The enzymes isolated from the bacteria Pseudomonas cichorii , Pseudomonas sp. ST-24 , Rhodobacter sphaeroides and Mesorhizobium loti catalyse the epimerization of various ketoses at the C-3 position, interconverting D-fructose and D-psicose, D-tagatose and D-sorbose, D-ribulose and D-xylulose, and L-ribulose and L-xylulose. The specificity depends on the species. The enzymes from Pseudomonas cichorii and Rhodobacter sphaeroides require Mn2+ [2,3].
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SYSTEMATIC NAME
IUBMB Comments
D-tagatose 3-epimerase
The enzymes isolated from the bacteria Pseudomonas cichorii [2], Pseudomonas sp. ST-24 [1], Rhodobacter sphaeroides [3] and Mesorhizobium loti [4] catalyse the epimerization of various ketoses at the C-3 position, interconverting D-fructose and D-psicose, D-tagatose and D-sorbose, D-ribulose and D-xylulose, and L-ribulose and L-xylulose. The specificity depends on the species. The enzymes from Pseudomonas cichorii and Rhodobacter sphaeroides require Mn2+ [2,3].
specificity is highest with D-fructose and decreases for other substrates in the order: D-tagatose, D-psicose, D-ribulose, D-xylulose and D-sorbose. The equilibrium ratio between D-psicose and D-fructose is 23:77 after 24 h at 40°C
epimerization of D-psicose at 60% compared to the activity with D-tagatose, epimerization of D-fructose at 20% compared to the activity with D-tagatose
epimerization of D-psicose at 60% compared to the activity with D-tagatose, epimerization of D-fructose at 20% compared to the activity with D-tagatose
epimerization of D-ribulose at 90% compared to the activity with D-tagatose, epimerization of D-xylulose at 40% compared to the activity with D-tagatose
epimerization of D-ribulose at 90% compared to the activity with D-tagatose, epimerization of D-xylulose at 40% compared to the activity with D-tagatose
epimerization of L-ribulose at 70% compared to the activity with D-tagatose, epimerization of L-xylulose at 20% compared to the activity with D-tagatose
epimerization of L-ribulose at 70% compared to the activity with D-tagatose, epimerization of L-xylulose at 20% compared to the activity with D-tagatose
RsDTE wild-type shows lower Michaelis-Menten constant (Km), lower turnover number (kcat), but higher catalytic efficiency (kcat/Km) values for D-fructose than for D-psicose. The kcat/Km for D-fructose is 5.5fold higher than for D-psicose, indicating that enzyme RsDTE highly catalyzes D-fructose, although it is a D-tagatose 3-epimerase
RsDTE wild-type shows lower Michaelis-Menten constant (Km), lower turnover number (kcat), but higher catalytic efficiency (kcat/Km) values for D-fructose than for D-psicose. The kcat/Km for D-fructose is 5.5fold higher than for D-psicose, indicating that enzyme RsDTE highly catalyzes D-fructose, although it is a D-tagatose 3-epimerase
RsDTE wild-type shows lower Michaelis-Menten constant (Km), lower turnover number (kcat), but higher catalytic efficiency (kcat/Km) values for D-fructose than for D-psicose. The kcat/Km for D-fructose is 5.5fold higher than for D-psicose, indicating that enzyme RsDTE highly catalyzes D-fructose, although it is a D-tagatose 3-epimerase
D-tagatose 3-epimerase (PcDTE) has a broad substrate specificity, it efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. Substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. 1-Deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. Ligand-binding structure at the catalytic site, overview. Binding structures of 6-deoxy L-psicose, 1-deoxy-3-oxo-D-galactitol, 1-deoxy-D-tagatose, 1-deoxy L-tagatose, L-erythrulose, D-talitol, and glycerol
D-tagatose 3-epimerase (PcDTE) has a broad substrate specificity, it efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. Substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. 1-Deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. Ligand-binding structure at the catalytic site, overview. Binding structures of 6-deoxy L-psicose, 1-deoxy-3-oxo-D-galactitol, 1-deoxy-D-tagatose, 1-deoxy L-tagatose, L-erythrulose, D-talitol, and glycerol
in the active site Mn2+ is coordinated by Glu152, Asp185, His211, and Glu246 at the end of the beta-barrel.O2 and O3 of D-tagatose and/or D-fructose coordinate Mn2+
the enzyme belongs to the D-tagatose 3-epimerase (D-TE) family enzymes. The overall fold of the subunit proves to be similar to those of the D-tagatose 3-epimerase from Pseudomonas cichorii and the D-psicose 3-epimerases from Agrobacterium tumefaciens and Clostridium cellulolyticum. But the situation at the subunit-subunit interface differs substantially from that in D-tagatose 3-epimerase family enzymes. In MJ1311p, Glu125, Leu126 and Trp127 from one subunit are located over the metal-ion-binding site of the other subunit and contribute to the active site, narrowing the substrate-binding cleft. Moreover, the nine residues comprising a trinuclear zinc centre in endonuclease IV are strictly conserved in MJ1311p, although a distinct groove involved in DNA binding is not present. The active-site architecture of MJ1311p is quite unique and is substantially different from those of D-tagatose 3-epimerase family enzymes and endonuclease IV
