGULATION, INTERACTION WITH VMA13.
[6]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[7]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]	"YND1 interacts with CDC55 and is a novel mediator of E4orf4-induced toxicity." Maoz T., Koren R., Ben-Ari I., Kleinberger T. J. Biol. Chem. 280:41270-41277(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ENZYMATIC ACTIVITY, INTERACTION WITH CDC55, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLU-152 AND SER-189.
[9]	"Cumulative mutations affecting sterol biosynthesis in the yeast Saccharomyces cerevisiae result in synthetic lethality that is suppressed by alterations in sphingolipid profiles." Valachovic M., Bareither B.M., Bhuiyan M.S.A., Eckstein J., Barbuch R., Balderes D., Wilcox L., Sturley S.L., Dickson R.C., Bard M. Genetics 173:1893-1908(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[10]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-579 AND SER-601, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF203695 Genomic DNA. Translation: AAF17573.1. U18778 Genomic DNA. Translation: AAB64538.1. AY692878 Genomic DNA. Translation: AAT92897.1. BK006939 Genomic DNA. Translation: DAA07655.1.
PIR	S50463.
RefSeq	NP_010920.3. NM_001178896.3.
3D structure databases
ProteinModelPortal	P40009.
SMR	P40009. Positions 7-447.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-7607N.
MINT	MINT-1354523.
STRING	4932.YER005W.
Proteomic databases
PaxDb	P40009.
PeptideAtlas	P40009.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YER005W; YER005W; YER005W.
GeneID	856722.
KEGG	sce:YER005W.
Organism-specific databases
CYGD	YER005w.
SGD	S000000807. YND1.
Phylogenomic databases
eggNOG	COG5371.
GeneTree	ENSGT00550000074435.
HOGENOM	HOG000246725.
KO	K14642.
OMA	YWHTTHE.
OrthoDB	EOG4WM83T.
Enzyme and pathway databases
BioCyc	MetaCyc:G3O-30192-MONOMER. YEAST:G3O-30192-MONOMER.
UniPathway	UPA00378.
Gene expression databases
Genevestigator	P40009.
GermOnline	YER005W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR000407. GDA1_CD39_NTPase. [Graphical view]
PANTHER	PTHR11782. PTHR11782. 1 hit.
Pfam	PF01150. GDA1_CD39. 1 hit. [Graphical view]
PROSITE	PS01238. GDA1_CD39_NTPASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	982817.

Entry information

Entry name

YND1_YEAST

Accession

Primary (citable) accession number: P40009
Secondary accession number(s): D3DLQ1, Q6B252

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 29, 2013
This is version 108 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program