Information on EC 2.7.1.45 - 2-dehydro-3-deoxygluconokinase

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

EC NUMBER
COMMENTARY hide
2.7.1.45
-
RECOMMENDED NAME
GeneOntology No.
2-dehydro-3-deoxygluconokinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 2-dehydro-3-deoxy-6-phospho-D-gluconate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3,6-anhydro-alpha-L-galactopyranose degradation
-
-
4-deoxy-L-threo-hex-4-enopyranuronate degradation
-
-
alginate degradation
-
-
D-fructuronate degradation
-
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D-galacturonate degradation I
-
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Entner-Doudoroff pathway III (semi-phosphorylative)
-
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degradation of sugar acids
-
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Entner Doudoroff pathway
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Pentose phosphate pathway
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Metabolic pathways
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Microbial metabolism in diverse environments
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-
SYSTEMATIC NAME
IUBMB Comments
ATP:2-dehydro-3-deoxy-D-gluconate 6-phosphotransferase
The enzyme shows no activity with 2-dehydro-3-deoxy-D-galactonate [1]. cf. EC 2.7.1.178, 2-dehydro-3-deoxyglucono/2-dehydro-3-deoxygalactonokinase.
CAS REGISTRY NUMBER
COMMENTARY hide
9026-54-4
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
no activity in Azobacter agilis
-
-
-
Manually annotated by BRENDA team
no activity in Neurospora crassa
-
-
-
Manually annotated by BRENDA team
no activity in Salmonella typhimurium
-
-
-
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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-
-
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
ATP + 2-dehydro-3-deoxy-D-gluconate
ADP + 2-dehydro-3-deoxy-6-phospho-D-gluconate
show the reaction diagram
-
-
-
?
ATP + 2-dehydro-3-deoxy-D-gluconate
ADP + 6-phospho-2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
ATP + 2-keto-D-gluconate
ADP + 6-phospho-2-keto-D-gluconate
show the reaction diagram
CTP + 2-dehydro-3-deoxy-D-gluconate
CDP + 6-phospho-2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
GTP + 2-dehydro-3-deoxy-D-gluconate
GDP + 6-phospho-2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
ITP + 2-dehydro-3-deoxy-D-gluconate
IDP + 6-phospho-2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
TTP + 2-dehydro-3-deoxy-D-gluconate
TDP + 6-phospho-2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
UTP + 2-dehydro-3-deoxy-D-gluconate
UDP + 6-phospho-2-dehydro-3-deoxy-D-gluconate
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
ATP + 2-dehydro-3-deoxy-D-gluconate
ADP + 2-dehydro-3-deoxy-6-phospho-D-gluconate
show the reaction diagram
D4GSE6
-
-
-
?
ATP + 2-dehydro-3-deoxy-D-gluconate
ADP + 6-phospho-2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
1.8fold activating at 0.1 M KCl
Ni2+
10 mM, required for activity, 92% relative activity compared to Mg2+; 92% of the activity with Mg2+
Zn2+
10 mM, required for activity, 75% relative activity compared to Mg2+; 75% of the activity with Mg2+
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Mn2+
-
divalent cation required, most effective at a ratio of Mn2+ and ATP of 1:3, deviation from this ratio is inhibitory at several concentration levels
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.027 - 1
2-dehydro-3-deoxy-D-gluconate
1.3 - 3.6
2-keto-D-gluconate
0.057 - 0.11
ATP
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8.26 - 11
2-dehydro-3-deoxy-D-gluconate
2.2 - 26.3
2-keto-D-gluconate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.104
-
recombinant cell extract after heat precipitation step
41.3
-
purified recombinant enzyme
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.6 - 6
-
acetate buffer
6 - 9
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broad optimum
additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.7 - 8
-
pH 4.7: about 50% of maximum activity, pH 8: about 85% of maximum activity, acetate buffer
6.5 - 8.5
half of the maximum activity is obtained at pHs 6.5 and 9.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
65% of maximum activity
90
25% of maximum activity
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
PDB
SCOP
CATH
ORGANISM
UNIPROT
Enterococcus faecalis (strain ATCC 700802 / V583)
