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Information on EC 3.6.1.1 - inorganic diphosphatase and Organism(s) Arabidopsis thaliana and UniProt Accession P31414
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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: Arabidopsis thaliana
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
PPA1
PPase
pyrophosphatase, inorganic
-
-
-
-
Pyrophosphate phospho-hydrolase
-
-
-
-
Pyrophosphate phosphohydrolase
-
-
-
-
Pyrophosphate-energized inorganic pyrophosphatase
-
-
-
-
H+-PPase
-
-
-
-
inorganic pyrophosphatase
-
-
-
-
PPase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
diphosphate + H2O = 2 phosphate
the catalytic mechanism of the HAD superfamily including a phosphorylated enzyme intermediate, overview
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
2-phosphorylethanolamine + H2O
ethanolamine + phosphate
low activity
-
-
?
4-nitrophenyl phosphate + H2O
4-nitrophenol + phosphate
low activity
-
-
?
D-glucose-6-phosphate + H2O
D-glucose + phosphate
low activity
-
-
?
diphosphate + H2O
2 phosphate
AtPPsPase1 catalyzes the specific cleavage
-
-
?
additional information
?
-
substrate specificity, overview. The enzyme is highly specific, no or poor activity with ribose-5-phosphate, phospho-L-serine, o-phosphocholine, phosphoenolpyruvate, L-glycerol-3-phosphate, beta-glycerol-phosphate, and phospho-L-tyrosine
-
-
?
additional information
?
-
-
substrate specificity, overview. The enzyme is highly specific, no or poor activity with ribose-5-phosphate, phospho-L-serine, o-phosphocholine, phosphoenolpyruvate, L-glycerol-3-phosphate, beta-glycerol-phosphate, and phospho-L-tyrosine
-
-
?
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
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
Mg2+
dependent on, can be partially substituted by Mn2+, both isozymes show similar catalytic constants and affinities for the Mg-pyrophosphate complex, while differed in their affinity for free Mg2+,
Mg2+
required, natural cofactor of AtPPA1, metal coordination and binding site
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
ordered binding of free Mg2+ and of the Mg-diphosphate complex. Both isozymes show similar catalytic constants and affinities for the Mg-diphosphate complex, while differed in their affinity for free Mg2+, kinetics, overview
-
0.0432
diphosphate
pH 7.5, 22°C, recombinant truncated mutant AtPPA1-DELTA(1-29)
0.059
diphosphate
pH 7.5, 25°C, isozyme PPa4 in a complex with Mg2+
0.069
diphosphate
pH 7.5, 25°C, isozyme PPa1 in a complex with Mg2+
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
21.4
diphosphate
pH 7.5, 22°C, recombinant truncated mutant AtPPA1-DELTA(1-29)
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
495.4
diphosphate
pH 7.5, 22°C, recombinant truncated mutant AtPPA1-DELTA(1-29)
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
distribution of expression of isozymes during development in different tissues, overview
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
isozyme PPa1, which contains an N-terminal mitochondrial target sequence with a putative cleavage site at Val31
the N-terminal peptide of immature AtPPA1 is mostly disordered. It can be cleaved during maturation. The cleaved peptide is a mitochondrial targeting signal
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
AtPPsPase1 belongs to the haloacid dehalogenase, HAD, superfamily
malfunction
the vacuolar H+-translocating pyrophosphatase (H+-PPase) loss-of-function fugu5 mutant is susceptible to drought and displays pleotropic postgerminative growth defects due to excess diphosphate. Stomatal closure after abscisic acid (ABA) treatment is delayed in vhp1-1, a fugu5 allele. In contrast, specific removal of diphosphate rescues all of the above fugu5 developmental and growth defects. Hydrolysis of PPi within guard cells alleviates delayed growth in fugu5-1. The GC1 promoter is properly expressed in guard cells in the fugu5-1 background. Stomatal development is mildly affected in fugu5-1. Dysfunction of H+-PPase in the fugu5 mutant leads to elevated cytosolic PPi levels and results in a pleiotropic phenotype. Mutant fugu5 plants exhibit seasonal fluctuations, growing better during the humid summer but exhibiting susceptibility to the dry winter. 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
physiological function
additional information
physiological function
tight control of AtPPsPase1 gene expression underlines its important role in the phosphate starvation response, cleavage of diphosphate is an immediate metabolic adaptation reaction
physiological function
inorganic diphosphatases (PPases), which hydrolyze inorganic diphosphate to phosphate in the presence of divalent metal cations, play a key role in maintaining phosphorus homeostasis in cells
physiological function
the H+-PPase contributes to stomatal functioning not only as a proton pump that acidifies the vacuoles, but also as an enzyme that maintains adequate PPi levels within guard cells. Regulation of PPi levels by H+-PPase is critical for proper resumption of postgerminative plant development. Diphosphate homeostasis is important for stomatal closure. Stomatal opening is independent of H+-PPase, but a balance between PPi level and vacuolar membrane potential is required for proper regulation of stomata, excess PPi selectively affects stomatal closure movement
additional information
