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2.7.4.6: nucleoside-diphosphate kinase

This is an abbreviated version!
For detailed information about nucleoside-diphosphate kinase, go to the full flat file.

Word Map on EC 2.7.4.6

Reaction

ATP
+
nucleoside diphosphate
=
ADP
+
nucleoside triphosphate

Synonyms

AfNDK, Afu5g03490, ASNDK, At4g09320, At4g11010, At5g63310, HsNDK, kinase, nucleoside diphosphate (phosphorylating), mitochondrial nucleoside diphosphate kinase, MJ1265, More, NDK, NDK B, NDK-1, NDKB, NDP kinase, NDP kinase A, NDP kinase alpha, NDP kinase beta, NDPK, NDPK B, NDPK I, NDPK II, NDPK III, NDPK IIpn, NDPK In, NDPK-3, NDPK-B, NDPK-C, NDPK-D, NDPK-In, NDPK1, NDPK2, NDPK3, NDPK3a, NDPKA, NDPKB, NM23, NM23 metastasis suppressor, Nm23-H1, NM23-H2, NM23-H4, NME1, NME2, NME3, NME4, nucleoside 5'-diphosphate kinase, nucleoside diphosphate (UDP) kinase, nucleoside diphosphate kinase, nucleoside diphosphate kinase 1, nucleoside diphosphate kinase 2, nucleoside diphosphate kinase 3, nucleoside diphosphate kinase 3a, nucleoside diphosphate kinase A, nucleoside diphosphate kinase B, nucleoside diphosphate kinase C, nucleoside diphosphate kinase D, nucleoside diphosphate kinase-1, nucleoside diphosphate kinase-2, nucleoside diphosphate kinases alpha, nucleoside diphosphate kinases beta, nucleoside diphosphate phosphotransferase, nucleoside diphosphokinase, nucleoside-diphosphate kinase 3, nucleotide diphosphate kinase, nucleotide phosphate kinase, ORF454, Os12g36194, OsNDPK2, SwoH, TcNDPK1, TcNDPK3, UDP kinase, uridine diphosphate kinase, WSL12, YSS2 protein

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.4 Phosphotransferases with a phosphate group as acceptor
                2.7.4.6 nucleoside-diphosphate kinase