Oceanicola granulosus (strain ATCC BAA-861 / DSM 15982 / KCTC 12143 / HTCC2516)
Oceanicola granulosus (strain ATCC BAA-861 / DSM 15982 / KCTC 12143 / HTCC2516)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30000
4 * 30000, gel filtration
32000
-
x * 32000, recombinant enzyme, SDS-PAGE, x * 33308, sequence calculation
33308
-
x * 32000, recombinant enzyme, SDS-PAGE, x * 33308, sequence calculation
34000
-
8 * 34000, denaturing SDS-PAGE
34480
4 * 34480, calculated, 4 * 35000, SDS-PAGE; calculated from amino acid sequence
35000
4 * 34480, calculated, 4 * 35000, SDS-PAGE; SDS-PAGE
36390
-
calculated from amino acid sequence
120000
gel filtration; gel filtration
160000
-
dynamic light scattering and gel filtration
260000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 32000, recombinant enzyme, SDS-PAGE, x * 33308, sequence calculation
hexamer
homooctamer
-
8 * 34000, denaturing SDS-PAGE
homotetramer
4 * 30000, gel filtration
tetramer
4 * 34480, calculated, 4 * 35000, SDS-PAGE
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
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dephosphorylation with potato acid phosphatase or bacterial alkaline phosphatase, leads to complete loss of activity
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2.05 A resolution. Comparison with strucuture of Thermus thermophilus
2 enzyme crystal forms, X-ray diffraction structure determination and analysis at 2.3 and 3.2 A resolution, respectively, molecular replacement, enzyme in complex with ATP, with 2-dehydro-3-deoxy-D-gluconate and ATP analogue adenosine 5'-(beta,gamma-imino)triphosphate, i.e. AMP-PNP, or with 2-dehydro-3-deoxy-D-gluconate and ATP, X-ray diffraction structure determination and analysis at 2.1 A resolution
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purified recombinant enzyme, free enzyme or in complex with ATP and 2-dehydro-3-deoxy-D-gluconate, method 1: automated microbatch method, 500 nl 23 mg/ml protein mixed with 500 nl screen solution containing 44% v/v methylpentanediol, 10% v/v dioxane, 0.1 M Na HEPES, pH 7.7, and covered with 0.015 ml silicone and parraffin oil mixture, 18C, crystals grow to final dimensions within 1 month after appearance, method 2: sitting drop vapour diffusion method at 25C, 0.001 ml 10 mg/ml protein solution mixed with equal volume of reservoir solution and equilibrated against 0.1 ml reservoir solution containing 28% v/v methylpentanediol, 10 mM CaCl2, 0.1 M trisodium citrate buffer, pH 5.6, or for cocrystallization of enzyme with ligands containing 0.35-0.45 M ammonium sulfate and 0.1 M Tris-HCl, pH 8.5, X-ray diffraction structure determination and analysis at 2.1-3.2 A resolution
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5
no activity
676988
10
no activity
676988
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
the activity at 50C is about 65% of the maximum
52
-
half-life: 6-7 min
80
1 h, no loss of activity; the purified recombinant enzyme is extremely thermostable and retains full activity after heating at 80C for 1 h
85
1 h, 50% residual activity
90
10 min, 10% residual activity; the activity at 90C is only about 25% of that at 80C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
dephosphorylation with potato acid phosphatase or bacterial alkaline phosphatase leads to complete loss of activity
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15C, retains more than 50% of activity after 2 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Butyl Toyopearl column chromatography and Superdex 200 column gel filtration; recombinant protein
DEAE Sepharose column chromatography, Q Sepharose column chromatography, Affi-gel blue column chromatography, Sephadex G-75 gel filtration, and Mono Q HR 5/5 column chromatography
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recombinant enzyme from Escherichia coli, by heat precipitation and gel filtration
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recombinant protein
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli strain BL21(DE3); expression in Escherichia coli
expression in Escherichia coli
gene kdgK as part of the ED gene cluster, expresssion in Escherichia coli
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gene kdgK as part of the ED gene cluster, expresssion in Escherichia coli as soluble proein at low rate
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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