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 hide
4.1.2.20
-
RECOMMENDED NAME
GeneOntology No.
2-dehydro-3-deoxyglucarate aldolase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Ascorbate and aldarate metabolism
-
-
D-galactarate degradation I
-
-
D-glucarate degradation I
-
-
degradation of sugar acids
-
-
Metabolic pathways
-
-
SYSTEMATIC NAME
IUBMB Comments
2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase (pyruvate-forming)
-
CAS REGISTRY NUMBER
COMMENTARY hide
37290-56-5
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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
COMMENTARY hide
LITERATURE
metabolism
-
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
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
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
-
-
-
?
2-dehydro-3-deoxy-D-glucarate
pyruvate + tartronate semialdehyde
show the reaction diagram
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
Pyruvate + D-glyceraldehyde
?
show the reaction diagram
-
-
-
-
-
pyruvate + glyceraldehyde
?
show the reaction diagram
-
-
-
?
pyruvate + glycolaldehyde
2-oxo-4,5-dihydroxy-L-pentanoic acid
show the reaction diagram
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
-
-
-
-
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
-
absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
Mo2+
-
absolute cation requirement, activation in the order of increasing effectiveness: Mg2+, Co2+, Fe2+, Mn2+, Mo2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
CN-
-
reversed by Mg2+ and Co2+, but not by Fe2+
diphosphate
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
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 - 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
-
-
additional information
additional information
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.34
2-dehydro-3-deoxy-6-phospho-D-gluconate
Picrophilus torridus
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
26.7
2-dehydro-3-deoxy-D-gluconate
Picrophilus torridus
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
0.4
2-dehydro-3-deoxy-L-rhamnonic acid
Escherichia coli
-
data for Mg2+-activated YfaU
0.3
2-keto-3-deoxy-L-lyxonate
0.54 - 299
4-hydroxy-2-ketoheptane-1,7-dioate
447
4-hydroxy-2-ketohexanoic acid
Escherichia coli
-
data for Ni2+-activated YfaU
396
4-hydroxy-2-ketopentanoic acid
Escherichia coli
-
data for Ni2+-activated YfaU
27.3
5-dehydro-4-deoxy-D-glucarate
Escherichia coli
-
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04
2-dehydro-3-deoxy-6-phospho-D-gluconate
Picrophilus torridus
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
8212
89
2-dehydro-3-deoxy-D-gluconate
Picrophilus torridus
-
at 60C in 50 mM sodium phosphate buffer (pH 6.2)
1172
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
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
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.7 - 8.6
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
120000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
-
crystallographic data
homotetramer
-
4 * 32000, SDS-PAGE
tetramer
x-ray crystallography
Crystallization/COMMENTARY
ORGANISM
UNIPROT
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
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
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 7.5
-
stable
5078
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
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
LITERATURE
ammonium sulfate precipitation, phenyl-Sepharose column chromatography, UnoQ5 column chromatography, and Superdex 200 gel filtration
-
DEAE-Sepharose column chromatography and Superdex 75 gel filtration
-
homogeneity
-
using metal affinity and size exclusion chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 (DE3) cells
expressed in Escherichia coli BL21 CodonPlus (DE3)-RIL cells
-
expression in Escherichia coli BL21
-
into the plasmid pT7 for expression in Escherichia coli B834DE3 pLacIRARE2 cells
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
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