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EC Tree
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
d-xylonate dehydratase, xylonate dehydratase, ccxydht,
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D-xylo-aldonate dehydratase
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dehydratase, D-xylonate
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CcXyDHT
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D-xylonate dehydratase
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D-xylonate dehydratase
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D-xylonate dehydratase
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YjhG
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D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O
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C-O bond cleavage by elimination of water
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D-xylonate hydro-lyase (2-dehydro-3-deoxy-D-xylonate-forming)
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D-gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
D-xylose
2-dehydro-3-deoxy-D-xylonate + H2O
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additional information
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D-gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
XAD catalyzes the dehydration of D-gluconate at a similar catalytic efficiency as compared with D-xylonate
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D-gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
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at 55% of the rate with D-xylonate
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D-gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
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at 55% of the rate with D-xylonate
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
XAD catalyzes the dehydration of D-xylonate at a similar catalytic efficiency as compared with D-gluconate
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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additional information
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D-galactonate is not utilized
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additional information
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D-galactonate is not utilized
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additional information
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not: D- and L-arabonate, D- and L-fuconate, 6-iodo-6-deoxygalactonate, D- and L-mannonate, D- and L-galactonate, L-gluconate, D-ribonate, D-glucuronate, D-galacturonate, D-galactarate
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additional information
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enzyme functions in the metabolism of D-xylose, but is probably not operative in glucose/gluconate metabolism
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additional information
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not: D- and L-arabonate, D- and L-fuconate, 6-iodo-6-deoxygalactonate, D- and L-mannonate, D- and L-galactonate, L-gluconate, D-ribonate, D-glucuronate, D-galacturonate, D-galactarate
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additional information
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enzyme functions in the metabolism of D-xylose, but is probably not operative in glucose/gluconate metabolism
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
additional information
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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D-xylonate
2-dehydro-3-deoxy-D-arabinonate + H2O
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additional information
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enzyme functions in the metabolism of D-xylose, but is probably not operative in glucose/gluconate metabolism
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additional information
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enzyme functions in the metabolism of D-xylose, but is probably not operative in glucose/gluconate metabolism
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[2Fe-2S]-center
each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion
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FeSO4
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addition of 5 mM to the EDTA-inhibited enzyme results in 75% of the original activity
MgCl2
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addition of 5 mM to the EDTA-inhibited enzyme results in 100% of the original activity
MgSO4
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addition of 5 mM to the EDTA-inhibited enzyme results in 100% of the original activity
PbCl2
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addition of 5 mM to the EDTA-inhibited enzyme results in 50% of the original activity
additional information
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absolute requirement for a divalent cation, no reactivation of EDTA-inhibited enzyme by CuSO4, CoCl2, ZnSO4 and NiCl2, all at 5 mM
Mg2+
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Mg2+
each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion
Mg2+
5 mM, required for activity, activates
Mn2+
5 mM, required for activity, activates
Mn2+
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addition of 5 mM to the EDTA-inhibited enzyme results in 13% of the original activity
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2-mercaptoethanol
1 mM, 44% loss of activity
dithiothreitol
1 mM, 70% loss of activity
additional information
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not inhibited by thiols, iodoacetic acid, p-mercuribenzoate or N-ethylmaleimide, all at 2 mM
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xylose
xylonate dehydratase activity is induced 2fold in xylose-grown cells
additional information
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enzyme is induced by growth on D-xylose, but not by D-gluconate, D-glucose, L-arabinose or D-fucose
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Dehydration
Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus.
Dehydration
In vitro reconstitution and characterisation of the oxidative D-xylose pathway for production of organic acids and alcohols.
