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Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus

Rahman, M.M.; Andberg, M.; Koivula, A.; Rouvinen, J.; Hakulinen, N.; Acta Crystallogr. Sect. F 72, 604-608 (2016)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
heterologously expressed in Escherichia coli
Caulobacter vibrioides
Crystallization (Commentary)
Crystallization
Organism
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°
Caulobacter vibrioides
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
D-xylonate
Caulobacter vibrioides
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
?
D-xylonate
Caulobacter vibrioides ATCC 19089
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Caulobacter vibrioides
Q9A9Z2
-
-
Caulobacter vibrioides ATCC 19089
Q9A9Z2
-
-
Purification (Commentary)
Commentary
Organism
-
Caulobacter vibrioides
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-xylonate
-
746662
Caulobacter vibrioides
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
D-xylonate
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
746662
Caulobacter vibrioides
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
D-xylonate
-
746662
Caulobacter vibrioides ATCC 19089
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
D-xylonate
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
746662
Caulobacter vibrioides ATCC 19089
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
Cloned(Commentary) (protein specific)
Commentary
Organism
heterologously expressed in Escherichia coli
Caulobacter vibrioides
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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°
Caulobacter vibrioides
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
D-xylonate
Caulobacter vibrioides
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
?
D-xylonate
Caulobacter vibrioides ATCC 19089
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
-
Caulobacter vibrioides
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
D-xylonate
-
746662
Caulobacter vibrioides
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
D-xylonate
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
746662
Caulobacter vibrioides
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
D-xylonate
-
746662
Caulobacter vibrioides ATCC 19089
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
D-xylonate
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
746662
Caulobacter vibrioides ATCC 19089
2-dehydro-3-deoxy-D-xylonate + H2O
-
-
-
?
General Information
General Information
Commentary
Organism
metabolism
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
Caulobacter vibrioides
General Information (protein specific)
General Information
Commentary
Organism
metabolism
the enzyme is involved in a nonphosphorylative oxidation pathway of pentose sugars
Caulobacter vibrioides
Other publictions for EC 4.2.1.82
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
749370
Rahman
The crystal structure of D-xy ...
Caulobacter vibrioides, Caulobacter vibrioides ATCC 19089
Sci. Rep.
8
865
2018
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1
1
-
-
-
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1
-
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4
-
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1
-
-
-
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2
1
1
-
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1
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1
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1
1
1
-
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-
1
-
-
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-
1
-
-
-
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2
1
1
-
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1
-
-
-
-
-
-
-
-
-
746662
Rahman
Crystallization and X-ray dif ...
Caulobacter vibrioides, Caulobacter vibrioides ATCC 19089
Acta Crystallogr. Sect. F
72
604-608
2016
-
-
1
1
-
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-
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2
-
6
-
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1
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4
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-
1
-
1
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2
-
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-
1
-
-
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-
4
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
747219
Jiang
Characterization of D-xylonat ...
Escherichia coli, Escherichia coli K12
Bioengineered
6
227-232
2015
-
-
-
-
-
-
4
1
-
2
1
2
-
3
-
-
1
-
-
-
-
-
2
-
1
1
1
-
1
1
-
-
-
-
-
-
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-
-
-
-
-
4
-
1
-
2
1
2
-
-
-
1
-
-
-
-
2
-
1
1
1
-
1
1
-
-
-
-
-
-
-
-
698940
Johnsen
D-xylose degradation pathway i ...
Haloferax volcanii
J. Biol. Chem.
284
27290-27303
2009
1
-
1
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-
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-
2
-
1
3
-
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10
-
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1
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1
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3
1
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-
-
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-
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1
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1
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2
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1
3
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1
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1
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3
1
-
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1
1
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-
-
701792
Meijnen
Establishment of oxidative D-x ...
Caulobacter vibrioides
Appl. Environ. Microbiol.
75
2784-2791
2009
-
-
1
-
-
-
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1
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4
-
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1
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1
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1
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1
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-
-
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1
1
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648798
Dahms
D-xylo-aldonate dehydratase ...
Pseudomonas sp., Pseudomonas sp. MSU-1
Methods Enzymol.
90
302-305
1982
1
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-
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2
2
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6
-
2
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8
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1
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1
1
8
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1
-
2
-
1
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-
1
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-
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-
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2
-
2
-
6
-
2
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1
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1
1
8
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1
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2
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1
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