Information on EC 4.2.1.6 - galactonate dehydratase

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

EC NUMBER
COMMENTARY
4.2.1.6
-
RECOMMENDED NAME
GeneOntology No.
galactonate dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
stereochemistry
-
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
it is proposed that the mechanism of the enzyme-catalyzed reaction is initiated by abstraction of the alpha-proton to form a stabilized enolic ion. If the substrate binds at the active site in the extended conformation the stereochemical course of the beta-elimination reaction is expected to be anti
-
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
the immediate dehydration product is the enol which undergoes spontaneous ketonization
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
D-galactonate degradation
-
-
degradation of sugar acids
-
-
Entner Doudoroff pathway
-
-
Galactose metabolism
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
SYSTEMATIC NAME
IUBMB Comments
D-galactonate hydro-lyase (2-dehydro-3-deoxy-D-galactonate-forming)
The enzyme shows no activity with D-gluconate [2]. cf. EC 4.2.1.140, gluconate/galactonate dehydratase.
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D-galactonate dehydrase
-
-
-
-
D-galactonate dehydratase
-
-
-
-
D-galactonate dehydratase
-
-
D-galactonate dehydratase
-
-
-
dehydratase, galactonate
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9024-38-8
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Escherichia coli K10
K10
-
-
Manually annotated by BRENDA team
strain PRL-R3
-
-
Manually annotated by BRENDA team
Klebsiella pneumoniae PRL-R3
strain PRL-R3
-
-
Manually annotated by BRENDA team
Mycobacterium butyricum
-
-
-
Manually annotated by BRENDA team
Mycobacterium friburgensis
-
-
-
Manually annotated by BRENDA team
Mycobacterium jucho
-
-
-
Manually annotated by BRENDA team
strain 279; strain 607
-
-
Manually annotated by BRENDA team
strain 607
-
-
Manually annotated by BRENDA team
Mycobacterium sp. 279
strain 279
-
-
Manually annotated by BRENDA team
Mycobacterium sp. 607
strain 607
-
-
Manually annotated by BRENDA team
no activity in Botrytis cinerea
-
-
-
Manually annotated by BRENDA team
ATCC 27855
-
-
Manually annotated by BRENDA team
Salmonella enterica subsp. enterica serovar Typhimurium LT-12
strain LT-12
-
-
Manually annotated by BRENDA team
L5-30; UR23
-
-
Manually annotated by BRENDA team
Sinorhizobium meliloti L5-30
L5-30
-
-
Manually annotated by BRENDA team
Sinorhizobium meliloti UR23
UR23
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-fuconate
2-keto-3-deoxy-D-fuconate + H2O
show the reaction diagram
Klebsiella pneumoniae, Klebsiella pneumoniae PRL-R3
-
30% of the activity with D-galactonate
-
?
D-galactonate
?
show the reaction diagram
-
-
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium butyricum
-
the enzyme catalyzes the first reaction in the D-galactonate catabolic pathway of non-pathogenic mycobacteria
-
-
-
D-galactonate
?
show the reaction diagram
-
induced by growth on D-galactose, D-galactonate, D-fucose, and L-arabinose over the level present in glucose-grown cells
-
-
-
D-galactonate
?
show the reaction diagram
-
growth on D-galactonate, L-arabinose and D-fucose increases the enzyme activity over the level of cells grown in nutrient broth
-
-
-
D-galactonate
?
show the reaction diagram
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium jucho, Mycobacterium butyricum, Mycobacterium friburgensis
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 607
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 279
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium jucho, Mycobacterium butyricum, Mycobacterium friburgensis
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
the enzyme is strictly specific for D-galactonate
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium butyricum
-
the enzyme is strictly specific for D-galactonate
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Sinorhizobium meliloti UR23
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Salmonella enterica subsp. enterica serovar Typhimurium LT-12
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Klebsiella pneumoniae PRL-R3
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium sp. 607
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium sp. 607
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Escherichia coli K10
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Sinorhizobium meliloti L5-30
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Salmonella enterica subsp. enterica serovar Typhimurium LT-2
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium sp. 279
-
-
-
?