the enzyme belongs to the D-tagatose 3-epimerase (D-TE) family enzymes. The overall fold of the subunit proves to be similar to those of the D-tagatose 3-epimerase from Pseudomonas cichorii and the D-psicose 3-epimerases from Agrobacterium tumefaciens and Clostridium cellulolyticum. But the situation at the subunit-subunit interface differs substantially from that in D-tagatose 3-epimerase family enzymes. In MJ1311p, Glu125, Leu126 and Trp127 from one subunit are located over the metal-ion-binding site of the other subunit and contribute to the active site, narrowing the substrate-binding cleft. Moreover, the nine residues comprising a trinuclear zinc centre in endonuclease IV are strictly conserved in MJ1311p, although a distinct groove involved in DNA binding is not present. The active-site architecture of MJ1311p is quite unique and is substantially different from those of D-tagatose 3-epimerase family enzymes and endonuclease IV
D-tagatose 3-epimerase (DTE) catalyzes epimerization between D-tagatose and D-sorbose. DTE from Pseudomonas cichorii (PcDTE) has a broad substrate specificity and efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose)
the hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. The sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through. Ligand-binding structure at the catalytic site, overview
the hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. The sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through. Ligand-binding structure at the catalytic site, overview
the O1 of substrate D-fructose forms hydrogen bonds with His192 and Glu162 to help the correct metal coordination of the substrate. The O2 forms hydrogen bonds with His192 and Arg221. Glu156 forms hydrogen bonds with O3, and Glu250 directs its OE2 atom to a hydrogen atom attached to C3. Because D-fructose has the same configurations of C1, C2 and C3 as D-tagatose, the interactions between D-fructose at the 1-, 2- and 3-positions and the enzyme are very similar to those in other DTE/DPE family enzymes. Residue R118 forms a hydrogen bond with O4 of D-fructose and may regulate the substrate specificity. The strengthened hydrophobic interaction may attribute to the recognition of D-tagatose, D-psicose, and D-sorbose. Enzyme homology modeling and structure comparisons, overview
the O1 of substrate D-fructose forms hydrogen bonds with His192 and Glu162 to help the correct metal coordination of the substrate. The O2 forms hydrogen bonds with His192 and Arg221. Glu156 forms hydrogen bonds with O3, and Glu250 directs its OE2 atom to a hydrogen atom attached to C3. Because D-fructose has the same configurations of C1, C2 and C3 as D-tagatose, the interactions between D-fructose at the 1-, 2- and 3-positions and the enzyme are very similar to those in other DTE/DPE family enzymes. Residue R118 forms a hydrogen bond with O4 of D-fructose and may regulate the substrate specificity. The strengthened hydrophobic interaction may attribute to the recognition of D-tagatose, D-psicose, and D-sorbose. Enzyme homology modeling and structure comparisons, overview
the O1 of substrate D-fructose forms hydrogen bonds with His192 and Glu162 to help the correct metal coordination of the substrate. The O2 forms hydrogen bonds with His192 and Arg221. Glu156 forms hydrogen bonds with O3, and Glu250 directs its OE2 atom to a hydrogen atom attached to C3. Because D-fructose has the same configurations of C1, C2 and C3 as D-tagatose, the interactions between D-fructose at the 1-, 2- and 3-positions and the enzyme are very similar to those in other DTE/DPE family enzymes. Residue R118 forms a hydrogen bond with O4 of D-fructose and may regulate the substrate specificity. The strengthened hydrophobic interaction may attribute to the recognition of D-tagatose, D-psicose, and D-sorbose. Enzyme homology modeling and structure comparisons, overview
the asymmetric unit contained two homologous subunits, and the dimer is generated by twofold symmetry. In MJ1311p, Glu125, Leu126 and Trp127 from one subunit are located over the metal-ion-binding site of the other subunit and contribute to the active site, narrowing the substrate-binding cleft. Three-dimensional structural analysis of MJ1311p, overview. The enzyme MJ1311p monomer is folded into an (alpha/beta)8 barrel carrying four additional helical segments, alpha1', alpha2', alpha4', and alpha6', which are inserted before alpha1, alpha2, alpha4, and alpha6, respectively. The quaternary-structural arrangement of MJ1311p is notably different from those of D-TE family enzymes
the asymmetric unit contained two homologous subunits, and the dimer is generated by twofold symmetry. In MJ1311p, Glu125, Leu126 and Trp127 from one subunit are located over the metal-ion-binding site of the other subunit and contribute to the active site, narrowing the substrate-binding cleft. Three-dimensional structural analysis of MJ1311p, overview. The enzyme MJ1311p monomer is folded into an (alpha/beta)8 barrel carrying four additional helical segments, alpha1', alpha2', alpha4', and alpha6', which are inserted before alpha1, alpha2, alpha4, and alpha6, respectively. The quaternary-structural arrangement of MJ1311p is notably different from those of D-TE family enzymes
