Information on EC 4.1.2.20 - 2-dehydro-3-deoxyglucarate aldolase

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The expected taxonomic range for this enzyme is: Bacteria, Archaea

EC NUMBER
COMMENTARY
4.1.2.20
-
RECOMMENDED NAME
GeneOntology No.
2-dehydro-3-deoxyglucarate aldolase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
show the reaction diagram
-
-
-
-
2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
show the reaction diagram
mechanism
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
elimination
-
-
elimination
-
-
of an aldehyde, C-C bond cleavage
-
PATHWAY
KEGG Link
MetaCyc Link
Ascorbate and aldarate metabolism
-
D-galactarate degradation I
-
D-glucarate degradation I
-
Metabolic pathways
-
SYSTEMATIC NAME
IUBMB Comments
2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase (pyruvate-forming)
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
2-dehydro-3-deoxygalactarate aldolase
-
-
-
-
2-dehydro-3-deoxygalactarate aldolase
-
-
2-keto-3-deoxy gluconate aldolase
P75682
-
2-keto-3-deoxy-glucarate aldolase
-
-
-
-
2-keto-3-deoxyglucarate aldolase
-
-
-
-
2-keto-3-deoxygluconate-specific aldolase
-
-
4-hydroxy-2-ketoheptane-1,7-dioate aldolase
-
-
5-KDGluc aldolase
-
-
-
-
5-Keto-4-deoxy-(D)-glucarate aldolase
-
-
-
-
5-keto-4-deoxy-D-glucarate aldolase
-
-
-
-
aldolase, 2-keto-3-deoxy-D-glucarate
-
-
-
-
DDG aldolase
-
-
-
-
DDG aldolase
-
-
KDG aldolase
P75682
-
KDG-specific aldolase
-
-
KDGA
P75682
-
KDGLucA
-
-
-
-
YagE
P75682
-
CAS REGISTRY NUMBER
COMMENTARY
37290-56-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
strain CR63MA
-
-
Manually annotated by BRENDA team
strain NCTC 10418
-
-
Manually annotated by BRENDA team
Escherichia coli CR63MA
strain CR63MA
-
-
Manually annotated by BRENDA team
Escherichia coli NCTC 10418
strain NCTC 10418
-
-
Manually annotated by BRENDA team
no activity in Bacillus subtilis
hexarate-grown
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
Picrophilus torridus degrades glucose via a strictly nonphosphorylative Entner-Doudoroff pathway with a 2-keto-3-deoxygluconate-specific aldolase
physiological function
P75682
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
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-dehydro-3-deoxy-6-phospho-D-gluconate
pyruvate + glyceraldehyde-3-phosphate
show the reaction diagram
-
-
-
-
?
2-dehydro-3-deoxy-D-galactonate
?
show the reaction diagram
P75682
-
-
-
?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
-
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
r
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
Escherichia coli CR63MA
-
-
-
-
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
Escherichia coli NCTC 10418
-
-
-
-
-
2-dehydro-3-deoxy-D-gluconate
pyruvate + glyceraldehyde
show the reaction diagram
-
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
-
-
?
2-dehydro-3-deoxy-L-rhamnonate
?
show the reaction diagram
-
-
-
-
?
2-keto-3-deoxy-L-lyxonate
?
show the reaction diagram
-
-
-
-
?
2-keto-3-deoxy-L-mannonate
?
show the reaction diagram
-
-
-
-
?
4-hydroxy-2-ketoheptane-1,7-dioate
pyruvate + succinic semialdehyde
show the reaction diagram
-
-
-
-
?
4-hydroxy-2-ketohexanoic acid
?
show the reaction diagram
-
-
-
-
?
4-hydroxy-2-ketopentanoic acid
?
show the reaction diagram
-
-
-
-
?
5-Dehydro-4-deoxy-D-glucarate
Pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
5-Dehydro-4-deoxy-D-glucarate
Pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
5-Dehydro-4-deoxy-D-glucarate
Pyruvate + tartronate semialdehyde
show the reaction diagram
-
-
-
-
Pyruvate + D-glyceraldehyde
?
show the reaction diagram
-
-
-
-
-
pyruvate + glyceraldehyde
?
show the reaction diagram
P75682
-
-
-
?
