Information on EC 4.1.2.14 - 2-dehydro-3-deoxy-phosphogluconate aldolase

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

EC NUMBER
COMMENTARY hide
4.1.2.14
-
RECOMMENDED NAME
GeneOntology No.
2-dehydro-3-deoxy-phosphogluconate aldolase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
condensation
elimination
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
D-fructuronate degradation
-
-
Entner-Doudoroff pathway I
-
-
D-galacturonate degradation I
-
-
D-glucosaminate degradation
-
-
Entner-Doudoroff pathway III (semi-phosphorylative)
-
-
4-deoxy-L-threo-hex-4-enopyranuronate degradation
-
-
3,6-anhydro-alpha-L-galactopyranose degradation
-
-
Entner Doudoroff pathway
-
-
Pentose phosphate pathway
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
SYSTEMATIC NAME
IUBMB Comments
2-dehydro-3-deoxy-6-phosphate-D-gluconate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
The enzyme shows no activity with 2-dehydro-3-deoxy-6-phosphate-D-galactonate. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase [2]. Also acts on 2-oxobutanoate [1].
CAS REGISTRY NUMBER
COMMENTARY hide
9024-53-7
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain Lhet2, strain PW2, strain KLB, strain OP and strain QBP
-
-
Manually annotated by BRENDA team
bifunctional enzyme Ec4.1.2.14/Ec4.1.3.16
-
-
Manually annotated by BRENDA team
strain CC409
-
-
Manually annotated by BRENDA team
strain CC409
-
-
Manually annotated by BRENDA team
strain RL3001
-
-
Manually annotated by BRENDA team
strain RL3001
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain NZP2213
-
-
Manually annotated by BRENDA team
strain NZP2213
-
-
Manually annotated by BRENDA team
strain A 3.12
-
-
Manually annotated by BRENDA team
strain CC224; strain SU391
-
-
Manually annotated by BRENDA team
strain CC224
-
-
Manually annotated by BRENDA team
strain SU391
-
-
Manually annotated by BRENDA team
strain CC365
-
-
Manually annotated by BRENDA team
strain CC365
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain SU216
-
-
Manually annotated by BRENDA team
strain SU216
-
-
Manually annotated by BRENDA team
serotype 2
UniProt
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
strain ZM4
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(4S)-2-oxo-4-hydroxy-4-(2'-pyridyl)butanoate
?
show the reaction diagram
-
-
-
-
r
2-dehydro-3-deoxy-6-phospho-D-gluconate
pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
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
?
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-4-hydroxy-4-(2'-pyridyl)butyrate
?
show the reaction diagram
-
-
-
-
?
2-dehydro-4-hydroxyoctonate
?
show the reaction diagram
-
-
-
-
?
2-keto-3-deoxy-6-phosphogalactonate
?
show the reaction diagram
-
-
-
-
?
2-oxobutyrate + 2-pyridine carboxaldehyde
?
show the reaction diagram
-
weak substrate for wild-type enzyme, good substrate for K133Q/T161K mutant
-
?
2-oxobutyrate + D-glyceraldehyde
?
show the reaction diagram
-
weak substrate
-
?
2-pyridinecarboxyaldehyde + pyruvate
(S)-4-hydroxy-2-keto-4-(2'-pyridyl)butyrate
show the reaction diagram
-
typical isolated yield of product is 80-90% after reverse-phase C18 purification. Reaction is also doable with substrates other than 2-pyridinecarboxyaldehyde. Enantiomeric excess greater than 99.7%
-
-
?
3-fluoropyruvate + 2-pyridine carboxaldehyde
?
show the reaction diagram
-
weak substrate for wild-type enzyme, good substrate for K133Q/T161K mutant
-
?
3-fluoropyruvate + D-glyceraldehyde
?
show the reaction diagram
-
weak substrate
-
?
