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Information on EC 3.6.1.1 - inorganic diphosphatase and Organism(s) Helicobacter pylori and UniProt Accession P56153
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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: Helicobacter pylori
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
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-
-
-
Pyrophosphate-energized inorganic pyrophosphatase
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-
-
-
inorganic pyrophosphatase
-
-
-
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PPase
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-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
diphosphate + H2O = 2 phosphate
catalytic mechanism involving residues Lys28, Tyr140, Glu20, Asp64, Asp69, Asp96, and Asp101, active site structure
-
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
diphosphate + H2O
2 phosphate
PPase plays an essential role in energy conservation and provides the energy for many biosynthetic pathways controlling the intracellular diphosphate levels
-
-
?
diphosphate + H2O
2 phosphate
diphosphate binding does not cause a significant conformational change in the diphosphate-PPase complex, structure, overview
-
-
?
diphosphate + H2O
2 phosphate
-
actual substrate is magnesium diphosphate or dimagnesium diphosphate
-
-
?
diphosphate + H2O
2 phosphate
-
diphosphate in form of Mg-diphosphate
-
-
?
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
PPase plays an essential role in energy conservation and provides the energy for many biosynthetic pathways controlling the intracellular diphosphate levels
-
-
?
diphosphate + H2O
2 phosphate
-
actual substrate is magnesium diphosphate or dimagnesium diphosphate
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
additional information
Mg2+
dependent on, other divalent cations substituted poorly for Mg2+
Mg2+
required, binds to diphosphate, effects on enzyme activity and kinetics, pH-dependence, overview
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
imidodiphosphoric acid
a nonhydrolyzable PPi analogue, inhibits by 50% at 2 mM
NaF
inhibits 46% and 91.4% of the activity at 0.04 mM and 0.5 mM, respectively
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
diphosphate
diphosphate binds Mg2+ to form a true substrate that activates the enzyme
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
effects of cysteine, homocysteine, and NaBH4 on kinetics of wild-type and mutant C16S enzymes, overview
-
additional information
additional information
-
effects of cysteine, homocysteine, and NaBH4 on kinetics of wild-type and mutant C16S enzymes, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
19272
-
6 * 19272, amino acid sequence calculation, structure-based phylogenetic tree of diphosphatases, overview
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hexamer
hexamer
additional information
hexamer
6 * 20675, recombinant His-tagged enzyme, mass spectrometry
hexamer
-
6 * 19272, amino acid sequence calculation, structure-based phylogenetic tree of diphosphatases, overview
additional information
structure analysis, PPase comprises three alpha-helices and nine beta-strands and folds as a barrel structure, it forms a hexamer in both the solution and crystal states, and each monomer has its own PPi-binding site
additional information
-
structure analysis, PPase comprises three alpha-helices and nine beta-strands and folds as a barrel structure, it forms a hexamer in both the solution and crystal states, and each monomer has its own PPi-binding site
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, free and in complex with diphosphate, hanging drop vapor diffusion method, for the free enzyme: 20 mg/ml protein in 20 mM Tris-HCl, pH 7.5, and 200 mM NaCl, precipitation with 1.44 M sodium citrate, and 100 mM Na HEPES, pH 7.4, 6 days at 25°C, for the diphosphate-bound enzyme: the diphosphate-PPase complex from the same buffer condition as the free enzyme with a 1:7.5 molar excess of K4diphosphate in the absence of divalent metal ion, the complex crystals are grown in the same buffer as free PPase using 3.6 M sodium formate as a precipitant, 3 days at 25°C, X-ray diffraction structure determination and analysis at 1.9 A and 2.3 A resolution, respectively, molecular replacement
purified recombinant His-tagged selenomethionine-enzyme, hanging drop vapour diffusion method, 14 mg/ml protein in 50 mM Tris-HCl, pH 7.0, 0.1 M NaCl, 1 mM 2-mercaptoethanol, and 10 mM MgCl2, against a reservoir solution containing 36% v/v methylpentanediol, 0.2 M MgCl2, and 0.1 M imidazole, pH 8.0, X-ray diffraction structure determination and analysis at 2.6 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C16S
site-directed mutagenesis, the mutant shows a loss of 50% activity and a reduction in sensitivity to reductants and oxidized glutathione compared to the wild-type enzyme. In addition, the replacement causes a considerable disruption in thermostability, C16S substitution destabilizes PPase through impairing trimer-trimer interactions
Y140F
site-directed mutagenesis, the mutant shows 78% reduced activity compared to the wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
15 min, the mutant enzyme loses 70% activity in absence of Mg2+, half-life is 4.2 min
additional information
additional information
residue Cys116 is involved in thermostability
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli to homogeneity by nickel affinity chromatography and gel filtration
recombinant His-tagged selenomethionine-enzyme from Escherichia coli strain B834(DE3) by metal affinity and anion exchange chromatography, and gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene Hp0620, structure-based phylogenetic tree of diphosphatases, expression of His-tagged enzyme in Escherichia coli strain B834(DE3) resulting in a selenomethionine-enzyme
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Oliva, G.; Romero, I.; Ayala, G.; Barrios-Jacobo, I.; Celis, H.
Characterization of the inorganic pyrophosphatase from the pathogenic bacterium Heliobacter pylori
Arch. Microbiol.
174
104-110
2000
Helicobacter pylori, Helicobacter pylori 8823
Wu, C.A.; Lokanath, N.K.; Kim, D.Y.; Park, H.J.; Hwang, H.Y.; Kim, S.T.; Suh, S.W.; Kim, K.K.
Structure of inorganic pyrophosphatase from Helicobacter pylori
Acta Crystallogr. Sect. D
D61
1459-1464
2005
Helicobacter pylori
Lee, M.J.; Huang, H.; Lin, W.; Yang, R.R.; Liu, C.L.; Huang, C.Y.
Activation of Helicobacter pylori inorganic pyrophosphatase and the importance of Cys16 in thermostability, enzyme activation and quaternary structure
Arch. Microbiol.
188
473-482
2007
Helicobacter pylori (P56153), Helicobacter pylori
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