Pyruvate + glycolaldehyde
2-Keto-4,5-dihydroxy-L-pentanoic acid
show the reaction diagram
-
-
-
-
-
Pyruvate + glycolaldehyde
2-Keto-4,5-dihydroxy-L-pentanoic acid
show the reaction diagram
Escherichia coli, Escherichia coli CR63MA
-
-
-
-
Pyruvate + glyoxylate
?
show the reaction diagram
-
-
-
-
-
Pyruvate + L-glyceraldehyde
?
show the reaction diagram
-
-
-
-
-
Pyruvate + tartronate semialdehyde
2-Dehydro-3-deoxy-D-glucarate
show the reaction diagram
-
-
-
-
Pyruvate + tartronate semialdehyde
5-Dehydro-4-deoxy-D-glucarate
show the reaction diagram
-
-
-
-
5-Dehydro-4-deoxy-D-glucarate
Pyruvate + tartronate semialdehyde
show the reaction diagram
Escherichia coli CR63MA
-
-
-
-
additional information
?
-
-
inducible enzyme
-
-
-
additional information
?
-
-
glucarate catabolic enzyme
-
-
-
additional information
?
-
Escherichia coli CR63MA
-
glucarate catabolic enzyme
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
additional information
?
-
-
inducible enzyme
-
-
-
additional information
?
-
-
glucarate catabolic enzyme
-
-
-
additional information
?
-
Escherichia coli CR63MA
-
glucarate catabolic enzyme
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Co2+
-
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+
Fe2+
-
absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Mg2+
-
absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Mg2+
-
required
Mg2+
-
requirement for divalent metal ion such as Mn2+, Mg2+ or Co2+
Mg2+
-
required
Mn2+
-
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+
Mn2+
-
required
Mo2+
-
absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
CN-
-
reversed by Mg2+ and Co2+, but not by Fe2+
diphosphate
-
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
8
-
2-dehydro-3-deoxy-6-phospho-D-gluconate
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
0.3
-
2-dehydro-3-deoxy-D-gluconate
-
at 60C 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
-
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
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
-
-
additional information
-
additional information
-
-
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.34
-
2-dehydro-3-deoxy-6-phospho-D-gluconate
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
26.7
-
2-dehydro-3-deoxy-D-gluconate
-
at 60C 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
-
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
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
-
-
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.04
-
2-dehydro-3-deoxy-6-phospho-D-gluconate
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
18772
89
-
2-dehydro-3-deoxy-D-gluconate
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
2381
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.14
-
-
crude extract, at 60C in 50 mM sodium phosphate buffer (pH 6.2)
48
-
-
after 343fold purification, at 60C in 50 mM sodium phosphate buffer (pH 6.2)
additional information
-
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.7
8.6
-
-
8
-
-
assay at
8
-
-
activity assay
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
120000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hexamer
-
crystallographic data
homotetramer
-
4 * 32000, SDS-PAGE
tetramer
P75682
x-ray crystallography
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
complexed with pyruvate
-
hanging drop vapor diffusion method
-
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
P75682
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
-
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
7.5
-
stable
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
70
90
-
at 70C, the enzyme does not lose activity upon incubation for 2 h. The half-lives of the enzyme at 80C and 90C are 20 min and 15 min, respectively
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
homogeneity
-
using metal affinity and size exclusion chromatography
-
DEAE-Sepharose column chromatography and Superdex 75 gel filtration
-
ammonium sulfate precipitation, phenyl-Sepharose column chromatography, UnoQ5 column chromatography, and Superdex 200 gel filtration
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli BL21 (DE3) cells
P75682
expression in Escherichia coli BL21
-
into the plasmid pT7 for expression in Escherichia coli B834DE3 pLacIRARE2 cells
-
expressed in Escherichia coli BL21 (DE3) cells
-
expressed in Escherichia coli BL21 CodonPlus (DE3)-RIL cells
-
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
analysis
-
enzymatic determination of D-glucaric acid
analysis
-
specific enzymatic assay for D-glucarate in human serum
analysis
Escherichia coli NCTC 10418
-
enzymatic determination of D-glucaric acid
-