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EC Tree
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
kdg aldolase, ddg aldolase, 2-dehydro-3-deoxygalactarate aldolase, 2-keto-3-deoxy gluconate aldolase, 5-keto-4-deoxy-(d)-glucarate aldolase, 5-keto-4-deoxy-d-glucarate aldolase, 4-hydroxy-2-ketoheptane-1,7-dioate aldolase, kdg-specific aldolase,
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2-dehydro-3-deoxygalactarate aldolase
2-keto-3-deoxy gluconate aldolase
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2-keto-3-deoxy-glucarate aldolase
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2-keto-3-deoxyglucarate aldolase
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2-keto-3-deoxygluconate-specific aldolase
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4-hydroxy-2-ketoheptane-1,7-dioate aldolase
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5-KDGluc aldolase
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5-Keto-4-deoxy-(D)-glucarate aldolase
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5-keto-4-deoxy-D-glucarate aldolase
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aldolase, 2-keto-3-deoxy-D-glucarate
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KDG-specific aldolase
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2-dehydro-3-deoxygalactarate aldolase
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2-dehydro-3-deoxygalactarate aldolase
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DDG aldolase
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KDGA
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2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
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2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
mechanism
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elimination
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elimination
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of an aldehyde, C-C bond cleavage
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2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase (pyruvate-forming)
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2-dehydro-3-deoxy-6-phospho-D-gluconate
pyruvate + glyceraldehyde-3-phosphate
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?
2-dehydro-3-deoxy-D-galactonate
?
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?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
2-dehydro-3-deoxy-D-gluconate
pyruvate + glyceraldehyde
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the enzyme is highly specific for 2-dehydro-3-deoxy-D-gluconate with up to 2000fold higher catalytic efficiency compared to 2-dehydro-3-deoxy-6-phosphogluconate
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-
?
2-dehydro-3-deoxy-L-rhamnonate
?
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-
?
2-keto-3-deoxy-L-lyxonate
?
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?
2-keto-3-deoxy-L-mannonate
?
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-
?
4-hydroxy-2-ketoheptane-1,7-dioate
pyruvate + succinic semialdehyde
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?
4-hydroxy-2-ketohexanoic acid
?
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-
?
4-hydroxy-2-ketopentanoic acid
?
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-
?
5-dehydro-4-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
Pyruvate + D-glyceraldehyde
?
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?
pyruvate + glyceraldehyde
?
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?
pyruvate + glycolaldehyde
2-oxo-4,5-dihydroxy-L-pentanoic acid
Pyruvate + glyoxylate
?
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?
Pyruvate + L-glyceraldehyde
?
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?
pyruvate + tartronate semialdehyde
2-dehydro-3-deoxy-D-glucarate
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-
?
pyruvate + tartronate semialdehyde
5-dehydro-4-deoxy-D-glucarate
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-
?
additional information
?
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2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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-
?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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-
?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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-
?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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r
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
5-dehydro-4-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
5-dehydro-4-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
5-dehydro-4-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
5-dehydro-4-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
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?
pyruvate + glycolaldehyde
2-oxo-4,5-dihydroxy-L-pentanoic acid
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?
pyruvate + glycolaldehyde
2-oxo-4,5-dihydroxy-L-pentanoic acid
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?
pyruvate + glycolaldehyde
2-oxo-4,5-dihydroxy-L-pentanoic acid
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?
additional information
?
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inducible enzyme
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?
additional information
?
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glucarate catabolic enzyme
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?
additional information
?
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glucarate catabolic enzyme
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?
additional information
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glucarate catabolic enzyme
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?
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additional information
?
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additional information
?
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inducible enzyme
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?
additional information
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glucarate catabolic enzyme
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?
additional information
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glucarate catabolic enzyme
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?
additional information
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glucarate catabolic enzyme
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?