4-hydroxy-2-oxooctonate
?
show the reaction diagram
-
-
-
-
r
D-2-dehydro-3-deoxygluconate
pyruvate + D-glyceraldehyde
show the reaction diagram
-
poor substrate
-
?
pyruvate + 2-pyridine carboxaldehyde
?
show the reaction diagram
pyruvate + 3-pyridine carboxaldehyde
?
show the reaction diagram
-
wild-type, 0.5% of activity with D-glyceraldehyde 3-phosphate, mutant T161S/S184L, 1% of wild-type activity with D-glyceraldehyde 3-phosphate
-
-
r
pyruvate + 4-pyridine carboxaldehyde
?
show the reaction diagram
-
wild-type, 3% of activity with D-glyceraldehyde 3-phosphate, mutant T161S/S184L, 2.5% of wild-type activity with D-glyceraldehyde 3-phosphate
-
-
r
pyruvate + benzaldehyde
?
show the reaction diagram
-
-
-
?
pyruvate + D-erythrose
?
show the reaction diagram
Pyruvate + D-erythrose 4-phosphate
3-Deoxy-D-riboheptulosonic acid 7-phosphate
show the reaction diagram
-
28% of the activity with D-glyceraldehyde 3-phosphate
-
-
pyruvate + D-glyceraldehyde
2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
Pyruvate + D-glyceraldehyde
?
show the reaction diagram
-
35% of the activity with D-glyceraldehyde 3-phosphate
-
-
-
Pyruvate + D-glyceraldehyde 3-phosphate
6-Phospho-2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
pyruvate + D-lactaldehyde
?
show the reaction diagram
-
-
-
?
pyruvate + D-threose
?
show the reaction diagram
-
weak substrate
-
?
pyruvate + DL-3-fluoro-2-hydroxypropanal
?
show the reaction diagram
-
-
-
?
pyruvate + DL-glyceraldehyde 3-phosphate
2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
-
-
-
?
pyruvate + glycoaldehyde
?
show the reaction diagram
Pyruvate + glyoxylate
?
show the reaction diagram
-
-
-
?
Pyruvate + glyoxylic acid
?
show the reaction diagram
-
93% of the activity with D-glyceraldehyde 3-phosphate
-
-
-
pyruvate + L-erythrose
?
show the reaction diagram
-
weak substrate
-
?
pyruvate + L-glyceraldehyde 3-phosphate
?
show the reaction diagram
-
weak substrate
-
?
pyruvate + L-threose
?
show the reaction diagram
-
weak substrate
-
?
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-6-phospho-D-gluconate
pyruvate + D-glyceraldehyde 3-phosphate
show the reaction diagram
2-dehydro-3-deoxy-D-galactonate
pyruvate + D-glyceraldehyde
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-keto-3-deoxy-6-phosphogalactonate
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
activates
Mg2+
-
activates
Mn2+
-
activates
Ni2+
-
activates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,4-dioxo-4-phenylbutanoic acid
-
-
2,4-dioxo-4-[2-(trifluoromethyl)phenyl]butanoic acid
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-
2,4-dioxo-4-[3-(trifluoromethyl)phenyl]butanoic acid
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-
2,4-dioxo-4-[4-(trifluoromethyl)phenyl]butanoic acid
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2-Keto-(3S)-3-bromopyruvate
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-
2-Keto-3-deoxy-6-phosphogalaconate
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-
2-keto-3-deoxygluconate
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-
4-(3-methoxyphenyl)-2,4-dioxobutanoic acid
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-
4-(4-methoxyphenyl)-2,4-dioxobutanoic acid
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-
5,5'-dithiobis(2-nitrobenzoate)
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-
5-Keto-4-deoxyglucarate
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-
acetylpyruvic acid
-
-
Bromopyruvate
-
pyruvate and 2-keto-3-deoxy-6-phosphogluconate protect
Cu2+
-
strong
Dinitrofluorobenzene
-
-
-
iodoacetamide
-
-
KCl
-
100 mM, 67% inhibition
KI
-
100 mM, 93% inhibition
NaBr
-