the asymmetric unit contained two homologous subunits, and the dimer is generated by twofold symmetry. In MJ1311p, Glu125, Leu126 and Trp127 from one subunit are located over the metal-ion-binding site of the other subunit and contribute to the active site, narrowing the substrate-binding cleft. Three-dimensional structural analysis of MJ1311p, overview. The enzyme MJ1311p monomer is folded into an (alpha/beta)8 barrel carrying four additional helical segments, alpha1', alpha2', alpha4', and alpha6', which are inserted before alpha1, alpha2, alpha4, and alpha6, respectively. The quaternary-structural arrangement of MJ1311p is notably different from those of D-TE family enzymes
purified enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 10.3 mg/ml protein in 10 mM potassium phosphate, pH 7.0, with 0.001 ml of reservoir solution composed of 0.2 M ammonium acetate, 30% isopropanol, 0.1 M Tris-HCl, pH 7.5, and equilibration against 0.1 ml reservoir solution, 3-7 days, 20°C, X-ray diffraction structure determination and analysis at 2.64 A resolution, heavy metal labeleing, single isomorphous replacement with anomalous scattering, and structure molecular modeling
crystal structures of the enzyme alone and in complexes with D-tagatose and D-fructose are determined at resolutions of 1.79, 2.28, and 2.06 A, respectively
crystals are obtained by the sitting-drop method at room temperature. The crystal belongs to the monoclinic space group P2(1), with unit-cell parameters a = 76.80, b = 94.92, c = 91.73 A , beta = 102.82°
recombinant enzyme mutant PcDTE_C66S in complexes with four deoxy rare sugars, 6-deoxy L-psicose, 1-deoxy 3-keto D-galactitol, 1-deoxy D-tagatose, and 1-deoxy L-tagatose, and with L-erythrulose (a sugar without groups at the 5- and 6-positions), hanging drop vapor diffusion method, mixing of 0.002 ml of 6-7 mg/ml protein in 5 mM Tris-HCl, pH 8.0, with 0.002 ml of reservoir solution containing 6.0-11.0 % w/v PEG 4000 and 100 mM CH3COONa, pH 4.6, and equilibration against 0.45 ml of reservoir solution, microgravity, X-ray diffraction structure determination and analysis at 1.59-2.3 A resolution, molecular replacement using crystal structure, PDB ID 1QUL, as a search model
the Vmax value of the mutant is about one-half of the Vmax value of the wild-type enzyme. The Km values for L-ribulose of the mutant and wild-type enzymes did not differ greatly
site-directed mutagenesis, the enzyme mutant recognizes deoxy sugars as substrates. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms are detected in the hydrophobic groove, while bound ligand molecules in the catalytic site are in the linear form
site-directed mutagenesis, the unique hydrogen bond between Arg118 and O4 of D-fructose is broken when Arg118 is mutated to Trp, the mutation improves the substrate recognition and activity of the enzyme. The mutant enzyme RsDTE_R118W shows decreased catalytic activity compared to the wild-type enzyme toward D-fructose, the kcat/Km for D-tagatose is about twofold higher than for D-psicose. Mutant R118W shows 1.5fold higher catalytic efficiency toward D-tagatose than the wild-type
site-directed mutagenesis, the unique hydrogen bond between Arg118 and O4 of D-fructose is broken when Arg118 is mutated to Trp, the mutation improves the substrate recognition and activity of the enzyme. The mutant enzyme RsDTE_R118W shows decreased catalytic activity compared to the wild-type enzyme toward D-fructose, the kcat/Km for D-tagatose is about twofold higher than for D-psicose. Mutant R118W shows 1.5fold higher catalytic efficiency toward D-tagatose than the wild-type
recombinant C-terminally His-tagged wild-type and mutant enzymes from Escherichia coli strain JM109 by nickel affinity chromatography and ultrafiltration
gene ycjR, DNA and amino acid sequence determination and analysis, sequence comparisons, phylogenetic analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli inclusion bodies by treatment with 20 ml 10 mM Tris-HCl buffer, pH 7.5, containing 1.0 mM EDTA, 4% Triton X-100, incubation at room temperature for 30 min, twice. Then the inclusion bodies are treated with denaturant solution containing 50 mM Tris-HCl buffer, pH 7.5, containing 6 M guanidine-HCl, 0.2 M NaCl, 1 mM EDTA overnight at 4°C. The solubilized enzyme (100 mg protein in 100 ml solution) is gently dropped into 1 l of refolding buffer containing 0.1 M Tris-HCl, pH 7.5, 1 mM MnCl2, and 0.4 M L-arginine, and incubated for 16 h at 4°C, followed by ultrafiltration
D-tagatose 3-epimerase is a useful enzyme for the production of expensive, rare sugars, e.g. D-sorbose and D-psicose, from inexpensive sugars, e.g. D-tagatose and D-fructose
D-tagatose 3-epimerase is a useful enzyme for the production of expensive, rare sugars, e.g. D-sorbose and D-psicose, from inexpensive sugars, e.g. D-tagatose and D-fructose