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Information on EC 3.6.1.1 - inorganic diphosphatase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P00817
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3.6.1.1 inorganic diphosphataseIUBMB Comments
Specificity varies with the source and with the activating metal ion. The enzyme from some sources may be identical with EC 3.1.3.1 (alkaline phosphatase) or EC 3.1.3.9 (glucose-6-phosphatase). cf. EC 7.1.3.1, H+-exporting diphosphatase.
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Word Map
- 3.6.1.1
- thiamine
- ppases
- vacuole
- apparatus
- nucleoside
-
tonoplast
- triphosphate
-
cytochemical
-
cisternae
- h+-atpase
- lysosome
- magnesium
- polyphosphate
- glucose-6-phosphatase
- orthophosphate
-
mung
- rubrum
-
cytochemistry
- rhodospirillum
- imidodiphosphate
-
saccule
-
nudix
-
h+-pumping
-
antiporter
- 5'-nucleotidase
-
proton-pumping
-
electrogenic
- vigna
- acpase
-
diadenosine
-
monophosphatase
- tripolyphosphate
-
v-type
- diphosphonate
- ap4a
-
chromatophores
-
dihydrate
- tetraphosphate
-
ectonucleotide
- exopolyphosphatase
-
vacuolar-type
- radiata
- phosphomonoesterase
- autotaxin
-
osmium
-
pyrophosphate-dependent
- n,n'-dicyclohexylcarbodiimide
-
decapping
-
pyrophosphohydrolase
-
sulfurylase
- molecular biology
- synthesis
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
pyrophosphatase, inorganic pyrophosphatase, v-ppase, h+-ppase, vacuolar h(+)-pyrophosphatase, sppase, e-ppase, vacuolar h(+)-ppase, soluble inorganic pyrophosphatase, ippase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
H+-PPase
-
-
-
-
inorganic diphosphatase
-
-
-
-
inorganic pyrophosphatase
PPase
-
-
-
-
pyrophosphatase, inorganic
-
-
-
-
Pyrophosphate phospho-hydrolase
-
-
-
-
Pyrophosphate phosphohydrolase
-
-
-
-
Pyrophosphate-energized inorganic pyrophosphatase
-
-
-
-
inorganic pyrophosphatase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
diphosphate + H2O = 2 phosphate
substrate binding structure and catalytic mechanism
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphorous acid anhydride hydrolysis
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
diphosphate phosphohydrolase
Specificity varies with the source and with the activating metal ion. The enzyme from some sources may be identical with EC 3.1.3.1 (alkaline phosphatase) or EC 3.1.3.9 (glucose-6-phosphatase). cf. EC 7.1.3.1, H+-exporting diphosphatase.
CAS REGISTRY NUMBER
COMMENTARY
9024-82-2
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
diphosphates + H2O
?
-
hydrolysis of organic diphosphates in the presence of Zn2+
-
-
?
additional information
?
-
-
no hydrolysis of ATP and traces of activity with tripolyphosphate in the presence of Mg2+
-
-
?
diphosphate + H2O
2 phosphate
the rate-determining step for the forward reaction with Mg2+ is hydrolysis of PPi, the wild-type active site shows a closed comformation with one of the two product phosphates already dissociated, active site residues Tyr93 and Asp115 are important, six-state catalytic mechanism, overview
in the reverse, net synthesis direction, the rate-determining step is not the condensation of the two phosphate ions but the previous step, which involves isomerization of the enzyme
-
r
diphosphate + H2O
2 phosphate
-
-
-
-
?
diphosphate + H2O
2 phosphate
-
high specificity with Mg2+ as cofactor
-
-
r
diphosphate + H2O
2 phosphate
-
important for energy metabolism, provides energy for biosynthetic reactions
-
-
?
diphosphate + H2O
2 phosphate
-
important for energy metabolism, provides energy for biosynthetic reactions, central enzyme of phosphorus metabolism
-
-
?
tripolyphosphate + H2O
?
-
hydrolysis only with Zn2+ or Mn2+ as cofactors
-
-
?
tripolyphosphate + H2O
?
