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3.6.1.1: inorganic diphosphatase

This is an abbreviated version!
For detailed information about inorganic diphosphatase, go to the full flat file.

Word Map on EC 3.6.1.1

Reaction

diphosphate
+
H2O
= 2 phosphate

Synonyms

acid PPase, AT727_13205, AtPPA1, AtPPsPase1, BT2127, CBS-PPase, CBS-PPase1, chloroplast inorganic pyrophosphatase 1, class A type PPA, cobalt-dependent inorganic pyrophosphatase, CPE2055, cytosolic PPase, D1C enzyme, dhPPase, E-PPase, EcPpA, EcPPiase, ehPPase, family I inorganic pyrophosphatase, family I PPase, family I pyrophosphatase, family II inorganic pyrophosphatase, family II PPase, H+-PPase, H+-pyrophosphatase, H+-translocating/vacuolar inorganic pyrophosphatase, Hpp1 protein, HVO_0729, HvPPA, hyperthermophilic inorganic pyrophosphatase, inorganic diphosphatase, inorganic PPase, inorganic pyrophosphatase, inorganic pyrophosphatase 1, inorganic pyrophosphatase-like protein, inorganic pyrophosphorylase, IPP, IPP1, Ipp1p, IPPase, LHPPase, M-PPase, manganese-dependent inorganic pyrophosphatase, MazG, MdPPa, membrane-integral inorganic pyrophosphatase, membrane-integral pyrophosphatase, miPPase, mitochondrial pyrophosphatase, Mn2+-bound canonical Family II PPase, More, Mtb PPiase, Mthe_0236, MtPPA1, MtPPiase, nucleotide-regulated pyrophosphatase, OVP1, p26.1a, p26.1b, PfPPase, PH1907, Pho-PPase, phospholysine phosphohistidine inorganic pyrophosphate phosphatase, phosphoprotein p26.1, PPA, PPA1, PpaC, PPase, PPase 1, PPase 2, ppase-1, PPase-2, PPase1, PPase2, PPase4, PPias, PPIase, proton-translocating inorganic pyrophosphatase, PYP-1, pyrophosphatase, pyrophosphatase, inorganic, Pyrophosphate phospho-hydrolase, pyrophosphate phospho-hydrolase 1, Pyrophosphate phosphohydrolase, Pyrophosphate-energized inorganic pyrophosphatase, RmPPase, Rv3628, siPPiase, soluble inorganic pyrophosphatase, soluble inorganic pyrophosphatase 2, soluble pyrophosphatase, soluble-type yeast PPase, sPPAse, ST2226, Tc-sPPase, TC004566, TcasGA2_TC004566, TgPPase, ThPP1, Tm-PPase, TM0913, V-PPase, vacuolar H(+)-PPase, vacuolar H(+)-pyrophosphatase, vacuolar H+-pyrophosphatase, vacuolar H+-translocating inorganic pyrophosphatase, vacuolar H+-translocating pyrophosphatase, vacuolar pyrophosphatase, VHP, VP1, VSP, VVPP1

ECTree

     3 Hydrolases
         3.6 Acting on acid anhydrides
             3.6.1 In phosphorus-containing anhydrides
                3.6.1.1 inorganic diphosphatase