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Fe2+
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absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Mo2+
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absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Co2+
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absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Co2+
requirement for divalent metal ion such as Mn2+, Mg2+ or Co2+
Mg2+
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Mg2+
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absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Mg2+
requirement for divalent metal ion such as Mn2+, Mg2+ or Co2+
Mn2+
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absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Mn2+
requirement for divalent metal ion such as Mn2+, Mg2+ or Co2+
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CN-
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reversed by Mg2+ and Co2+, but not by Fe2+
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8
2-dehydro-3-deoxy-6-phospho-D-gluconate
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at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
0.3
2-dehydro-3-deoxy-D-gluconate
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at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
0.078
2-dehydro-3-deoxy-L-rhamnonic acid
data for Mg2+-activated YfaU
0.8
2-keto-3-deoxy-L-lyxonate
data for Mg2+-activated YfaU
0.14
2-keto-3-deoxy-L-mannonate
data for Mg2+-activated YfaU
0.1 - 0.15
4-hydroxy-2-ketoheptane-1,7-dioate
0.05
4-hydroxy-2-ketohexanoic acid
data for Ni2+-activated YfaU
0.1
4-hydroxy-2-ketopentanoic acid
data for Ni2+-activated YfaU
0.000065
5-dehydro-4-deoxy-D-glucarate
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additional information
additional information
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0.1
4-hydroxy-2-ketoheptane-1,7-dioate
data for Ni2+-activated YfaU
0.15
4-hydroxy-2-ketoheptane-1,7-dioate
data for Mg2+-activated YfaU
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0.34
2-dehydro-3-deoxy-6-phospho-D-gluconate
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at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
26.7
2-dehydro-3-deoxy-D-gluconate
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at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
0.4
2-dehydro-3-deoxy-L-rhamnonic acid
data for Mg2+-activated YfaU
0.3
2-keto-3-deoxy-L-lyxonate
data for Mg2+-activated YfaU
0.3
2-keto-3-deoxy-L-mannonate
data for Mg2+-activated YfaU
0.54 - 299
4-hydroxy-2-ketoheptane-1,7-dioate
447
4-hydroxy-2-ketohexanoic acid
data for Ni2+-activated YfaU
396
4-hydroxy-2-ketopentanoic acid
data for Ni2+-activated YfaU
27.3
5-dehydro-4-deoxy-D-glucarate
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0.54
4-hydroxy-2-ketoheptane-1,7-dioate
data for Mg2+-activated YfaU
299
4-hydroxy-2-ketoheptane-1,7-dioate
data for Ni2+-activated YfaU
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0.04
2-dehydro-3-deoxy-6-phospho-D-gluconate
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at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
89
2-dehydro-3-deoxy-D-gluconate
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at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
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0.14
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crude extract, at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
48
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after 343fold purification, at 60°C in 50 mM sodium phosphate buffer (pH 6.2)
additional information
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8
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assay at
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brenda
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brenda
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brenda
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no activity in Bacillus subtilis
hexarate-grown
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brenda
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brenda
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brenda
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Uniprot
brenda
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UniProt
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brenda
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metabolism
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Picrophilus torridus degrades glucose via a strictly nonphosphorylative Entner-Doudoroff pathway with a 2-keto-3-deoxygluconate-specific aldolase
physiological function
overexpression of YagE increases cell viability in the presence of certain bactericidal antibiotics, indicating a putative biological role of YagE as a prophage encoded virulence factor enabling the survival of bacteria in the presence of certain antibiotics
