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4.1.99.12: 3,4-dihydroxy-2-butanone-4-phosphate synthase

This is an abbreviated version!
For detailed information about 3,4-dihydroxy-2-butanone-4-phosphate synthase, go to the full flat file.

Word Map on EC 4.1.99.12

Reaction

D-ribulose 5-phosphate
=
formate
 +
L-3,4-dihydroxybutan-2-one 4-phosphate

Synonyms

3,4-dihydroxy 2-butanone-4-phosphate synthase, 3,4-dihydroxy-2-butanone 4-phosphate synthase, 3,4-dihydroxy-2-butanone-4-phosphate synthase, AtRIBA1, AtRIBA2, bifunctional GCHYII/DHBP, bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase, DBPS, DHBP synthase, DHBPS, DHBPS/GCHII, dihydroxybutanone phosphate synthase, L-3,4-dihydroxy-2-butanone 4-phosphate synthase, L-3,4-dihydroxy-2-butanone-4-phosphate synthase, LcRIBA, More, Mtb-DHBPS, Mtb-ribA2, NbRibA, Rib3, ribA, ribA2, ribB, Sp0176, vDHBPS, vribB

ECTree

     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.99 Other carbon-carbon lyases
                4.1.99.12 3,4-dihydroxy-2-butanone-4-phosphate synthase

Crystallization

Crystallization on EC 4.1.99.12 - 3,4-dihydroxy-2-butanone-4-phosphate synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant apoenzyme in complex with the substrate ribulose 5-phosphate, sitting drop vapour diffusion method, 0.003 ml of 17-34 mg/ml protein in 50 mM Tris-HCl, pH 7.5, is mixed with 0.001 ml of reservoir solution containing 85 mM sodium citrate, pH 5.0, and 17% PEG 8000, with or without 5 mM EDTA, equilibration against 0.3 ml reservoir solution, 0.003 ml of the complex solution is mixed with 0.001 ml of 90 mM Mes/NaOH, pH 6.0, containing 18% PEG 8000, addition of 2 mM D-ribulose 5-phosphate, 20°C, X-ray diffraction structure determination and analysis at 1.6-1.7 A resolution, molecular replacement, modelling
reinterpretation of the space-group symmetry is reported for two crystal structures, PDB codes 1tks and 1tku
purified recombinant enzyme, hanging drop vapour diffusion method at room temperature, 4-5 days, 0.0022 ml of protein solution containing 24 mg/ml protein in 50 mM Tris-HCl pH 7.5, is mixed with 0.0007 ml of precipitating well solution containing 3 M CsCl, 3 M Cs-formate, 20 mM Bis-Tris-propane-NaOH, pH 6.9, or 6 M sodium formate, 25 mM HEPES-NaOH, pH 7.0, labeling with 1.5 mM Au(CN)2, X-ray diffraction structure determination and analysis at 1.4-2.4 A resolution, multiwavelength anomalous diffraction
purified enzyme mutant H147S in complex with substrate ribulose 5-phosphate, monoclinic crystal form, X-ray diffraction structure determination and analysis at 1.55-1.7 A resolution
-
purified recombinant bifunctional enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 20-25 mg/ml protein in 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM DTT, with 0.001 ml of reservoir solutioncontaining 0.1 M Na HEPES pH 7.5, 15%(w/v) PEG 8000, equilibration against 0.04 ml reservoir solution, 20°C, 2-4 days, X-ray diffraction structure determination and analysis at 3.0 A resolution
three crystal structures of Mtb-DHBPS domain in complex with phosphate and glycerol at pH 6.0, with sulfate at pH 4.0 and with zinc and sulfate at pH 4.0 are determined at 1.8, 2.06 and 2.06 A resolution, respectively
purified recombinant enzyme, crystallization of different enzyme complexes: E-SO42-, E-SO42-Mg2+, E-SO42-Mn2+, E-SO42-Mn2+-glycerol, and E-SO42-Zn2+ complexes with X-ray diffraction structure determination and and analysis at resolutions that extend to 1.55 A, 0.98 A, 1.60 A, 1.16 A, and 1.00 A, respectively, divalent cation-free enzyme from 24-30% PEG 5000 monomethyl ether, 0.2 M Li2SO4, and 0.1 M MES-NaOH, pH 6.0-6.5, by the hanging drop vapor diffusion method, to prepare divalent cation-containing crystals, 200 mM MgCl2, 200 mM MnCl2, or 200 mM zinc acetate are added to the crystals for 8-16 h in soaking solutions of the well solutions omitting Li2SO4 and 4% higher in the concentration of PEG 5000 monomethyl ether
-
purified recombinnat enzyme divalent cation free, soaked in Zn2+ or soaked in Mg2+, hanging drop vapor diffusion method, room temperature, 0.001 ml of 7 mg/ml protein in 50 mM Tris-HCl, pH 7.5, is mixed with 0.001 ml well solution containing 24-30% PEG monomethyl ether, 0.2 M Li2SO4, and 0.1 M MES-NaOH, pH 6.0-6.5, 1 week-3 months, rectangular plates, X-ray diffraction structure determination and analysis at 1.5 A, 1.0 A, and 1.8 A resolution, respectively
-
the crystal structures of Salmonella DHBPS in complex with sulfate, D-ribulose 5-phosphate and sulfate-zinc ion is determined at a resolution of 2.80, 2.52, and 1.86 A, respectively. Analysis of these crystal structures reveals that the acidic loop (residues 34-39) responsible for the acid-base catalysis is disordered in the absence of substrate or metal ion at the active site. Upon binding either substrate or sulfate and metal ions, the acidic loop becomes stabilized, adopts a closed conformation and interacts with the substrate
purified recombinant His-tagged enzyme, hanging-drop vapor diffusion method, mixing of 0.001 ml of 5 mg/ml protein in 5 mM Tris-HCl, pH 8.0, and 50 mM NaCl, with 0.001 ml of reservoir solution containing ammonium sulfate 2.0 M and 0.1 M BisTris pH7.02, X-ray diffraction structure determination and analysis at 2.0 A resolution
purified enzyme in apoform or in complex with inhibitor 4-phospho-D-erythronohydroxamic acid, or substrate and substrate plus metal ions, sitting drop vapor diffusion method, mixing of 0.001 ml of 20 mg/ml protein in 25 mM Tris-HCl, pH 8.0, with 0.01 ml crystallization solution, containing for the apo form enzyme 0.2 M Na2HPO4, pH 9.1, and 20% PEG 3350, for phosphate-bound enzyme 0.2 M NaH2PO4, pH 4.5 and 20% PEG 3350, the Ru5P and 4PEH complex crystals are obtained by mixing vDHBPS with 10 mM Ru5P or 4PEH and incubation for 30 min at 20°C, grown in 0.2 M Na2HPO4, pH 9.1 and 20% PEG3350, the enzyme-Ru5P-Zn2+ and enzyme-4PEH-Zn2+ complex crystals are obtained by soaking complex crystals in 100 mM ZnCl2 for 12 h at 20°C, X-ray diffraction structure determination and analysis at 1.96 A, 1.86 A, 1.59 A, and 2.04 A resolution, respectively, modelling