AtPPA1 three-dimensional structure analysis and modelling, overview
additional information
-
AtPPA1 three-dimensional structure analysis and modelling, overview
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
24484
x * 24484, isozyme PPa1, DNA sequence calculation, x * 24576, isozyme PPa4, DNA sequence calculation
24576
x * 24484, isozyme PPa1, DNA sequence calculation, x * 24576, isozyme PPa4, DNA sequence calculation
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
x * 24484, isozyme PPa1, DNA sequence calculation, x * 24576, isozyme PPa4, DNA sequence calculation
additional information
additional information
circular dichroism spectrum, secondary structure of isozymes, overview
additional information
topology and conformation of the PPA1 subunits, comparison to the enzyme from Medicago truncatula. The N-terminal peptide of immature AtPPA1 is mostly disordered
additional information
-
topology and conformation of the PPA1 subunits, comparison to the enzyme from Medicago truncatula. The N-terminal peptide of immature AtPPA1 is mostly disordered
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphoprotein
the enzyme shares the catalytic mechanism of the HAD superfamily including a phosphorylated enzyme intermediate
proteolytic modification
the N-terminal peptide is autocatalytically cleaved, presence of three N-terminal variants, truncated at Leu23, Ser25 and Leu26. The growth of AtPPA1 crystal iis strongly correlated with the progression of proteolysis
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, hanging drop vapor diffusion method, mixing of 7.5-10 mg/ml protein with precipitant solution containing 100 mM succinic acid, pH 7.0, and 15% PEG3350, or 100 mM bicine, pH 9.0, 7% PEG 6000, and 3 mM MgCl2 for the Mg2+-bound enzyme, 2 weeks, 19°C, 20% glycerol or PEG400 as cryoprotectants, X-ray diffraction structure determination and analysis at 1.93 A and 1.83 A resolution, respectively, structure modelling. Growth of AtPPA1 crystal is strongly correlated with the progression of proteolysis
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
construction of an N-truncated variant of AtPPA1 with residues 1-29 deleted (DELTA(1-29)) produced using construct pMCSG48-AtPPA1-DELTA(1-29)
additional information
-
construction of an N-truncated variant of AtPPA1 with residues 1-29 deleted (DELTA(1-29)) produced using construct pMCSG48-AtPPA1-DELTA(1-29)
additional information
construction of the vacuolar H+-translocating pyrophosphatase (H+-PPase) loss-of-function fugu5 mutant that is susceptible to drought and displays pleotropic postgerminative growth defects due to excess diphosphate. Specific removal of PPi from a fugu5 mutant background (i.e. in the pAVP1::IPP1 transgenic line) rescues all recognized developmental defects and vigorously enhances growth. The GC1 promoter is properly expressed in guard cells in the fugu5-1 background. Construction and phenotypic analyses of the pGC1::IPP1 line in the fugu5-1 background expressing the soluble PPase from Saccharomyces cerevisiae strain 288c. pGC1::IPP1/fugu5-1 displays typical oblong cotyledons reminiscent of fugu5 mutants, but expression of IPP1 in the guard cells of the pGC1::IPP1/fugu5-1 lines does not affect the palisade cell phenotype, phenotypes, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant GST-tagged isozymes from Escherichia coli by glutathione affinity chromatography, elution with ethylene glcol and Mg2+
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography, dialysis, tag cleavage by TEV protease, followed by gel filtration and ultrafiltration
recombinant His6-tagged enzyme from Escherichia coli strain BL21 (DE3) by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
At1g73010, DNA and amino acid sequence determination and analysis, expression of His6-tagged enzyme in Escherichia coli strain Bl21 (DE3)
gene ppa1, isozyme PPase 1, DNA and amino acid sequence determination and analysis, subcloning in Escherichia coli
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Gomez-Garcia, M.R.; Losada, M.; Serrano, A.
A novel subfamily of monomeric inorganic pyrophosphatases in photosynthetic eukaryotes
Biochem. J.
395
211-221
2006
Chlamydomonas reinhardtii (Q93Y52), Chlamydomonas reinhardtii (Q949J1), Chlamydomonas reinhardtii, Arabidopsis thaliana (Q9LXC9)
Navarro-De la Sancha, E.; Coello-Coutino, M.P.; Valencia-Turcotte, L.G.; Hernandez-Dominguez, E.E.; Trejo-Yepes, G.; Rodriguez-Sotres, R.
Characterization of two soluble inorganic pyrophosphatases from Arabidopsis thaliana
Plant Sci.
172
796-807
2007
Arabidopsis thaliana (Q9LXC9)
May, A.; Berger, S.; Hertel, T.; Koeck, M.
The Arabidopsis thaliana phosphate starvation responsive gene AtPPsPase1 encodes a novel type of inorganic pyrophosphatase
Biochim. Biophys. Acta
1810
178-185
2011
Arabidopsis thaliana (Q67YC0), Arabidopsis thaliana, Arabidopsis thaliana Col-0 (Q67YC0)
Grzechowiak, M.; Sikorski, M.; Jaskolski, M.
Inorganic pyrophosphatase (PPase) from a higher plant
Biotechnologia
94
35-37
2013
Arabidopsis thaliana
-
Grzechowiak, M.; Ruszkowski, M.; Sliwiak, J.; Szpotkowski, K.; Sikorski, M.; Jaskolski, M.
Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity
Biochem. J.
476
2297-2319
2019
Medicago truncatula (I3STR7), Medicago truncatula, Arabidopsis thaliana (Q93V56), Arabidopsis thaliana
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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