Information on EC 4.1.2.55 - 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.1.2.55
-
RECOMMENDED NAME
GeneOntology No.
2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3,6-anhydro-alpha-L-galactopyranose degradation
-
-
4-deoxy-L-threo-hex-4-enopyranuronate degradation
-
-
D-fructuronate degradation
-
-
D-galactonate degradation
-
-
D-galacturonate degradation I
-
-
D-glucosaminate degradation
-
-
Entner-Doudoroff pathway I
-
-
Entner-Doudoroff pathway III (semi-phosphorylative)
-
-
Galactose metabolism
-
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L-glucose degradation
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
Pentose phosphate pathway
-
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degradation of sugar acids
-
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Entner Doudoroff pathway
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SYSTEMATIC NAME
IUBMB Comments
2-dehydro-3-deoxy-6-phosphate-D-gluconate/2-dehydro-3-deoxy-6-phosphate-D-galactonate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
In the archaeon Sulfolobus solfataricus the enzyme is involved in glucose and galactose catabolism via the branched variant of the Entner-Doudoroff pathway. It utilizes 2-dehydro-3-deoxy-6-phosphate-D-gluconate and 2-dehydro-3-deoxy-6-phosphate-D-galactonate with similar catalytic efficiency. In vitro the enzyme can also catalyse the cleavage of the non-phosphorylated forms 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate with much lower catalytic efficiency. cf. EC 4.1.2.21, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, and EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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-D-galactonate
pyruvate + D-glyceraldehyde
show the reaction diagram
2-dehydro-3-deoxy-D-galactonate 6-phosphate
pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
2-dehydro-3-deoxy-D-gluconate
pyruvate + D-glyceraldehyde
show the reaction diagram
2-dehydro-3-deoxy-D-gluconate 6-phosphate
pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
2-dehydro-3-deoxy-D-xylonate
pyruvate + glycolaldehyde
show the reaction diagram
2-dehydro-3-deoxy-L-arabinonate
pyruvate + glycolaldehyde
show the reaction diagram
pyruvate + 2-azidoacetaldehyde
?
show the reaction diagram
-
-
-
?
pyruvate + 3-azido-2-hydroxypropanal
?
show the reaction diagram
-
-
-
?
pyruvate + D-erythrose
(4S,5S,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate
show the reaction diagram
-
formation of (4S,5S,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate and (4S,5S,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate in the ratio 35:65
-
-
?
pyruvate + D-glyceraldehyde
2-dehydro-3-deoxy-D-galactonate
show the reaction diagram
pyruvate + D-glyceraldehyde
2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
pyruvate + D-glyceraldehyde
3-deoxy-D-erythro-hex-2-ulosonate
show the reaction diagram
-
formation of 3-deoxy-D-erythro-hex-2-ulosonate and 3-deoxy-D-threo-hex-2-ulosonate in the ratio 45:55
-
-
?
pyruvate + D-glyceraldehyde
3-deoxy-D-threo-hex-2-ulosonate
show the reaction diagram
-
formation of 3-deoxy-D-erythro-hex-2-ulosonate and 3-deoxy-D-threo-hex-2-ulosonate in the ratio 45:55
-
-
?
pyruvate + D-glyceraldehyde 3-phosphate
2-dehydro-3-deoxy-D-galactonate 6-phosphate
show the reaction diagram
-
higher activity with D-glyceraldehyde 3-phosphate compared to D-glyceraldehyde
-
-
r
pyruvate + D-glyceraldehyde 3-phosphate
2-dehydro-3-deoxy-D-gluconate 6-phosphate
show the reaction diagram
pyruvate + D-glyceraldehyde acetonide
3-deoxy-5,6-O-(1-methylethylidene)-D-erythro-hex-2-ulosonate
show the reaction diagram
-
highly stereoselective formation of 3-deoxy-5,6-O-(1-methylethylidene)-D-erythro-hex-2-ulosonate in 92% diastereomeric excess
-
-
?
pyruvate + D-threose
(4R,5R,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate
show the reaction diagram
-
formation of (4S,5R,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate and (4R,5R,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate in the ratio 40:60
-
-
?
pyruvate + D-threose
(4S,5R,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate
show the reaction diagram
-
formation of (4S,5R,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate and (4R,5R,6R)-4,5,6,7-tetrahydroxy-2-oxoheptanoate in the ratio 40:60
-
-
?
pyruvate + glycolaldehyde
2-dehydro-3-deoxy-D-xylonate
show the reaction diagram
pyruvate + glycolaldehyde
2-dehydro-3-deoxy-L-arabinonate
show the reaction diagram
pyruvate + glycolaldehyde
?
show the reaction diagram
-
-
-
?
