Information on EC 4.2.1.39 - Gluconate dehydratase

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

EC NUMBER
COMMENTARY hide
4.2.1.39
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RECOMMENDED NAME
GeneOntology No.
Gluconate dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O
show the reaction diagram
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Entner-Doudoroff pathway II (non-phosphorylative)
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Entner-Doudoroff pathway III (semi-phosphorylative)
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Metabolic pathways
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Microbial metabolism in diverse environments
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Pentose phosphate pathway
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Entner Doudoroff pathway
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SYSTEMATIC NAME
IUBMB Comments
D-gluconate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
The enzyme shows no activity with D-galactonate [2]. cf. EC 4.2.1.140, gluconate/galactonate dehydratase.
CAS REGISTRY NUMBER
COMMENTARY hide
37290-75-8
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain M250, properties are conspiciously different from those of Clostridium pasteurianum
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Manually annotated by BRENDA team
strain M250, properties are conspiciously different from those of Clostridium pasteurianum
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
not in many other methylotrophic bacteria
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
i.e. Rhodopseudomonas sphaeroides
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-arabonate
?
show the reaction diagram
D-fuconate
?
show the reaction diagram
D-galactoheptonate
2-dehydro-3-deoxy-D-galactoheptonate + H2O
show the reaction diagram
-
1.6% of the activity with D-gluconate
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-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
D-galactonate
?
show the reaction diagram
-
85% of activity with D-gluconate
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-
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D-gluconate
2-dehydro-3-deoxy-D-gluconate
show the reaction diagram
D-gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
show the reaction diagram
D-gluconate
?
show the reaction diagram
D-mannonate
?
show the reaction diagram
D-ribonate
?
show the reaction diagram
-
substrate specifity 11%
-
-
?
D-xylonate
?
show the reaction diagram
DL-isovalerate
?
show the reaction diagram
-
substrate specifity 11%
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-
?
gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
show the reaction diagram
-
-
-
?
L-arabonate
?
show the reaction diagram
L-mannonate
?
show the reaction diagram
-
substrate specifity 10%
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-
?
additional information
?
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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
D-gluconate
2-dehydro-3-deoxy-D-gluconate + H2O
show the reaction diagram
D-gluconate
?
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cd2+
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the enzyme is activated by the presence of Co2+, Mg2+, Ni2+, Cd2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
dithiothreitol
Fe2+
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deactivates the enzyme
glutathione
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1 mM, 41% inhibition
L-cysteine
p-chloromercuribenzoate
sulfhydryl compounds
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
sulfhydryl compounds
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2
D-galactonate
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0.45 - 20.8
D-gluconate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
760
D-gluconate
Sulfolobus solfataricus
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.001
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cell-free extracts, gluconate-grown
0.002
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nitrogen source urea
0.01
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cell-free extracts, gluconate-grown
0.011
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carbon source DL-glutamate
0.013
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carbon source DL-alanine
0.019
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nitrogen source bacto peptone
0.023
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cell-free extracts, glucose-grown
0.025
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carbon source D-glucose
0.027
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carbon source D-galactose; nitrogen source yeast extract
0.031
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nitrogen source glucosamine; nitrogen source (NH4)SO4
0.036
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nitrogen source H4NO3
0.038
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carbon source D-galactonate
0.04
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nitrogen source casamino acid
0.041
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cell-free extracts, gluconate-grown
0.042
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carbon source maltose
0.046
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carbon source D-arabinose
0.05
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nitrogen source NH4Cl
0.057
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carbon source sucrose
0.08
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cell-free extracts, gluconate-grown
0.083
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cell-free extracts, gluconate-grown
0.111
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nitrogen source malt extract
0.13
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carbon source D-gluconate
0.5
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cell-free extract, fructose grown
10
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cell-free extract, gluconate grown
483
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cell-free sucrose-grown
1420
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cell-free extracts, gluconate-grown
2000
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cell-free extracts
additional information
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buffer-dependent
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.8
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enzyme assay at
8
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enzyme assay at
8.4 - 8.8
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8.6
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enzyme assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5 - 8.1
50% of activity at pH 8.1 and at pH 4.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55
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enzyme assay at
70
half-life is about 15 min
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70 - 95
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70°C: about 40% of maximal activity, 95°C: about 40% of maximal activity
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
44040
-
x * 44040, calculated from sequence
44730
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rGNAD, His-tagged, calculated
45000
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rGNAD, His-tagged, determined by SDS-PAGE
56000
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rGNAD, Trx-fusion, determined by SDS-PAGE
62000
-
determined by SDS-PAGE
63410
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calculated
64000
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2 * 64000, SDS-PAGE
71000
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rGNAD, GST-fusion, determined by SDS-PAGE
118000
-
sucrose density gradient centrifugation
131000
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sedimentation equilibrium, gel filtration
270000
340000
gel filtration
350000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x * 44000, SDS-PAGE; x * 44040, calculated from sequence
dimer
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2 * 64000, SDS-PAGE
homooctamer
8 * 44000, SDS-PAGE
octamer
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8 * 44000, SDS-PAGE
additional information
-
number of sulfhydryl groups
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
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phosphorylation and dephosphorylation control the activity of D-gluconate dehydratase, loss of activity by dephosphorylation
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60
no loss of activity upon incubation for 2 h
70
-
half-life: 7 h
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
rather labile
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
inactivation by O2, activity restored by sulfhydryl compounds in the presence of Fe2+
-
5684
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, Tris-HCl buffer, 50% glycerol, 30% loss of activity within 5 months
-20°C, Tris-HCl buffer, pH 8.0, cell-free extract with inactivated enzyme, several weeks
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0°C, Tris-HCl buffer, pH 8.0-8.8, MgCl2, sodium-D-gluconate, 50% loss of activity after 7 days
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4°C, Tris-HCl buffer, pH 7.1, reactivated enzyme, at least 3 weeks under anaerobic conditions
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
after ammonium sulfate precipitation chromatography on a Phenyl-Sepharose, a Q-Sepharose, a Mono Q, and a HiTrap desalting column is performed
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by centrifugation and gel filtration, 190fold to apparent homogeneity
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
into the pGEM-T easy vector for sequencing
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vectors for constructing different fusion proteins are used, pET-21a, 6xHis, pET-32a, thioredoxin, Trx, pET-42a, glutathione-S-transferase, GST, and pET-43.1a, N-utilization substance A, NusA
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
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