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
3,6-anhydro-alpha-L-galactopyranose degradation
-
-
4-deoxy-L-threo-hex-4-enopyranuronate degradation
-
-
D-fructuronate degradation
-
-
D-galacturonate degradation I
-
-
D-glucosaminate degradation
-
-
Entner Doudoroff pathway
-
-
Entner-Doudoroff pathway I
-
-
Entner-Doudoroff pathway III (semi-phosphorylative)
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
Pentose phosphate pathway
-
-
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
-
-
-
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
Rhizobium lupini
strain RL3001
-
-
Manually annotated by BRENDA team
Rhizobium lupini RL3001
strain RL3001
-
-
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-oxooctonoate
?
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
-
-
2,4-dioxo-4-[3-(trifluoromethyl)phenyl]butanoic acid
-
-
2,4-dioxo-4-[4-(trifluoromethyl)phenyl]butanoic acid
-
-
2-Keto-(3S)-3-bromopyruvate
-
-
2-Keto-3-deoxy-6-phosphogalaconate
-
-
2-keto-3-deoxygluconate
-
-
4-(3-methoxyphenyl)-2,4-dioxobutanoic acid
-
-
4-(4-methoxyphenyl)-2,4-dioxobutanoic acid
-
-
5,5'-dithiobis(2-nitrobenzoate)
-
-
5-Keto-4-deoxyglucarate
-
-
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-oxooctonoate
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
Thermotoga maritima
-
-
1.5 - 3.1
4-hydroxy-2-oxooctonoate
533
6-phospho-2-dehydro-3-deoxy-D-gluconate
Pseudomonas fluorescens
-
-
0.000001
benzaldehyde
Escherichia coli
-
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-oxooctonoate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.07
2,4-dioxo-4-phenylbutanoic acid
-
pH 7.6, 25C
0.04
2,4-dioxo-4-[2-(trifluoromethyl)phenyl]butanoic acid
-
pH 7.6, 25C
0.03
2,4-dioxo-4-[3-(trifluoromethyl)phenyl]butanoic acid
-
pH 7.6, 25C
0.38
2,4-dioxo-4-[4-(trifluoromethyl)phenyl]butanoic acid
-
pH 7.6, 25C
0.075
4-(3-methoxyphenyl)-2,4-dioxobutanoic acid
-
pH 7.6, 25C
0.18
4-(4-methoxyphenyl)-2,4-dioxobutanoic acid
-
pH 7.6, 25C
0.25
acetylpyruvic acid
-
pH 7.6, 25C
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 K12)
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
22920
calculated
23000
determined by SDS-PAGE
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
-15C or 4C activity of the crystalline enzyme is stable for months
-
4C, 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 4C 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 (3066 entries)
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