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2.7.1.35: pyridoxal kinase

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

Word Map on EC 2.7.1.35

Reaction

ATP
+
pyridoxal
=
ADP
 +
pyridoxal 5'-phosphate

Synonyms

ePL kinase, ePL kinase 1, hPL kinase, HPLK, kinase (phosphorylating), pyridoxal, kinase, pyridoxal (phosphorylating), LdPdxK, PdxK, pdxY, PKH, PL kinase, PLK, Plk1, PM kinase, PN kinase, PN/PL/PM kinase, pyridoxal 5-phosphate-kinase, pyridoxal kinase, pyridoxal kinase 1, pyridoxal kinase PKL, pyridoxal kinase-like protein SOS4, pyridoxal phosphokinase, pyridoxal/pyridoxine kinase, pyridoxamine kinase, pyridoxine kinase, pyridoxine/pyridoxal/pyridoxamine kinase, salt overly sensitive4, SAV0580, Sos4, StPLK, vitamin B6 kinase

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.1 Phosphotransferases with an alcohol group as acceptor
                2.7.1.35 pyridoxal kinase

Crystallization

Crystallization on EC 2.7.1.35 - pyridoxal kinase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method using 28% PEG 4000, 0.17 M sodium acetate trihydrate, and 0.1 M Tris-HCl (pH 8.5)
-
with 28% (w/v) PEG 4000, 0.17 M sodium acetate trihydrate, 0.1 M Tris-HCl (pH 8.5) as the precipitant in the presence of 10 mM ADP and 10 mM MgCl
-
hanging drop vapour diffusion method using 20 mM potassium phosphate, pH 7.5, 5 mM beta-mercaptoethanol, 0.2 mM EDTA, and 21% PEG 4K, 100 mM Tris-HCl, pH 8.5, 200 mM Na acetate, 40 mM MgSO4, and 10% glycerol
hanging drop vapour diffusion method using 0.1 mM Tris-HCl pH 8.0, 1.8 M NH4Ac, and 3% glycol
hanging drop vapour diffusion method using 100 mM Tris-HCl pH 8.0 and 50% 2-methyl-2,4-pentanediol
in complex with ginkgotoxin and theophylline, hanging drop vapor diffusion method, using 48-50% (w/v) 2-methyl-1,3 propanediol as precipitant, at 22°C
unliganded enzyme and in complex with MgATP, diffraction to 2.0 and 2.2 A rsolution, respectively. both Structures show similar open conformations. Mg2+ and Na+ act in tandem to anchor the ATP at the active site, which itself acts as a sink to bind several molecules of 2-methyl-2,4-pentanediol
purified recombinant His-tagged enzyme in complex with ADP, and subsstrate pyridoxamine or pyridoxine or ginkgotoxin, mixing of 0.0015 ml of protein solution containing 6.5 mg/ml protein, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 2 mM ADP, and 2 mM ligand, with reservoir solution containing 0.1 M sodium cacodylate, pH 6.0, 0.32 M calcium acetate, 4% glycerol, and 18% PEG 8000, and equilibration against 0.5 ml reservoir, 22°C, 2 days, X-ray diffraction structure determination and analysis at 1.85-2.0 A resolution, molecular replacement. Method optimization, overview. The apoform of the enzyme does not crystallize
crystallized in the orthorhombic form using the hanging-drop vapour-diffusion method with sodium citrate as the precipitant, crystals are transferred into a soaking liquid without citrate and two-heavy-atom derivatives are prepared
-
crystals are grown in the presence of 100 mM potassium phosphate, pH 7.2, and 120 mM ammonium sulfate and crystals grown in the presence of 600 mM potassium phosphate, pH 7.2, and in the absence of ammonium sulfate. The crystals are quite stable to X-rays and diffract at 2.2 A resolution
-
hanging drop vapor diffusion method in complex with adenosine 5’-(beta, gamma-methylenetriphosphate)-pyridoxamine, ADP-pyriodoxal 5’-phosphate, and ADP
-
hanging drop vapor diffusion method, in complex with (R)-roscovitine and N6-methyl-(R)-roscovitine
purified enzyme in apoform and in complex with AMP-PNP and pyridoxal (PL), hanging drop vapour diffusion method, for apoform mixing of protein solution with reservoir solution containing 0.1 M HEPES, pH 7.75, 0.2 M CaCl2, 31% v/v PEG 400, and 5% v/v glycerol, and soaking of crystals in solution with 5 mM ligand, at 20°C, X-ray diffraction structure determination and analysis at 2.15 A resolution, molecular replacement using the the coordinates of PdxK from sheep brain as a search model (PDB ID 1RFU), and modelling. The fold is retained and both AMP-PNP and PL occupy the same binding sites when compared to the human orthologue
sitting drop vapor diffusion method, using 0.1 M Tris, pH 8.5, 1 M LiCl2, and 15% (w/v) PEG 6000
-
unliganded StPLK (P212121) and two different tetragonal (P43212) crystal forms (form I and form II) of its complex with PL, ADP, and Mg2+, X-ray diffraction structure determination and analysis at 2.2-2.6 A resolution, modelling
native protein and in complex with its substrates to 1.4?1.85 A resolution. The protein shows a typical ribokinase fold with a central large beta-sheet consisting of nine strands, flanked by three and five structurally conserved alpha-helices