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
-
-
D-galacturonate degradation I
-
-
Entner-Doudoroff pathway III (semi-phosphorylative)
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
Pentose phosphate pathway
-
-
degradation of sugar acids
-
-
Entner Doudoroff pathway
-
-
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
-
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
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)
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
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 32000, recombinant enzyme, SDS-PAGE, x * 33308, sequence calculation
hexamer
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(alphabeta)3; (alphabeta)3, each subunit is composed of a larger alpha/beta domain and a smaller beta-sheet
homooctamer
-
8 * 34000, denaturing SDS-PAGE
homotetramer
4 * 30000, gel filtration
tetramer
4 * 34480, calculated, 4 * 35000, SDS-PAGE
additional information
-
each subunit is composed of a larger alpha/beta domain and a smaller beta-sheet
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
-
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, 18°C, crystals grow to final dimensions within 1 month after appearance, method 2: sitting drop vapour diffusion method at 25°C, 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
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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 50°C 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 80°C for 1 h
85
1 h, 50% residual activity
90
10 min, 10% residual activity; the activity at 90°C is only about 25% of that at 80°C
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
-15°C, 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
-
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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