Reviewed, UniProtKB/Swiss-Prot P00817 (IPYR_YEAST)

Names and origin

Protein names

Recommended name:
    Inorganic pyrophosphatase
    EC=3.6.1.1
Alternative name(s):
    Pyrophosphate phospho-hydrolase
      Short name=PPase

Gene names

Name:	IPP1
Synonyms:	PPA, PPA1
Ordered Locus Names:	YBR011C
ORF Names:	YBR0202

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	287 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	Diphosphate + H2O = 2 phosphate.
Cofactor	Binds 4 magnesium ions per subunit. Other metal ions can support activity, but at a lower rate. Two magnesium ions are required for the activation of the enzyme and are present before substrate binds, two additional magnesium ions form complexes with substrate and product By similarity.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm.
Miscellaneous	Present with 68400 molecules/cell in log phase SD medium. Ref.9
Sequence similarities	Belongs to the PPase family.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Magnesium Metal-binding
Molecular function	Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	phosphate metabolic process Inferred by curator. Source: SGD
Cellular component	cytosol Traceable author statement. Source: SGD
Molecular function	inorganic diphosphatase activity Inferred from direct assay. Source: SGD magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein homodimerization activity Inferred from mutant phenotype. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	P53839	1	EBI-9338,EBI-28263
ACB1	P31787	1	EBI-9338,EBI-2060
ADE16	P54113	1	EBI-9338,EBI-14213
ADE17	P38009	1	EBI-9338,EBI-14223
ADE4	P04046	1	EBI-9338,EBI-14238
ALO1	P54783	1	EBI-9338,EBI-2519
ARC18	Q05933	1	EBI-9338,EBI-2764
ARC19	P33204	1	EBI-9338,EBI-2757
ARP2	P32381	1	EBI-9338,EBI-2927
AUS1	Q08409	1	EBI-9338,EBI-35723
CAF20	P12962	1	EBI-9338,EBI-9010
CAP2	P13517	1	EBI-9338,EBI-4013
CUP1-1	P07215	1	EBI-9338,EBI-11541
DPH5	P32469	1	EBI-9338,EBI-6095
DYS1	P38791	1	EBI-9338,EBI-5871
EFT1	P32324	1	EBI-9338,EBI-6333
EHT1	P38295	1	EBI-9338,EBI-20890
ERG11	P10614	1	EBI-9338,EBI-5127
ESS1	P22696	1	EBI-9338,EBI-6679
GCD7	P32502	1	EBI-9338,EBI-6260
GCN1	P33892	1	EBI-9338,EBI-7442
GLO2	Q05584	1	EBI-9338,EBI-7672
GPD2	P41911	1	EBI-9338,EBI-7791
GRE3	P38715	1	EBI-9338,EBI-7884
GSY2	P27472	1	EBI-9338,EBI-8036
HCH1	P53834	1	EBI-9338,EBI-28288
HUG1	Q6Q5K6	1	EBI-9338,EBI-392766
IDI1	P15496	1	EBI-9338,EBI-8902
INO1	P11986	1	EBI-9338,EBI-9257
KTI11	Q3E840	1	EBI-9338,EBI-2055307
LIA1	P47120	1	EBI-9338,EBI-25526
LSP1	Q12230	1	EBI-9338,EBI-34978
MPG1	P41940	1	EBI-9338,EBI-11191
PGM2	P37012	1	EBI-9338,EBI-13296
PRO2	P54885	1	EBI-9338,EBI-13872
PRO3	P32263	1	EBI-9338,EBI-13885
PST2	Q12335	1	EBI-9338,EBI-14064
PUP2	P32379	1	EBI-9338,EBI-13971
RAD25	Q00578	1	EBI-9338,EBI-14683
RAS2	P01120	1	EBI-9338,EBI-14838
RIB5	P38145	1	EBI-9338,EBI-2083267
RSP5	P39940	1	EBI-9338,EBI-16219
SAC6	P32599	1	EBI-9338,EBI-6931
SCL1	P21243	1	EBI-9338,EBI-13975
SDH4	P37298	1	EBI-9338,EBI-16796
SIS1	P25294	1	EBI-9338,EBI-17244
SMI1	P32566	1	EBI-9338,EBI-17452
SNA3	P14359	1	EBI-9338,EBI-26122
SNC2	P33328	1	EBI-9338,EBI-17512
SSD1	P24276	1	EBI-9338,EBI-18153
SSM4	P40318	1	EBI-9338,EBI-18208
TPD3	P31383	1	EBI-9338,EBI-1936
TRP2	P00899	1	EBI-9338,EBI-19575
TRP4	P07285	1	EBI-9338,EBI-2096870
URA7	P28274	1	EBI-9338,EBI-20128
URN1	Q06525	1	EBI-9338,EBI-35138
VMA7	P39111	1	EBI-9338,EBI-20272
VPS21	P36017	1	EBI-9338,EBI-29399
YHB1	P39676	1	EBI-9338,EBI-6905
YKL054C	P35732	1	EBI-9338,EBI-26695
YOP1	Q12402	1	EBI-9338,EBI-37092
YPR1	Q12458	1	EBI-9338,EBI-29490
YRF1-4	O13559	1	EBI-9338,EBI-29562