Pyruvate + glyoxylate
?
show the reaction diagram
-
-
-
-
r
pyruvate + L-erythrose
(4R,5R,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate
show the reaction diagram
-
formation of (4S,5R,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate and (4R,5R,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate in the ratio 60:40
-
-
?
pyruvate + L-erythrose
(4S,5R,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate
show the reaction diagram
-
formation of (4S,5R,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate and (4R,5R,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate in the ratio 60:40
-
-
?
pyruvate + L-glyceraldehyde
2-dehydro-3-deoxy-L-galactonate
show the reaction diagram
-
condensation of pyruvate with L-glyceraldehyde proceeds with no stereocontrol, yielding a 53:47 diastereoisomeric mixture of 2-dehydro-3-deoxy-L-gluconate (anti-(4S,5R)-3-deoxy-2-hexulosonate) and 2-dehydro-3-deoxy-L-galactonate (syn-(4S,5S)-3-deoxy-2-hexulosonate)
-
-
?
pyruvate + L-glyceraldehyde
2-dehydro-3-deoxy-L-gluconate
show the reaction diagram
-
condensation of pyruvate with L-glyceraldehyde proceeds with no stereocontrol, yielding a 53:47 diastereoisomeric mixture of 2-dehydro-3-deoxy-L-gluconate (anti-(4S,5R)-3-deoxy-2-hexulosonate) and 2-dehydro-3-deoxy-L-galactonate (syn-(4S,5S)-3-deoxy-2-hexulosonate)
-
-
?
pyruvate + L-glyceraldehyde
3-deoxy-D-erythro-hex-2-ulosonate
show the reaction diagram
-
formation of 3-deoxy-L-threo-hex-2-ulosonate and 3-deoxy-L-erythro-hex-2-ulosonate in the ratio 50:50
-
-
?
pyruvate + L-glyceraldehyde
3-deoxy-D-threo-hex-2-ulosonate
show the reaction diagram
-
formation of 3-deoxy-L-threo-hex-2-ulosonate and 3-deoxy-L-erythro-hex-2-ulosonate in the ratio 50:50
-
-
?
pyruvate + L-glyceraldehyde acetonide
3-deoxy-5,6-O-(1-methylethylidene)-L-threo-hex-2-ulosonate
show the reaction diagram
-
highly stereoselective formation of 3-deoxy-5,6-O-(1-methylethylidene)-L-threo-hex-2-ulosonate in 94% diastereomeric excess
-
-
?
pyruvate + L-threose
(4R,5S,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate
show the reaction diagram
-
formation of (4S,5S,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate and (4R,5S,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate in the ratio 90:10
-
-
?
pyruvate + L-threose
(4S,5S,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate
show the reaction diagram
-
formation of (4S,5S,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate and (4R,5S,6S)-4,5,6,7-tetrahydroxy-2-oxoheptanoate in the ratio 90:10
-
-
?
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
2-dehydro-3-deoxy-D-galactonate
pyruvate + D-glyceraldehyde
show the reaction diagram
2-dehydro-3-deoxy-D-galactonate 6-phosphate
pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
2-dehydro-3-deoxy-D-gluconate
pyruvate + D-glyceraldehyde
show the reaction diagram
2-dehydro-3-deoxy-D-gluconate 6-phosphate
pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
2-dehydro-3-deoxy-D-xylonate
pyruvate + glycolaldehyde
show the reaction diagram
2-dehydro-3-deoxy-L-arabinonate
pyruvate + glycolaldehyde
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
activity is unaffected by the presence of 0.1 mM ZnCl2
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Hydroxypyruvate
-
-
NaBH4
-
69% inactivation in the presence of NaBH% and pyruvate, complete inactivation when the reaction time is increased to 20 min
additional information
-
no decrease in activity in the presence of 50 mM EDTA
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9.9
2-dehydro-3-deoxy-D-galactonate
0.17
2-dehydro-3-deoxy-D-galactonate 6-phosphate
-
60°C, pH not specified in the publication
25.7
2-dehydro-3-deoxy-D-gluconate
0.1
2-dehydro-3-deoxy-D-gluconate 6-phosphate
-
60°C, pH not specified in the publication
33.3
2-dehydro-3-deoxy-D-xylonate
-
pH 6.5, 50°C
17.6
2-dehydro-3-deoxy-L-arabinonate
-
pH 6.5, 50°C
2.1 - 9.1
D-glyceraldehyde
5.5 - 22.7
D-glyceraldehyde acetonide
7.1
L-Glyceraldehyde
-
pH 6, 70°C
0.7 - 39.6
pyruvate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6.8
2-dehydro-3-deoxy-D-galactonate
34.8
2-dehydro-3-deoxy-D-galactonate 6-phosphate
Sulfolobus solfataricus
-
60°C, pH not specified in the publication
28.2
2-dehydro-3-deoxy-D-gluconate
61.9
2-dehydro-3-deoxy-D-gluconate 6-phosphate
Sulfolobus solfataricus
-
60°C, pH not specified in the publication
15
2-dehydro-3-deoxy-D-xylonate
Sulfolobus solfataricus
-
pH 6.5, 50°C
9.3
2-dehydro-3-deoxy-L-arabinonate
