P00817 (IPYR_YEAST) Reviewed, UniProtKB/Swiss-Prot

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 (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	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.
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 Reference proteome
Gene Ontology (GO)
Biological_process	phosphate-containing compound metabolic process Inferred by curator PubMed 8224193. Source: SGD
Cellular_component	cytosol Traceable author statement PubMed 12451180. Source: SGD
Molecular_function	inorganic diphosphatase activity Inferred from direct assay PubMed 8224193. Source: SGD magnesium ion binding Inferred from electronic annotation. Source: InterPro protein homodimerization activity Inferred from mutant phenotype PubMed 11854292. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RSP5	P39940	2	EBI-9338,EBI-16219

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5

Chain

2 – 287

286

Inorganic pyrophosphatase

PRO_0000137588

Sites

Active site

90

1

Proton donor Ref.8 Ref.9

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

Diphosphate

Amino acid modifications

Modified residue

61

1

Phosphothreonine Ref.13

Modified residue

65

1

Phosphothreonine Ref.14

Modified residue

247

1

Phosphothreonine Ref.14

Modified residue

251

1

Phosphothreonine Ref.11 Ref.12 Ref.14

Modified residue

253

1

Phosphothreonine Ref.14

Modified residue

255

1

Phosphoserine Ref.14

Modified residue

266

1

Phosphoserine Ref.13 Ref.14

Modified residue

286

1

Phosphoserine Ref.11

Experimental info

Sequence conflict

41

1

N → D AA sequence Ref.5

Sequence conflict

72

1

D → N AA sequence Ref.5

Sequence conflict

75

1

Missing AA sequence Ref.5

Sequence conflict

124

1

E → Q AA sequence Ref.5

Sequence conflict

137

1

Q → E AA sequence Ref.5

Sequence conflict

187

1

N → D AA sequence Ref.5

Sequence conflict

225

1

D → N AA sequence Ref.5

Sequence conflict

267

1

P → L in CAA31629. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

287

Helix Strand Turn

Details...

Beta strand

3 – 10

8

Beta strand

13 – 15

3

Beta strand

17 – 22

6

Beta strand

25 – 27

3

Turn

29 – 32

4

Beta strand

35 – 38

4

Turn

39 – 42

4

Beta strand

43 – 50

8

Beta strand

58 – 60

3

Beta strand

62 – 64

3

Beta strand

69 – 71

3

Beta strand

75 – 77

3

Beta strand

85 – 87

3

Beta strand

91 – 96

6

Beta strand

106 – 108

3

Turn

109 – 112

4

Beta strand

113 – 115

3

Beta strand

117 – 119

3

Beta strand

121 – 124

4

Beta strand

126 – 128

3

Beta strand

135 – 144

10

Beta strand

146 – 148

3

Beta strand

155 – 160

6

Beta strand

163 – 165

3

Helix

166 – 168

3

Helix

172 – 178

7

Helix

182 – 192

11

Helix

195 – 197

3

Helix

205 – 208

4

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 [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[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]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-287.
[6]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 26-36 AND 240-252. Strain: ATCC 204508 / S288c.
[7]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 240-250. Strain: ATCC 38531 / Y41.
[8]	"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] [Europe PMC] [Abstract] Cited for: ACTIVE SITE TYR-90.
[9]	"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] [Europe PMC] [Abstract] Cited for: ACTIVE SITE.
[10]	"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].
[11]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-251 AND SER-286, MASS SPECTROMETRY. Strain: YAL6B.
[12]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-251, MASS SPECTROMETRY. Strain: ADR376.
[13]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-61 AND SER-266, MASS SPECTROMETRY.
[14]	"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 THR-65; THR-247; THR-251; THR-253; SER-255 AND SER-266, MASS SPECTROMETRY.
[15]	"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).
[16]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[17]	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).
[18]	"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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF MUTANTS LYS-79 AND LYS-118.
[19]	"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] [Europe PMC] [Abstract] Cited for: SIMILARITY TO E.COLI AND K.LACTIS PPASES.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X13253 Genomic DNA. Translation: CAA31629.1.
Z35880 Genomic DNA. Translation: CAA84949.1.
AY692953 Genomic DNA. Translation: AAT92972.1.
BK006936 Genomic DNA. Translation: DAA07132.1.

PIR

PWBY. S45864.

RefSeq

NP_009565.1. NM_001178359.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P00817.

SMR

P00817. Positions 2-285.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5753N.

IntAct

P00817. 40 interactions.

MINT

MINT-614477.

STRING

4932.YBR011C.

2D gel databases

COMPLUYEAST-2DPAGE

P00817.

SWISS-2DPAGE

P00817.

Proteomic databases

PaxDb

P00817.

PeptideAtlas

P00817.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YBR011C; YBR011C; YBR011C.

GeneID

852296.

KEGG

sce:YBR011C.

Organism-specific databases

SGD

S000000215. IPP1.

Phylogenomic databases

eggNOG

COG0221.

GeneTree

ENSGT00390000017004.

HOGENOM

HOG000195569.

KO

K01507.

OMA

KSTHQCW.

OrthoDB

EOG4MGWHC.

Gene expression databases

Genevestigator

P00817.

GermOnline

YBR011C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.90.80.10. 1 hit.

InterPro

IPR008162. Pyrophosphatase.
[Graphical view]

PANTHER

PTHR10286. PTHR10286. 1 hit.

Pfam

PF00719. Pyrophosphatase. 1 hit.
[Graphical view]

SUPFAM

SSF50324. Pyrophosphatase. 1 hit.

PROSITE

PS00387. PPASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00817.

NextBio

970952.

Entry information

Entry name

IPYR_YEAST

Accession

Primary (citable) accession number: P00817
Secondary accession number(s): D6VQ12

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 24, 2007
Last modified:	April 3, 2013
This is version 151 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program