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32000
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4 * 32000, SDS-PAGE
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hexamer
crystallographic data
homotetramer
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4 * 32000, SDS-PAGE
tetramer
x-ray crystallography
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hanging drop vapor diffusion method
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micro batch method, cocrystallization of YagE with 2-keto-3-deoxy galactonate and with pyruvate and glyceraldehyde in 100 mM HEPES pH 6.5, 200 mM MgCl2, 15% (w/v) PEG 3350, 50 mM pyruvate, and 50 mM glyceraldehyde
the crystal structure of apo-YfaU is determined to 1.39 A resolution and the structure of a Mg2+-pyruvate product complex to 1.93 A resolution
hanging drop vapour diffusion method with 10% PEG 8000, 100 mM Tris-HCl buffer pH 6.8 and 20 mM MnCl2
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70 - 90
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at 70°C, the enzyme does not lose activity upon incubation for 2 h. The half-lives of the enzyme at 80°C and 90°C are 20 min and 15 min, respectively
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ammonium sulfate precipitation, phenyl-Sepharose column chromatography, UnoQ5 column chromatography, and Superdex 200 gel filtration
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DEAE-Sepharose column chromatography and Superdex 75 gel filtration
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using metal affinity and size exclusion chromatography
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expressed in Escherichia coli BL21 (DE3) cells
expressed in Escherichia coli BL21 CodonPlus (DE3)-RIL cells
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expression in Escherichia coli BL21
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into the plasmid pT7 for expression in Escherichia coli B834DE3 pLacIRARE2 cells
expressed in Escherichia coli BL21 (DE3) cells
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expressed in Escherichia coli BL21 (DE3) cells
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analysis
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enzymatic determination of D-glucaric acid
analysis
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specific enzymatic assay for D-glucarate in human serum
analysis
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enzymatic determination of D-glucaric acid
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Wood, W.A.
2-Keto-3-deoxy-6-phosphogluconic and related aldolases
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
7
281-302
1972
Escherichia coli, no activity in Bacillus subtilis
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brenda
Fish, D.C.; Blumenthal, H.J.
2-keto-3-deoxy-D-Glucarate aldolase
Methods Enzymol.
9
529-534
1966
Escherichia coli, Escherichia coli CR63MA
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brenda
Jeffcoat, R.; Dagley, S.
Bacterial hydrolases and aldolases in evolution
Nature New Biol.
241
186-187
1973
Klebsiella aerogenes
brenda
Marsh, C.A.
An enzymatic determination of D-glucaric acid by conversion to pyruvate
Anal. Biochem.
145
266-272
1985
Escherichia coli, Escherichia coli NCTC 10418
brenda
Blumenthal, H.J.; Lucuta, V.L.; Blumenthal, D.C.
Specific enzymatic assay for D-glucarate in human serum
Anal. Biochem.
185
286-293
1990
Escherichia coli
brenda
Hubbard, B.K.; Koch, M.; Palmer, D.R.J.; Babbitt, P.C.; Gerlt, J.A.
Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli
Biochemistry
37
14369-14375
1998
Escherichia coli
brenda
Blackwell, N.C.; Cullis, P.M.; Cooper, R.A.; Izard, T.
Rhombohedral crystals of 2-dehydro-3-deoxygalactarate aldolase from Escherichia coli
Acta Crystallogr. Sect. D
55
1368-1369
1999
Escherichia coli
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brenda
Izard, T.; Blackwell, N.C.
Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism
EMBO J.
19
3849-3856
2000
Escherichia coli (P23522), Escherichia coli
brenda
Li, X.; Huang, H.; Song, X.; Wang, Y.; Xu, H.; Teng, M.; Gong, W.
Purification, crystallization and preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from Leptospira interrogans
Acta Crystallogr. Sect. F
62
1269-1270
2006
Leptospira interrogans
brenda
Rea, D.; Hovington, R.; Rakus, J.F.; Gerlt, J.A.; Fueloep, V.; Bugg, T.D.; Roper, D.I.
Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12
Biochemistry
47
9955-9965
2008
Escherichia coli (P23522)
brenda
Reher, M.; Fuhrer, T.; Bott, M.; Schoenheit, P.
The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate-specific aldolase
J. Bacteriol.
192
964-974
2010
Picrophilus torridus
brenda
Bhaskar, V.; Kumar, M.; Manicka, S.; Tripathi, S.; Venkatraman, A.; Krishnaswamy, S.
Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis
Proteins
79
1132-1142
2011
Escherichia coli (P75682), Escherichia coli
brenda
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