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0.4
D-gluconate
at 42°C, in 0.1 M Tris-HCl buffer, pH 7.5, 2.5 M KCl, 50 mM MgCl2
0.55
D-xylonate
at 42°C, in 0.1 M Tris-HCl buffer, pH 7.5, 2.5 M KCl, 50 mM MgCl2
4.88
D-xylonate
pH 8.0, 30°C
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1.1
100fold purified enzyme, with D-xylonate or D-gluconate as substrate
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8
assay at
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6.7 - 8.5
pH 6.7: about 65% of maximal activity, pH 8.5: about 65% of maximal activity
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30
assay at
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20 - 42
20°C: about 60% of maximal activity, 42°C: about 50% of maximal activity, activity is almost undetectable above 60x01C°
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UniProt
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SwissProt
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SwissProt
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UniProt
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UniProt
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malfunction
in-frame deletion mutant has lost its ability to grow on xylose, but it shows the same phenotype as the wild-type during growth on glucose
metabolism
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is essential for establishing an oxidative D-xylose catabolic pathway in Pseudomonas putida S12, but coexpression of the putative 2-keto-3-deoxy-D-xylonate dehydratase (XylX) improves the biomass yield by approximately 10%, while the growth rate is not altered. When XylA, catalyzing the next and final step in the pathway, is also coexpressed, both the biomass yield and the maximum growth rate increase. Lower-pathway activities of strains S12xylXD and S12xylD, which rely on endogenous semialdehyde dehydrogenase, are about one-half the activity of the strain that coexpresses the alpha-KGSA dehydrogenase (S12xylXAD)
metabolism
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
metabolism
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the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
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45500
8 * 45500, sequence analysis. 8 * 52000, gel filtration
52000
8 * 45500, sequence analysis. 8 * 52000, gel filtration
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homooctamer
8 * 45500, sequence analysis. 8 * 52000, gel filtration
tetramer
crystallographic data, each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion
tetramer
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crystallographic data, each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion
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hanging-drop vapour-diffusion method at 20°C. Crystals that diffracted to 2.66 A resolution are obtained using sodium formate and polyethylene glycol 3350. They belong to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 A, beta = 97.38°
the crystal structure of D-xylonate dehydratase from Caulobacter crescentus is described at 2.7 A resolution and it is compares with other available enzyme structures from the IlvD/EDD protein family
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70
the enzyme is denatured to precipitation above 70°C
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frozen state, several months, stable
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by centrifugation, gel filtration, ammonium sulfate precipitation and ultrafiltration, 100fold. Recombinant XAD purified by Ni-NTA chromatography
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heterologously expressed in Escherichia coli
PCR product cloned into pET19b. The resulting plasmid harvested from Escherichia coli JM109, sequenced, and transformed into Escherichia coli Rosetta(DE3)-pLysS expression strain. In-frame deletion mutant amplified and ligated into pTA131, sequenced, and transformed in Haloferax volcanii H26 DELTApyrE2
xylXABCD, xylXAD, xylXD, xylD or xylX ligated into the vector pJTmcs using the KpnI, XbaI, and XmaJI restriction sites, under the control of the constitutive tac promoter, expressed in Pseudomonas putida S12
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heterologously expressed in Escherichia coli
heterologously expressed in Escherichia coli
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Dahms, A.S.; Donald, A.
D-xylo-aldonate dehydratase
Methods Enzymol.
90
302-305
1982
Pseudomonas sp., Pseudomonas sp. MSU-1
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Johnsen, U.; Dambeck, M.; Zaiss, H.; Fuhrer, T.; Soppa, J.; Sauer, U.; Schoenheit, P.
D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii
J. Biol. Chem.
284
27290-27303
2009
Haloferax volcanii (D4GP40), Haloferax volcanii
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Meijnen, J.P.; de Winde, J.H.; Ruijssenaars, H.J.
Establishment of oxidative D-xylose metabolism in Pseudomonas putida S12
Appl. Environ. Microbiol.
75
2784-2791
2009
Caulobacter vibrioides
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Rahman, M.M.; Andberg, M.; Koivula, A.; Rouvinen, J.; Hakulinen, N.
Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus
Acta Crystallogr. Sect. F
72
604-608
2016
Caulobacter vibrioides (Q9A9Z2), Caulobacter vibrioides, Caulobacter vibrioides ATCC 19089 (Q9A9Z2)
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Jiang, Y.; Liu, W.; Cheng, T.; Cao, Y.; Zhang, R.; Xian, M.
Characterization of D-xylonate dehydratase YjhG from Escherichia coli
Bioengineered
6
227-232
2015
Escherichia coli (P39358), Escherichia coli, Escherichia coli K12 (P39358)
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Rahman, M.M.; Andberg, M.; Koivula, A.; Rouvinen, J.; Hakulinen, N.
The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family
Sci. Rep.
8
865
2018
Caulobacter vibrioides (Q9A9Z2), Caulobacter vibrioides, Caulobacter vibrioides ATCC 19089 (Q9A9Z2)
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