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-galactonate
?
show the reaction diagram
-
-
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium butyricum
-
the enzyme catalyzes the first reaction in the D-galactonate catabolic pathway of non-pathogenic mycobacteria
-
-
-
D-galactonate
?
show the reaction diagram
-
induced by growth on D-galactose, D-galactonate, D-fucose, and L-arabinose over the level present in glucose-grown cells
-
-
-
D-galactonate
?
show the reaction diagram
-
growth on D-galactonate, L-arabinose and D-fucose increases the enzyme activity over the level of cells grown in nutrient broth
-
-
-
D-galactonate
?
show the reaction diagram
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium jucho, Mycobacterium butyricum, Mycobacterium friburgensis
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 607
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 279
-
enzyme of D-galactonate catabolism
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+
Mg2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+; optimal concentration: 1 mM
Mg2+
Mycobacterium butyricum
-
highest activity at 0.3 mM MgCl2, Mg2+ or Mn2+ required
Mg2+
-
optimal concentration: 1 mM
Mg2+
-
activates
Mn2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+
Mn2+
Mycobacterium butyricum
-
highest activity at 0.02 mM MnCl2, Mn2+ or Mg2+ required
Ni2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
CdSO4
Mycobacterium butyricum
-
-
CuSO4
Mycobacterium butyricum
-
-
HgCl2
Mycobacterium butyricum
-
-
iodoacetamide
-
-
iodoacetate
Mycobacterium butyricum
-
-
NaF
Mycobacterium butyricum
-
-
PCMB
Mycobacterium butyricum
-
-
ZnSO4
Mycobacterium butyricum
-
reactivated by chelating agents
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.3
D-fuconate
-
-
0.9
D-galactonate
-
-
1
D-galactonate
Mycobacterium butyricum
-
-
1.14
D-galactonate
-
-
8.33
D-galactonate
-
-
8.9
D-galactonate
-
pH 7, temperature not specified in the publication, Vmax: 8.52 nkat per mg of extracted protein
21.74
D-galactonate
-
pH 7, temperature not specified in the publication, Vmax: 2.21 nkat per mg of extracted protein
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.56
Mycobacterium butyricum
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.1
-
glycylglycine buffer
7.8 - 8
Mycobacterium butyricum
-
in 100 mM tris-HCl buffer or 50 mM phosphate buffer
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.9 - 8
-
pH 5.9: about 40% of maximal activity, pH 8.0: about 25% of maximal activity
6 - 9
-
about 25% of maximal activity at pH 6.0 and at pH 9.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
20 - 60
-
about 45% of maximal activity at 20C and 60C
PDB
SCOP
CATH
ORGANISM
Ralstonia pickettii (strain 12J)
Ralstonia pickettii (strain 12J)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
240000 - 245000
-
gel filtration, sucrose density gradient centrifugation
33932
240000 - 245000
-
-
33934
270000
Mycobacterium butyricum
-
gel filtration
33933
270000
-
-
5092
290000
-
gel filtration
33936
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hexamer
-
6 * 46000, SDS-PAGE
hexamer
Klebsiella pneumoniae PRL-R3
-
6 * 46000, SDS-PAGE
-
tetramer
-
-
tetramer
-
4 * 57000, SDS-PAGE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
53
-
half-life: more than 1 h
33932
60
-
5 min, 6% loss of activity, 60 min, 30% loss of activity
33942
70
Mycobacterium butyricum
-
15 min, about 10% loss of activity
33933
70
-
5 min, 60% loss of activity. 60 min, 70% loss of activity
33942
75
Mycobacterium butyricum
-
10 min, about 60% loss of activity. 15 min, about 90% loss of activity
33933
81
-
half-life: 10 min
33932
95
-
half-life: 3 min
33932
additional information
-
Mg2+, dithiothreitol and D-galactonate increase the rate of thermal inactivation
33932
additional information
Mycobacterium butyricum
-
dithiothreitol increases heat sensitivity
33933
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
insensitive to repeated freeze-thaw cycles
-
stable to lyophilization in 0.05 M glycine/0.01 M sodium cacodylate, pH 8.8
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C or -20C, stable for at least 1 month
-
-20C, 0.05 M glycine-0.01 M sodium cacodylate, pH 8.8, stable for 6 months
-
-20C, 6 months, stable
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
-
Mycobacterium butyricum
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Saccharomyces cerevisiae
-