100 mM, 88% inhibition
NaCl
-
100 mM, 76% inhibition
NaF
-
100 mM, 45% inhibition
NaI
-
100 mM, 93% inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.6 - 43
(4S)-2-oxo-4-hydroxy-4-(2'-pyridyl)butanoate
0.05 - 1.7
2-dehydro-3-deoxy-6-phospho-D-gluconate
1.5 - 2.3
2-dehydro-3-deoxy-D-gluconate
0.006 - 1.2
2-dehydro-3-deoxy-D-gluconate 6-phosphate
3 - 32
2-dehydro-4-hydroxy-4-(2'-pyridyl)butyrate
26 - 150
2-dehydro-4-hydroxyoctonate
0.1
2-keto-3-deoxy-6-phosphogluconate
-
-
2 - 146
4-hydroxy-2-oxooctonate
0.038 - 10.5
6-phospho-2-dehydro-3-deoxy-D-gluconate
26.3
benzaldehyde
-
pH 7.5, K133Q/T161K mutant
2 - 285
D-2-dehydro-deoxygluconate
10
pyruvate
-
pH 7.5, wild-type and K133Q/T161K mutant
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
11 - 240
(4S)-2-oxo-4-hydroxy-4-(2'-pyridyl)butanoate
27 - 83
2-dehydro-3-deoxy-6-phospho-D-gluconate
0.019 - 0.11
2-dehydro-3-deoxy-D-gluconate
0.00029 - 284
2-dehydro-3-deoxy-D-gluconate 6-phosphate
6 - 40
2-dehydro-4-hydroxy-4-(2'-pyridyl)butyrate
1.8 - 2.9
2-dehydro-4-hydroxyoctonate
80
2-keto-3-deoxy-6-phosphogluconate
-
-
1.5 - 3.1
4-hydroxy-2-oxooctonate
533
6-phospho-2-dehydro-3-deoxy-D-gluconate
-
-
0.000001
benzaldehyde
-
pH 7.5, K133Q/T161K mutant
0.016 - 6.08
D-2-dehydro-deoxygluconate
0.0000046 - 0.0121
pyruvate
additional information
additional information
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.33 - 150
(4S)-2-oxo-4-hydroxy-4-(2'-pyridyl)butanoate
24 - 830
2-dehydro-3-deoxy-6-phospho-D-gluconate
0.014 - 0.72
4-hydroxy-2-oxooctonate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.07
2,4-dioxo-4-phenylbutanoic acid
-
pH 7.6, 25°C
0.04
2,4-dioxo-4-[2-(trifluoromethyl)phenyl]butanoic acid
-
pH 7.6, 25°C
0.03
2,4-dioxo-4-[3-(trifluoromethyl)phenyl]butanoic acid
-
pH 7.6, 25°C
0.38
2,4-dioxo-4-[4-(trifluoromethyl)phenyl]butanoic acid
-
pH 7.6, 25°C
0.075
4-(3-methoxyphenyl)-2,4-dioxobutanoic acid
-
pH 7.6, 25°C
0.18
4-(4-methoxyphenyl)-2,4-dioxobutanoic acid
-
pH 7.6, 25°C
0.25
acetylpyruvic acid
-
pH 7.6, 25°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.7
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain B / BL21-DE3)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Vibrio fischeri (strain ATCC 700601 / ES114)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
21505
-
x * 21505, SDS-PAGE
22000
-
3 * 22000, SDS-PAGE
22920
calculated
23000
determined by SDS-PAGE
23942
-
x * 23942, calculation from amino acid sequence determined by Edman method
49500
-
2 * 49500, equilibrium sedimentation after treatment with NaBH4 or guanidine hydrochloride
60000
determined by gel filtration, trimer
72000 - 73300
-
meniscus depletion method, low speed equilibrium sedimentation, disc gel electrophoresis
72000 - 78000
-
disc gel electrophoresis
72000
-
high speed equilibrium sedimentation
86150
-
equilibrium sedimentation
87830
-
equilibrium sedimentation
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
2 * 49500, equilibrium sedimentation after treatment with NaBH4 or guanidine hydrochloride
trimer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method
-
sitting drop vapor diffusion method
-
microdialysis against sequentially higher concentrations of ammonium sulfate
-
structure at 2.8 A resolution
-
the structure of 2-keto-3-deoxy-6-phosphogluconate aldolase is solved at a resolution of 2.8 A
enzyme in complex with pyruvate, 2-dehydro-3-deoxy-D-gluconate or 2-dehydro-3-deoxy-D-galactonate, determination of the structural basis for substrate promiscuity
-
the crystal structure of the apoprotein is determined to a resolution of 2.0 A, the structure of the protein covalently linked to pyruvate is determined to 2.2 A