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4

Chain

2 – 287

286

Inorganic pyrophosphatase

PRO_0000137588

Sites

Active site

90

1

Proton donor Ref.7 Ref.8

Metal binding

116

1

Magnesium 1

Metal binding

121

1

Magnesium 1

Metal binding

121

1

Magnesium 2

Metal binding

153

1

Magnesium 1

Binding site

79

1

Inorganic pyrophosphate Ref.8

Amino acid modifications

Modified residue

61

1

Phosphothreonine Ref.12

Modified residue

65

1

Phosphothreonine Ref.13

Modified residue

247

1

Phosphothreonine Ref.13

Modified residue

251

1

Phosphothreonine Ref.13 Ref.10 Ref.11

Modified residue

253

1

Phosphothreonine Ref.13

Modified residue

255

1

Phosphoserine Ref.13

Modified residue

266

1

Phosphoserine Ref.12 Ref.13

Modified residue

286

1

Phosphoserine Ref.10

Experimental info

Sequence conflict

41

1

N → D AA sequence Ref.4

Sequence conflict

72

1

D → N AA sequence Ref.4

Sequence conflict

75

1

Missing AA sequence Ref.4

Sequence conflict

124

1

E → Q AA sequence Ref.4

Sequence conflict

137

1

Q → E AA sequence Ref.4

Sequence conflict

187

1

N → D AA sequence Ref.4

Sequence conflict

225

1

D → N AA sequence Ref.4

Sequence conflict

267

1

P → L in CAA31629. Ref.1

Secondary structure

1

.

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.

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.

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287

Helix Strand Turn

Details...