-
reaction only in the presence of Mn2+ or Zn2+
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
diphosphate + H2O
2 phosphate
-
important for energy metabolism, provides energy for biosynthetic reactions
-
-
?
diphosphate + H2O
2 phosphate
-
important for energy metabolism, provides energy for biosynthetic reactions, central enzyme of phosphorus metabolism
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
the pyrophosphatase requires four divalent metal cations for catalysis, magnesium provides the highest activity
Cd2+
-
4 Cd2+ sites per subunit, enzyme activity lower compared to Mg2+
Co2+
-
supports the hydrolysis of ATP and tripolyphosphate, very weak activation of diphosphate hydrolysis
Mg2+
Mn2+
Zn2+
Mn2+
-
supports the hydrolysis of ATP and tripolyphosphate, very weak activation of diphosphate hydrolysis
Zn2+
-
supports the hydrolysis of ATP and tripolyphosphate, very weak activation of diphosphate hydrolysis
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
metal binding affinities and kinetics of wild-type and mutant enzymes, overview
-
additional information
additional information
-
metal binding affinities and kinetics of wild-type and mutant enzymes, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.005
ATP
-
less than 0.005/sec, pH 7.2, 25°C, in the presence of Mg2+
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
64080
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant wild-type enzyme or mutants E48D, Y93F, D115E, D117E, D120E, D120N, and D152E in 60 mM MES, pH 6.0, and 10 mM Mg2+, 4°C, 0.008 ml sitting drops in the presence of 5 mM Mg2+, 1 mM PO43-, and a MPD concentration gradient from 16 to 19%, 2-4 weeks, cryoprotection by soaking of crystals at 4°C in 32% MPD, 30 mM MES, 10 mM Mg2+, and 1 mM PO43- for a few min, X-ray diffraction structure determination and analysis at 1.5-1.9 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D115E
site-directed mutagenesis, the mutation affects metal binding and the hydrogen bonding network in the active, in contrary to the wild-type enzyme, the mutant shows an open conformation variant of the hitherto unobserved two-phosphate and two bridging water active site, crystal structure determination with bound phosphate and Mg2+, and comparison to the wild-type enzyme structure
D117E
site-directed mutagenesis, crystal structure determination with bound phosphate and Mg2+, and comparison to the wild-type enzyme structure
D120E
site-directed mutagenesis, crystal structure determination with bound phosphate and Mg2+, and comparison to the wild-type enzyme structure
D120N
site-directed mutagenesis, crystal structure determination with bound phosphate and Mg2+, and comparison to the wild-type enzyme structure
D152E
site-directed mutagenesis, crystal structure determination with bound phosphate and Mg2+, and comparison to the wild-type enzyme structure
E48D
site-directed mutagenesis, crystal structure determination with bound phosphate and Mg2+, and comparison to the wild-type enzyme structure
Y93F
site-directed mutagenesis, the mutation affects metal binding and the hydrogen bonding network in the active, crystal structure determination with bound phosphate and Mg2+, and comparison to the wild-type enzyme structure
additional information
additional information
construction and analysis of the pGC1::IPP1 line, in which the soluble-type yeast PPase inorganic pyrophosphatase (IPP1) is specifically expressed in Arabidopsis thaliana guard cells in the H+-PPase loss-of-function mutant fugu5 background. pGC1::IPP1/fugu5-1 displays typical oblong cotyledons reminiscent of fugu5 mutants, but recombinant expression of IPP1 in the guard cells of the pGC1::IPP1/fugu5-1 lines does not affect the palisade cell phenotype. Effect of pGC1::IPP1 expression on palisade tissue development and hypocotyl elongation, overview
additional information
-
construction and analysis of the pGC1::IPP1 line, in which the soluble-type yeast PPase inorganic pyrophosphatase (IPP1) is specifically expressed in Arabidopsis thaliana guard cells in the H+-PPase loss-of-function mutant fugu5 background. pGC1::IPP1/fugu5-1 displays typical oblong cotyledons reminiscent of fugu5 mutants, but recombinant expression of IPP1 in the guard cells of the pGC1::IPP1/fugu5-1 lines does not affect the palisade cell phenotype. Effect of pGC1::IPP1 expression on palisade tissue development and hypocotyl elongation, overview
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene IPP1, recombinant expression in Arabidopsis thaliana fugu5 mutant guard cells
RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Welsh, K.M.; Cooperman, B.S.