hanging drop vapor diffusion method, using 25% (w/v) polyethylene glycol 3350, and 0.1 M bis-tris pH 5.5
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1
-
4 h, stable
4965
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9
-
inactivation above
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
highly stable when frozen in phosphate buffer
-
Mg2+ stabilizes
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C or 4°C activity of the crystalline enzyme is stable for months
-
4°C, HEPES (100 mM, pH 7.5), NaCl (100 mM), 10% glycerol, at concentrations ranging from 1 to 16 mM, up to 1 year, remains stable
-
protein can be stored at 4°C for up to 6 months without a significant loss in activity.
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni2+-charged chelating Sepharose Fast Flow column chromatography
-
one-step procedure
-
purified by using Ni2+ affinity column
-
using a nickel-affinity and a Superdex 200 column
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
-
expressed in Escherichia coli BL21(DE3) cells
-
expressed in Escherichia coli K-12 cells
-
expression in Escherichia coli
-
His6-tagged KDPG aldolase is cloned in Escherichia coli BL21
-
into the plasmid vector pRStac
-
into the vector pET21a for expression in Escherichia coli BL21DE3 cells
using the pET expression system
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E9K/V118A
-
KA1-4 variant, improved cleavage of D-2-dehydro-deoxygluconate
G40A/V188A
-
KA1-1 variant, improved cleavage of D-2-dehydro-deoxygluconate
K133Q
-
no aldolase activity
K133Q/T161K
-
reduced catalytic efficiency
S184A
-
the mutation decreases the efficiency of KDPG retro-aldol cleavage only modestly
S184D
-
the mutation leads to strongly reduced enzymatic activity
S184F
-
active site mutation, enhances the substrate specificity to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butanoate
S184L
-
the mutation is located in the substrate-binding pocket, interacts with the phosphate moiety of KDPG, and improves the catalytic efficiency for the synthesis of a precursor for nikkomycin by 40fold
T161A
-
strongly reduced activity
T161S
-
active site mutation, enhances the substrate specificity to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butanoate
T161S/S184F
-
active site mutation, working additively to enhance the substrate specificity to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butanoate
T161S/S184L
-
active site mutation, working additively to enhance the substrate specificity to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butanoate. Mutations improve the value of kcat/KM (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butanoate by more than 450fold, resulting in a catalytic efficiency that is comparable to that of the wild-type enzyme with the natural substrate while retaining high stereoselectivity
T161V
-
strongly reduced activity
T84A/I92F
-
KA1-2 variant, improved cleavage of D-2-dehydro-deoxygluconate
T84A/I92F/V118A
-
KA2 variant, improved kcat, Km and thermal stability
T84A/I92F/V118A/E138V
-
KA3 variant, small change of melting temperature
T84A/I92F/V118A/G141S/T105I
-
KA3-L2 variant, slightly less stable than wild-type
T84A/I92F/V118A/T161A
-
KA3-L1 variant, enhanced activity towards negatively charged glyoxylate and glyceraldehyde-3-phosphate
V118A
-
KA1-3 variant, improved cleavage of D-2-dehydro-deoxygluconate
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
2-keto-3-deoxy-6-phosphogluconate aldolase is an attractive target for drug therapy in the case of human Streptococcus suis infections
synthesis
Show AA Sequence (3004 entries)
Please use the Sequence Search for a specific query.