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Information on EC 5.1.3.31 - D-tagatose 3-epimerase and Organism(s) Pseudomonas cichorii and UniProt Accession O50580
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5.1.3.31 D-tagatose 3-epimeraseIUBMB Comments
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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Word Map
- 5.1.3.31
- d-fructose
- d-psicose
-
epimerization
- d-allulose
- cichorii
-
ketohexose
- tumefaciens
-
izumoring
- l-fuculose
- d-arabinose
- d-sorbose
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aldohexose
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bioproduction
- dpease
- l-xylulose
- synthesis
- loti
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mesorhizobium
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epimerizes
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low-calorie
- d-ribulose
The taxonomic range for the selected organisms is: Pseudomonas cichorii
The expected taxonomic range for this enzyme is: Bacteria, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
d-tagatose 3-epimerase, l-ribulose 3-epimerase, ketose 3-epimerase, rsdte, pcdte, mj1311p, mj1311, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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].
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
1-deoxy 3-keto D-galactitol
1-deoxy 3-keto D-allitol
7% activity compared to the activity with D-tagatose
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-
r
1-deoxy D-tagatose
1-deoxy D-sorbose
0.12% activity compared to the activity with D-tagatose
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-
r
1-deoxy L-tagatose
1-deoxy L-sorbose
0.14% activity compared to the activity with D-tagatose
-
-
r
6-deoxy L-psicose
6-deoxy L-fructose
15.7% activity compared to the activity with D-tagatose
-
-
r
additional information
?
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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
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-
?
additional information
?
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-
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
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mn2+
additional information
Mn2+
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+
additional information
metal enzyme, divalent cations are required for activity
additional information
-
metal enzyme, divalent cations are required for activity
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.127
recombinant enzyme mutant C66S, substrate 1-deoxy D-sorbose, pH 9.0, 60°C
0.15
recombinant enzyme mutant C66S, substrate 1-deoxy L-sorbose, pH 9.0, 60°C
108
recombinant enzyme mutant C66S, substrate D-tagatose, pH 9.0, 60°C
16.9
recombinant enzyme mutant C66S, substrate 6-deoxy L-fructose, pH 9.0, 60°C
7.6
recombinant enzyme mutant C66S, substrate 1-deoxy 3-keto D-allitol, pH 9.0, 60°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the enzyme belongs to the D-tagatose 3-epimerase (D-TE) family
physiological function
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)
additional information
additional information
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
additional information
-
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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
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°
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C66S
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His-tagged wild-type and mutant enzymes from Escherichia coli strain JM109 by nickel affinity chromatography and ultrafiltration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene dte, recombinant expression of C-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain JM109
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
enzyme PcDTE is used industrially to produce D-psicose from the more abundant sugar D-fructose
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yoshida, H.; Yamada, M.; Nishitani, T.; Takada, G.; Izumori, K.; Kamitori, S.
Purification, crystallization and preliminary X-ray diffraction studies of D-tagatose 3-epimerase from Pseudomonas cichorii
Acta Crystallogr. Sect. F
63
123-125
2007
Pseudomonas cichorii
Uechi, K.; Takata, G.; Fukai, Y.; Yoshihara, A.; Morimoto, K.
Gene cloning and characterization of L-ribulose 3-epimerase from Mesorhizobium loti and its application to rare sugar production
Biosci. Biotechnol. Biochem.
77
511-515
2013
Mesorhizobium loti (N0DP12), Mesorhizobium loti, Pseudomonas cichorii (O50580)
Yoshida, H.; Yamada, M.; Nishitani, T.; Takada, G.; Izumori, K.; Kamitori, S.
Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose
J. Mol. Biol.
374
443-453
2007
Pseudomonas cichorii (O50580), Pseudomonas cichorii
Yoshida, H.; Yoshihara, A.; Ishii, T.; Izumori, K.; Kamitori, S.
X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates
Appl. Microbiol. Biotechnol.
100
10403-10415
2016
Pseudomonas cichorii (O50580), Pseudomonas cichorii
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