Yeast inorganic pyrophosphatase. A model for active-site structure based on 113Cd2+ and 31P NMR studies
Biochemistry
23
4947-4955
1984
Saccharomyces cerevisiae
Cooperman, B.S.
The mechanism of action of yeast inorganic pyrophosphatase
Methods Enzymol.
87
526-548
1982
Saccharomyces cerevisiae
Yano, Y.; Irie, M.
Renaturation of yeast inorganic pyrophosphatase denatured in urea and guanidine hydrochloride
J. Biochem.
78
1001-1011
1975
Saccharomyces cerevisiae
Bunick, G.; McKenna, G.P.; Colton, R.; Voet, D.
The x-ray structure of yeast inorganic pyrophosphatase. Crystal properties
J. Biol. Chem.
249
4647-4649
1974
Saccharomyces cerevisiae
Butler, L.G.
Yeast and other inorganic pyrophosphatases
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
4
529-541
1971
Saccharomyces cerevisiae
-
Bunick, G.; McKenna, G.P.; Scarbrough, F.E.; Uberbacher, E.C.; Voet, D.
The x-ray structure of yeast inorganic pyrophosphosphatase at 5.5. Ang. Resolution
Acta Crystallogr. Sect. B Struct. Sci.
34
3210-3215
1978
Saccharomyces cerevisiae
-
Cohen, S.A.; Sterner, R.; Keim, P.S.; Heinrickson, R.L.
Covalent structural analysis of yeast inorganic pyrophosphatase
J. Biol. Chem.
253
889
1978
Saccharomyces cerevisiae
Lundin, M.; Deopujari, S.W.; Lichko, L.; da Silva, L.P.; Baltscheffsky, H.
Characterization of a mitochondrial inorganic pyrophosphatase in Saccharomyces cerevisiae
Biochim. Biophys. Acta
1098
217-223
1992
Saccharomyces cerevisiae
Zyryanov, A.B.; Shestakov, A.S.; Lahti, R.; Baykov, A.A.
Mechanism by which metal cofactors control substrate specificity in pyrophosphatase
Biochem. J.
367
901-906
2002
Saccharomyces cerevisiae, Escherichia coli, Rattus norvegicus, Streptococcus mutans, Escherichia coli MRE 600
Halonen, P.; Baykov, A.A.; Goldman, A.; Lahti, R.; Cooperman, B.S.
Single-turnover kinetics of Saccharomyces cerevisiae inorganic pyrophosphatase
Biochemistry
41
12025-12031
2002
Saccharomyces cerevisiae
Oksanen, E.; Ahonen, A.K.; Tuominen, H.; Tuominen, V.; Lahti, R.; Goldman, A.; Heikinheimo, P.
A complete structural description of the catalytic cycle of yeast pyrophosphatase
Biochemistry
46
1228-1239
2007
Saccharomyces cerevisiae (P00817), Saccharomyces cerevisiae
Drake, R.; Serrano, A.; Perez-Castineira, J.R.
N-Terminal chimaeras with signal sequences enhance the functional expression and alter the subcellular localization of heterologous membrane-bound inorganic pyrophosphatases in yeast
Biochem. J.
426
147-157
2010
Saccharomyces cerevisiae, Trypanosoma cruzi (Q9NDF0), Trypanosoma cruzi, Trypanosoma cruzi Y (Q9NDF0)
Asaoka, M.; Inoue, S.I.; Gunji, S.; Kinoshita, T.; Maeshima, M.; Tsukaya, H.; Ferjani, A.
Excess pyrophosphate within guard cells delays stomatal closure
Plant Cell Physiol.
60
875-887
2019
Arabidopsis thaliana (A8MQH1), Saccharomyces cerevisiae (P00817), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (P00817)
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