Sulfolobus solfataricus
-
pH 6.5, 50°C
0.06 - 15.7
D-glyceraldehyde
0.7 - 5.4
D-glyceraldehyde acetonide
9.9
L-Glyceraldehyde
Sulfolobus solfataricus
-
pH 6, 70°C
0.07 - 15
pyruvate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.7
2-dehydro-3-deoxy-D-galactonate
3965
207
2-dehydro-3-deoxy-D-galactonate 6-phosphate
Sulfolobus solfataricus
-
60°C, pH not specified in the publication
7986
1.1
2-dehydro-3-deoxy-D-gluconate
1172
643
2-dehydro-3-deoxy-D-gluconate 6-phosphate
Sulfolobus solfataricus
-
60°C, pH not specified in the publication
1596
0.45
2-dehydro-3-deoxy-D-xylonate
Sulfolobus solfataricus
-
pH 6.5, 50°C
9012
0.53
2-dehydro-3-deoxy-L-arabinonate
Sulfolobus solfataricus
-
pH 6.5, 50°C
7095
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.3
Hydroxypyruvate
-
pH 6.0, 70°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
1.1 U/mg, pH 6.0, 70°C
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
assay at, 2-dehydro-3-deoxy-D-xylonate and 2-dehydro-3-deoxy-L-arabinonate are less thermally stable than these C6 analogues (2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate), and so their kinetic assays are carried out at 50°C
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 60
-
the mutant enzyme V193A is more active than wild-type
50 - 90
-
50°C: about 65% of maximal activity, 90°C: about 70% of maximal activity, mutant enzyme V193A
60 - 90
-
60°C: about 50% of maximal activity, 90°C: about 95% of maximal activity, wild-type enzyme
70 - 100
-
70°C: about 40% of maximal activity, 100°C: about 95% of maximal activity
PDB
SCOP
CATH
ORGANISM
UNIPROT
Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32980
-
4 * 32980, calculated from sequence
33000
-
4 * 33000, crystallographic data
133000
-
equilibrium centrifugation analysis
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging-drop method, the enzyme crystallizes in two space groups, P3(1)21 and P6(5)22, for which diffraction data are obtained to a maximum resolution of 1.8 and 2.5 A
-
hanging drop diffusion method, three crystal forms: orthorhombic crystals of space group P2(1)2(1)2(1), which diffract to beyond 2.15 A, monoclinic crystals of space group C2, which diffract to 2.2 A, and cubic crystals of space group P4(2)32, which diffract to 3.4 A
-
trapping of Schiff base complexes with natural substrates pyruvate, 2-dehydro-3-deoxy-D-gluconate, 2-dehydro-3-deoxy-D-galactonate and pyruvate plus D-glyceraldehyde at physiological pH by rapid soaking at low temperature followed by flash freezing prior to X-ray data collection. The complexes explain the substrate promiscuity of the enzyme with a rigid ligand-binding site able to accommodate both 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate
-
X-ray crystallographic analysis of the active site of the aldolase bound to pyruvate, 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate at 4°C, reveals that its catalytic mechanism is typical of the N-acetylneuraminic acid lyase superfamily
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90
-
activity half-life of wild-type enzyme is 100 min, activity half-life of mutant enzyme V193A is 120 min
95
-
half-life: 7.8 h
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
-
expression in Escherichia coli
-
overexpression in Escherichia
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
V193A
-
the mutant enzyme displays a threefold increase in activity compared with wild type enzyme. Increased specific activity at 40–60 °C of this mutant is observed, not only for the condensation of pyruvate with glyceraldehyde, but also for several unnatural acceptor aldehydes. The optimal temperature for activity of SacKdgAV193A is lower than for the wild type enzyme, but enzymatic stability of the mutant is similar to that of the wild type
T157C
-
improved for 2-dehydro-3-deoxy-D-gluconate with a 75% diastereoisomeric ratio
T157C/Y132V
-
diastereoselective formation of 2-dehydro-3-deoxy-D-gluconate with much improved (91%) diastereoisomeric ratio
T157F/Y132V
-
diastereoselective formation of 2-dehydro-3-deoxy-D-gluconate with much improved (93%) diastereoisomeric ratio
T157V/A198L/D181Q
-
diastereoselective formation of 2-dehydro-3-deoxy-D-galactonate with much improved (88%) diastereoisomeric ratio
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
-
stereoselectivity is induced into aldol reactions of this naturally promiscuous enzyme by employing D-glyceraldehyde acetonide and L-glyceraldehyde acetonide as substrates