Beta strand

3 – 13

11

Beta strand

17 – 22

6

Beta strand

25 – 27

3

Turn

29 – 32

4

Beta strand

35 – 38

4

Helix

39 – 41

3

Beta strand

43 – 50

8

Beta strand

58 – 60

3

Beta strand

62 – 64

3

Beta strand

69 – 71

3

Beta strand

91 – 96

6

Beta strand

106 – 108

3

Turn

109 – 112

4

Beta strand

113 – 115

3

Beta strand

121 – 124

4

Beta strand

135 – 144

10

Beta strand

146 – 148

3

Beta strand

155 – 160

6

Helix

166 – 168

3

Helix

172 – 178

7

Helix

182 – 192

11

Helix

195 – 197

3

Beta strand

203 – 205

3

Helix

206 – 208

3

Beta strand

210 – 212

3

Helix

213 – 231

19

Beta strand

245 – 247

3

Helix

256 – 258

3

Turn

259 – 261

3

Beta strand

266 – 268

3

Helix

275 – 278

4

Sequences

	Sequence		Length	Mass (Da)
	P00817-1 [UniParc]. Last modified July 24, 2007. Version 4. Checksum: 1DC19A702A389BA9	FASTA	287	32,300
	10 20 30 40 50 60 MTYTTRQIGA KNTLEYKVYI EKDGKPVSAF HDIPLYADKE NNIFNMVVEI PRWTNAKLEI 70 80 90 100 110 120 TKEETLNPII QDTKKGKLRF VRNCFPHHGY IHNYGAFPQT WEDPNVSHPE TKAVGDNDPI 130 140 150 160 170 180 DVLEIGETIA YTGQVKQVKA LGIMALLDEG ETDWKVIAID INDPLAPKLN DIEDVEKYFP 190 200 210 220 230 240 GLLRATNEWF RIYKIPDGKP ENQFAFSGEA KNKKYALDII KETHDSWKQL IAGKSSDSKG 250 260 270 280 IDLTNVTLPD TPTYSKAASD AIPPASPKAD APIDKSIDKW FFISGSV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning, molecular characterization and chromosome localization of the inorganic pyrophosphatase (PPA) gene from S. cerevisiae." Kolakowski L.F. Jr., Schloesser M., Cooperman B.S. Nucleic Acids Res. 16:10441-10452(1988) [PubMed: 2849749] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 26109 / X2180.
[2]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed: 7813418] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"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: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"Covalent structural analysis of yeast inorganic pyrophosphatase." Cohen S.A., Sterner R., Keim P.S., Heinrikson R.L. J. Biol. Chem. 253:889-897(1978) [PubMed: 340461] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-287.
[5]	"Protein identifications for a Saccharomyces cerevisiae protein database." Garrels J.I., Futcher B., Kobayashi R., Latter G.I., Schwender B., Volpe T., Warner J.R., McLaughlin C.S. Electrophoresis 15:1466-1486(1994) [PubMed: 7895733] [Abstract] Cited for: PROTEIN SEQUENCE OF 26-36 AND 240-252. Strain: ATCC 204508 / S288c.
[6]	"Protein expression during exponential growth in 0.7 M NaCl medium of Saccharomyces cerevisiae." Norbeck J., Blomberg A. FEMS Microbiol. Lett. 137:1-8(1996) [PubMed: 8935650] [Abstract] Cited for: PROTEIN SEQUENCE OF 240-250. Strain: ATCC 38531 / Y41.
[7]	"Tyrosine-89 is important for enzymatic activity of S. cerevisiae inorganic pyrophosphatase." Raznikov A.V., Sklyankina V.A., Avaeva S.M. FEBS Lett. 308:62-64(1992) [PubMed: 1322842] [Abstract] Cited for: ACTIVE SITE TYR-90.
[8]	"Identification of an arginine important for enzymatic activity within the covalent structure of yeast inorganic pyrophosphatase." Bond M.W., Chiu N.Y., Cooperman B.S. Biochemistry 19:94-102(1980) [PubMed: 6101539] [Abstract] Cited for: ACTIVE SITE.
[9]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed: 15665377] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-251 AND SER-286, MASS SPECTROMETRY.
[11]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-251, MASS SPECTROMETRY.
[12]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-61 AND SER-266, MASS SPECTROMETRY.
[13]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-65; THR-247; THR-251; THR-253; SER-255 AND SER-266, MASS SPECTROMETRY.
[14]	"X-ray diffraction study of inorganic pyrophosphatase from baker's yeast at the 3-A resolution." Arutiunian E.G., Terzian S.S., Voronova A.A., Kuranova I.P., Smirnova E.A., Vainstein B.K., Hohne W.E., Hansen G. Dokl. Akad. Nauk SSSR 258:1481-1492(1981) Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
[15]	"The structural basis for pyrophosphatase catalysis." Heikinheimo P., Lehtonen J., Baykov A., Lahti R., Cooperman B.S., Goldman A. Structure 4:1491-1508(1996) [PubMed: 8994974] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[16]	Swaminathan K., Cooperman B.S., Lahti R., Voet D. Submitted (DEC-1997) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
[17]	"The R78K and D117E active-site variants of Saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implications." Tuominen V., Heikinheimo P., Kajander T., Torkkel T., Hyytia T., Kapyla J., Lahti R., Cooperman B.S., Goldman A. J. Mol. Biol. 284:1565-1580(1998) [PubMed: 9878371] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF MUTANTS LYS-79 AND LYS-118.
[18]	"Conservation of functional residues between yeast and E. coli inorganic pyrophosphatases." Lahti R., Kolakowski L.F. Jr., Heinonen J., Vihinen M., Pohjanoksa K., Cooperman B.S. Biochim. Biophys. Acta 1038:338-345(1990) [PubMed: 2160278] [Abstract] Cited for: SIMILARITY TO E.COLI AND K.LACTIS PPASES.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X13253 Genomic DNA. Translation: CAA31629.1.
Z35880 Genomic DNA. Translation: CAA84949.1.
AY692953 Genomic DNA. Translation: AAT92972.1.