Crystallization

Crystallization on EC 2.7.4.6 - nucleoside-diphosphate kinase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with nucleotides, vapor diffusion method, using 40-45% (v/v) 2-methyl-2,4-pentane-d12-diol in 0.1 M HEPES (pH 7.5) or 0.1 M MOPS (pH 7.4)
purified recombinant tagged wild-type and mutant enzymes, hanging-drop vapor diffusion method, mixing of 0.001 ml of spontanously degraded 200 mg/ml protein in 50 mmol/L Tris, pH 8.0, 150 mmol/l NaCl, and 5 mmol/l MgCl2, with 0.001 ml of reservoir solution containing 0.1 mol/l potassium sodium tartrate tetrahydrate, and 18% w/v PEG 3350 for the wild-type enzyme and 1 mol/l sodium malonate, pH 7.0, 0.1 mol/l HEPES, pH 7.0, and 0.5% v/v Jeffamine ED-2001, pH 7.0 for the truncated mutant enzymes, X-ray diffraction structure determination and analysis, molecular replacement method using Burkholderia thailandensis NDK, PDB ID 4DUT, as starting model
-
hanging drop vapour diffusion
hanging-drop vapor diffusion method
hanging drop vapour-diffusion method, 0.002 ml protein solution consisting of 10 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 50 mM NaCl, 5 mM EDTA equilibrated against 0.5 ml reservoir solution consisting of 2.25 M ammonium formate and 0.1 M HEPES buffer, pH 7.25, X-ray diffraction structure determination at 2.0 A resolution
sitting-drop vapor-diffusion method, structures are solved of both the apoenzyme and a liganded form with ADP and vanadate ligands
in complex with 3Â’-fluoro-2Â’,3Â’-dideoxyUDP
purified recombinant His-tagged wild-type and selenomethionine-labeled enzymes, sitting drop vapor diffusion method, mixing of 0.001 ml of 10 mg/ml protein in 50 mM Tris, 500 mM NaCl, pH 8.0, with 0.001 ml of precipitatant solution, followed by equilibration aganst 0.1 ml reservoir solution containing 60% v/v Tacsimate, pH 7.0, 20°C, X-ray diffraction structure determination and analysis at 1.39-1.94 A resolution
in the enzyme tetramer, subunits interact by an interface harboring the Kpn loop as in hexamers, but at the opposite side of this loop
purified recombinant enzyme, sitting drop vapor diffusion method, mixing 200 nL of protein solution, containing 15 mg/mL protein, with 200 nL of reservoir solution containing 0.2 M ammonium sulphate, 0.1 M sodium acetate/acetic acid buffer, pH 4.6, with either 30% PEG 2000 monomethyl ether or 25% PEG 4000, 20°C, a few hours, X-ray diffraction structure determination and analysis at 1.62 A resolution
-
sitting drop vapor diffusion method, using 100 mM HEPES-NaOH buffer (pH 7.6), 18% (w/v) PEG 400, and 10 mM EDTA, at 20°C
hanging-drop vapor diffusion method at 18°C. Crystallized in a free state and a substrate-bound form with CDP. The structures are solved to a resolution of 2.35 and 2.2 A, respectively. Crystals with the apo-form are obtained with His6-tagged enzyme, whereas the untagged form is used for co-crystallization with the nucleotide
sitting drop vapor diffusion method, crystal form 1 is a cubic shaped crystal grown from 0.2M ammonium acetate, 0.1M sodium citrate tribasic dehydrate at pH 5.6, and 30%(w/v) polyethylene glycol (PEG) 4000, while crystal form 2 is a rod-shaped crystal grown from 0.19M sodium acetate, 0.09M Tris HCl at pH 8.5, and 28%(w/v) PEG 4000
mutant H118G/F60W in complex with ADP, Ca2+ and phosphate
-
wild-type and mutant S120G in complex with ADP, no significant changes between wild-type and mutant even in the surroundings of the catalytic His residue
-
sitting drop vapor diffusion method, using 100 mM citrate-HCl pH 5.6 and 1850 mM ammonium sulfate
-
crystallized at 24°C using polyethylene glycol 4000 as precipitant. The crystal is hexagonal, belonging to the space group P63, with unit-cell parameters a = b = 72.89, c = 100.87 A. The asymmetric unit contains two subunits of NDP kinase
mutant enzyme D93N crystallizes to hexagonal plates with 2.0 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.5, and to rods with 2.0 M ammonium sulfate, 2% (w/v) PEG400, 0.1 M HEPES, pH 7.5
purified recombinant enzyme mutant R80N, mixing of 200 nl of 11 mg/ml protein in 20 mM Tris-HCl, pH 7.5, and 20 mM MgCl2 with 200 nl of reservoir solution containing 30% w/v PEG 4000, 0.2 M ammonium acetate, and 0.1 M trisodium citrate, pH 5.6, a few hours, 20°C, X-ray diffraction structure determination and analysis at 1.9 A resolution, molecular replacement method using the wild-type Mt-NDPK structure as search model, PDB ID 1k44, modelling
-
crystal structure and crystal-ADP interaction
-
hanging-drop vapor-diffusion method
purified recombinant enzyme in binary complexes with purine and pyrimidine nucleoside diphosphates, acceptors dADP and dCDP and donor ADP, mixing of 0.001 ml of 20 mg/ml protein in 100 mM NaCl, 40 mM MgCl2, 4mM DTT, and 20 mM nucleotides with 0.001 ml of reservoir solution containing 0.2 M magnesium chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000 or 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000, or 0.2 M ammonium acetate, 0.1 M Tris-HCl, pH 8.5, 30% v/v 2-propanol, 3-7 days, 16°C, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution, molecular replacement
hanging drop vapor diffusion method at room temperature
hanging drop vapor diffusion method
-