Crystallization

Crystallization on EC 3.6.1.1 - inorganic diphosphatase

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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
purified recombinant wild-type and mutant enzymes in complex with substrate analogue imidodiphosphate, PNP, and/or inhibitor fluoride, 35-40 mg/ml protein in 83mM TES/K+, pH 7.2, 17 mM KCl and 0.05 mM EGTA is mixed with 5 mM MgCl2 and 10 mM NaF, 1 mM PNP, sitting drop vapour diffusion method, 4°C, 3:2 ratio of protein to well solution, the latter containing 100 mM HEPES/K+, pH 7.5, 2.3-2.5 M ammonium sulfate, 3-4% PEG 400, 2-3 days, X-ray diffraction structure determination and anaylsis at 1.75-2.15 A resolution, the mutant H98Q crystals do not contain fluoride ions
purified recombinant His-tagged wild-type and mutant BT2127 variants, sitting-drop vapor diffusion method, X-ray diffraction structure determination and analysis at
regulatory part of Clostridium perfringens CBS-PPase complexed with AMP, PDB ID 3L31
different forms depending on the presence of NH4Cl or (NH4)2SO4 (alpha3'alpha3'')
-
purified enzyme, X-ray diffraction structure determination and analysis
-
wild-type enzyme with bound fluoride trapped in an intermediate conformation, and mutant R43Q with one phosphate and four Mn2+ bound, 7-8 mg/ml protein, with 0.2 M sodium acetate, pH 5.5, using 1.5 M-1.7 M NaCl as precipitant, X-ray diffraction structure determination and analysis at 1.05-1.68 A resolution
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
-
purified recombinant enzyme, hanging drop vapor diffusion method, mixing of 7.7 mg/ml bromelain-treated protein with precipitant solution containing 1.6% Tacsimate, pH 5.0, 80 mM tribasic sodium citrate, pH 5.6, 12.8% PEG 3350, and 20% glycerol, 2 days, 19°C, X-ray diffraction structure determination and analysis at 1.84-2.89A resolution, structure modelling
purified enzyme bound to catalytic metals, to substrate diphosphate, and to one or two inorganic phosphate ions, hanging drop vapour diffusion method, mixing of 0.001 ml of 14 mg/ml protein in 40 mM Tris-HCl, pH 8.0, and 100 mM NaCl, with 0.001 ml of reservoir solution containing 1.65 M NaKHPO4, 100 mM HEPES, pH 7.75, and 2 mM CaCl2, xthe crystals of Mtb PPiase in complex with two phosphate ions are obtained with the reservoir solution composed of 1.6 M KH2PO4, 100 mM HEPES, pH 7.75, and 2 mM CaCl2, and the crystals of Mtb PPiase in complex with one phosphate are obtained with the reservoir solution containing 1.57 M NaKHPO4, 100 mM HEPES pH 7.75 and 2 mM MnCl2, 22°C, X-ray diffraction structure determination and analysis at 1.85-3.30 A resolution, molecular replacement with the structure of the Mtb PPiase-Mg2+ complex as a search model
purified recombinant detagged enzyme in complex with inhibitor 2,4-bis(aziridin-1-yl)-6-(1-phenylpyrrol-2-yl)-S-triazine or N2,N4-dimethyl-6-(1-phenyl-1H-pyrrol-2-yl)-1,3,5-triazine-2,4-diamine, hanging drop vapour diffusion method, mixing of 7 mg/ml protein in 40 mM Tris-HCl pH 8.0, 100 mM NaCl, and 2 mM 2-mercaptoethanol, with reservoir solution containing 0.1 M HEPES pH 7.5, 1.6 M NaH2PO4, and 0.2 M KH2PO4, or 0.1 M HEPES pH 7.75, 1.4 M KH2PO4, and 2 mM CaCl2, respectively, 22°C, overnight, X-ray diffraction structure determination and analysis at 2.65 A and 2.45 A resolution, respectively. 2,4-Bis(aziridin-1-yl)-6-(1-phenylpyrrol-2-yl)-S-triazine is co-crystallized, while N2,N4-dimethyl-6-(1-phenyl-1H-pyrrol-2-yl)-1,3,5-triazine-2,4-diamine is bound by soaking
purified recombinant Rv3628, hanging drop vapour diffusion method, mixing of 0.001 ml protein in150 mM Na HEPES, pH 7.0, and 0.001 ml reservoir solution, containing 1.6 M NaKHPO4, pH 7.0, and equilibration against 1 ml reservoir solution, X-ray diffraction structure determination and analysis at 1.5 A resolution, modeling
purified recombinant detagged wild-type enzyme complexed with Mg2+, vapor diffusion method, 10 mg/ml seleno-methionine substituted PfPPase in buffer are mixed with condition 8% Tacsimate, pH 8.0, and 20% PEG 3350, 20°C, 4 days, X-ray diffraction structure determination and analysis at 2.35 A resolution
purified recombinant enzyme, 20 mg/ml protien hanging drop vapour diffusion method, 3,8% PEG 4000, 0.1 M Na-acetate, pH 5.0-5.2, and 0.02 M MgCl2, asymmetric trimeric crystals, dimerization to hexamers, X-ray diffraction structure determination and analysis at 2.66 A resolution
-
purified recombinant enzyme, hanging drop vapour diffusion method, 20 mg/ml protein in 5 mM Tris-HCl, pH 8.0, and 50 mM NaCl, 18°C, 0.001 ml versus 0.001 ml reservoir solution containing 8% PEG 4000, 0.1 M sodium acetate, pH 4.5, for needle-shaped crystals, and 3.8% PEG 4000, 0.1 M sodium acetate, pH 5.0-5.2, for large crystals, X-ray diffraction structure determination and analysis at 2.7 A resolution
-
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
isoform PpaC in complex with Mn2+, hanging drop vapor diffusion method, using 1.32 M ammonium citrate tribasic
complexed enzyme with each enzyme monomer containing the diphosphate analogue imidodiphosphate and three metal ions per active site: two Mn2+ ions in sites M1 and M2 and an Mg2+ ion in site M3, X-ray diffraction structure determination and analysis at 2.8 A resolution, molecular replacement
purified recombinant enzyme, 5-20 mg/ml protein in 20 mM Tris-HCl, pH 7.0, hanging drop vapour diffusion method, 0.001 ml of protein and well solution are mixed, 2 weeks at room temperature, X-ray diffraction structure determination and analysis at 2.8 A resolution
at 2.7 A resolution. Comparison with Thermus thermophilus and Escherichia coli enzymes
CD and FTIR spectra demonstrate a similar overall fold for enzyme and PPases from Escherichia coli and Thermus thermophilus
-
strucutural model based on structure of Thermus thermophilus enzyme
-
sitting drop vapor diffusion method, using 25% (w/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate pH 4.6, 10 mM calcium chloride, 2 mM ammonium sulfate
purified enzyme, vapour diffusion method, mixing of 10 mg/ml protein solution with 10% PEG 4000, 20% glycerol, 0.03 M glycols, and 0.1 M HEPES/MOPS, pH 7.5, 20°C, 6-8 days, X-ray diffraction structure determination and analysis at 2.35 A resolution, molecular replacement method using ScPPase (PDB ID 1WGJ) as a template
-
vapor diffusion method, using 15-20% (w7v) 2,4-methylpentanediol, and 3% (w/v) PEG4000
-