PIR

PWBY. S45864.

RefSeq

NP_009565.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
117E	X-ray	2.15	A/B	2-287	[»]
1E6A	X-ray	1.90	A/B	2-286	[»]
1E9G	X-ray	1.15	A/B	2-286	[»]
1HUJ	X-ray	2.10	A/B	2-282	[»]
1HUK	X-ray	2.20	A/B	2-282	[»]
1M38	X-ray	1.80	A/B	1-287	[»]
1PYP	X-ray	3.00	A/B	2-287	[»]
1WGI	X-ray	2.20	A/B	2-287	[»]
1WGJ	X-ray	2.00	A/B	2-287	[»]
1YPP	X-ray	2.40	A/B	2-286	[»]
2IHP	X-ray	1.50	A/B	2-286	[»]
2IK0	X-ray	1.70	A/B	2-286	[»]
2IK1	X-ray	1.70	A/B	2-286	[»]
2IK2	X-ray	1.80	A/B	2-286	[»]
2IK4	X-ray	1.80	A/B	2-286	[»]
2IK6	X-ray	1.80	A/B	2-286	[»]
2IK7	X-ray	1.90	A/B	2-286	[»]
2IK9	X-ray	1.50	A/B	2-286	[»]
8PRK	X-ray	1.85	A/B	1-287	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:5753N.

IntAct

P00817. 116 interactions.

2-D gel databases

SWISS-2DPAGE

P00817.

COMPLUYEAST-2DPAGE

P00817.

Proteomic databases

PeptideAtlas

P00817.

PRIDE

P00817.

Genome annotation databases

Ensembl

YBR011C. Saccharomyces cerevisiae. [Contig view]

GeneID

852296.

GenomeReviews

Gene locus YBR011C in contig Y13134_GR.

KEGG

sce:YBR011C.

NMPDR

fig|4932.3.peg.260.

Organism-specific databases

CYGD

YBR011c.

SGD

S000000215. IPP1.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P00817.

OMA

P00817. WFFISGS.

Enzyme and pathway databases

BRENDA

3.6.1.1. 250.

Gene expression databases

ArrayExpress

P00817.

GermOnline

YBR011C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR008162. Pyrophosphatase.
[Graphical view]

PANTHER

PTHR10286. Pyrophosphatase. 1 hit.

Pfam

PF00719. Pyrophosphatase. 1 hit.
[Graphical view]

ProDom

PD002014. Inorg_pphsph. 1 hit.
[Graphical view] [Entries sharing at least one domain]

PROSITE

PS00387. PPASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

970952.

Entry information

Entry name

IPYR_YEAST

Accession

Primary (citable) accession number: P00817

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 24, 2007
Last modified:	June 16, 2009
This is version 115 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)